Publications

Harezlak, J, Ruppert, D & Wand, MP 2018, Semiparametric Regression with R, Springer New York.
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This easy-to-follow applied book expands upon the authors’ prior work on semiparametric regression to include the use of R software. In 2003, authors Ruppert and Wand co-wrote Semiparametric Regression with R.J. Carroll, which introduced the techniques and benefits of semiparametric regression in a concise and user-friendly fashion. Fifteen years later, semiparametric regression is applied widely, powerful new methodology is continually being developed, and advances in the R computing environment make it easier than ever before to carry out analyses. Semiparametric Regression with R introduces the basic concepts of semiparametric regression with a focus on applications and R software. This volume features case studies from environmental, economic, financial, and other fields. The examples and corresponding code can be used or adapted to apply semiparametric regression to a wide range of problems. It contains more than fifty exercises, and the accompanying HRW package contains all datasets and scripts used in the book, as well as some useful R functions. This book is suitable as a textbook for advanced undergraduates and graduate students, as well as a guide for statistically-oriented practitioners, and could be used in conjunction with Semiparametric Regression. Readers are assumed to have a basic knowledge of R and some exposure to linear models. For the underpinning principles, calculus-based probability, statistics, and linear algebra are desirable.

Mozaner Bordin, D, Junqueira Dorta, D, Yonamine, M, da Costa, JL & Spinosa de Martinis, B 2018, Toxicologia forense.

Scammell, H 2018, Interplay of Quantum and Statistical Fluctuations in Critical Quantum Matter, Springer.
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This book explores critical phenomena in highly correlated quantum matter.

Thenkabail, PS, Lyon, JG & Huete, A 2018, Hyperspectral Indices and Image Classifications for Agriculture and Vegetation.
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Written by leading global experts, including pioneers in the field, the four-volume set on Hyperspectral Remote Sensing of Vegetation, Second Edition, reviews existing state-of- the-art knowledge, highlights advances made in different areas, and provides guidance for the appropriate use of hyperspectral data in the study and management of agricultural crops and natural vegetation. Volume II, Hyperspectral Indices and Image Classifications for Agriculture and Vegetation evaluates the performance of hyperspectral narrowband or imaging spectroscopy data with specific emphasis on the uses and applications of hyperspectral narrowband vegetation indices in characterizing, modeling, mapping, and monitoring agricultural crops and vegetation. This volume presents and discusses topics such as the non-invasive quantification of foliar pigments, leaf nitrogen concentration of cereal crop, the estimation of nitrogen content in crops and pastures, and forest leaf chlorophyll content, among others. The concluding chapter provides readers with useful guidance on the highlights and essence of Volume II through the editors’ perspective. Key Features of Volume II: Provides the fundamentals of hyperspectral narrowband vegetation indices and hyperspectral derivative vegetation indices and their applications in agriculture and vegetation studies. Discusses the latest advances in hyperspectral image classification methods and their applications. Explains the massively big hyperspectral sensing data processing on cloud computing architectures. Highlights the state-of-the-art methods in the field of hyperspectral narrowband vegetation indices for monitoring agriculture, vegetation, and their properties such as plant water content, nitrogen, chlorophyll, and others at leaf, canopy, field, and landscape scales. Includes best global expertise on hyperspectral remote sensing of agriculture, crop water use, plant species detection, crop productivity and water productivity mapping, and modeling.

Aneece, IP, Thenkabail, PS, Lyon, JG, Huete, A & Slonecker, T 2018, 'Spaceborne Hyperspectral EO-1 Hyperion Data Pre-Processing' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 251-272.
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Awasthi, R, Singh, AK, Mishra, G, Maurya, A, Chellappan, DK, Gupta, G, Hansbro, PM & Dua, K 2018, 'An Overview of Circular RNAs' in Advances in Experimental Medicine and Biology, Springer Singapore, Germany, pp. 3-14.
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© 2018, Springer Nature Singapore Pte Ltd. Circular RNAs (cirRNAs) are long, noncoding endogenous RNA molecules and covalently closed continuous loop without 5′–3′ polarity and polyadenylated tail which are largely concentrated in the nucleus. CirRNA regulates gene expression by modulating microRNAs and functions as potential biomarker. CirRNAs can translate in vivo to link between their expression and disease. They are resistant to RNA exonuclease and can convert to the linear RNA by microRNA which can then act as competitor to endogenous RNA. This chapter summarizes the evolutionary conservation and expression of cirRNAs, their identification, highlighting various computational approaches on cirRNA, and translation with a focus on the breakthroughs and the challenges in this new field.

Brodersen, KE, Kühl, M, Nielsen, DA, Pedersen, O & Larkum, AWD 2018, 'Rhizome, Root/Sediment Interactions, Aerenchyma and Internal Pressure Changes in Seagrasses' in Seagrasses of Australia, Springer International Publishing, Germany, pp. 393-418.
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© Springer International Publishing AG, part of Springer Nature 2018. Life in seawater presents several challenges for seagrasses owing to low O 2 and CO 2 solubility and slow gas diffusion rates. Seagrasses have evolved numerous adaptations to these environmental conditions including porous tissue providing low-resistance internal gas channels (aerenchyma) and carbon concentration mechanisms involving the enzyme carbonic anhydrase. Moreover, seagrasses grow in reduced, anoxic sediments, and aerobic metabolism in roots and rhizomes therefore has to be sustained via rapid O 2 transport through the aerenchyma. Tissue aeration is driven by internal concentration gradients between leaves and belowground tissues, where the leaves are the source of O 2 and the rhizomes and roots function as O 2 sinks. Inadequate internal aeration e.g., due to low O 2 availability in the surrounding water during night time, can lead to sulphide intrusion into roots and rhizomes, which has been linked to enhanced seagrass mortality. Under favourable conditions, however, seagrasses leak O 2 and dissolved organic carbon into the rhizosphere, where it maintains oxic microzones protecting the plant against reduced phytotoxic compounds and generates dynamic chemical microgradients that modulate the rhizosphere microenvironment. Local radial O 2 loss from belowground tissues of seagrasses leads to sulphide oxidation in the rhizosphere, which generates protons and results in local acidification. Such low-pH microniches can lead to dissolution of carbonates and protolytic phosphorus solubilisation in carbonate-rich sediments. The seagrass rhizosphere is also characterised by numerous high-pH microniches indicative of local stimulation of proton consuming microbial processes such as sulphate reduction via root/rhizome exudates and/or release of alkaline substances. High sediment pH shifts the sulphide speciation away from H 2 S towards non-tissue-penetrating HS - ions, which can alleviate the be...

Choi, AH, Akyol, S, Bendavid, A & Ben-Nissan, B 2018, 'Nanobioceramic thin films: Surface modifications and cellular responses on titanium implants' in Titanium in Medical and Dental Applications, Elsevier, pp. 147-173.
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© 2018 Elsevier Inc. All rights reserved. The relationship between biological responses and surface properties of materials is one of the main issues in biomedical materials research. A major disadvantage of current synthetic implants is their failure to adapt to the local tissue environment. In the dental and orthopedic fields, improvements in biocompatibility and the reliability of titanium and its alloys can be achieved through surface modifications. The purpose of altering the surfaces of metallic materials using biomedical thin films and nanocoatings is to promote bioactivity, reliability, and biocompatibility while at the same time eliminating or reducing corrosion and metal ion release. Important factors in determining the capability and performance of coated implants under physiological environments are the mechanical and adhesion properties. The design and success of an implant depends on a number of factors that includes materials, tissue implant interactions, biomechanical factors, and a patient’s health, which should be properly assessed. Furthermore, theoretical modeling approaches such as finite element analysis (FEA) are vital in the progress of understanding thin film-substrate interfacial behavior, which may result in better design and selection of thin film and substrate materials.

Choi, AH, Conway, RC, Cazalbou, S & Ben-Nissan, B 2018, 'Maxillofacial bioceramics in tissue engineering: Production techniques, properties, and applications' in Fundamental Biomaterials: Ceramics, Elsevier, pp. 63-93.
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Bioceramics prior to the 1970s were employed as implants to perform singular and biologically inert roles. The limitations with these synthetic materials as tissue substitutes were emphasized with the growing realization that the cells and tissues of the body perform many other vital regulatory and metabolic roles. Since then, the demands of bioceramics have changed, from maintaining an essentially physical function without eliciting a host response to providing a more positive interaction with the host. This has been accompanied by increasing demands on medical devices that they not only improve the quality of life but also extend its duration. More importantly, the exciting and potential opportunities associated with the use of nanobioceramics as body interactive materials, helping the body to heal, or promoting the regeneration of tissues, thus restoring physiological functions. This review covers the type of bioceramics currently used in maxillofacial surgery as well as their production methods and properties. The bioceramics covered include glass ceramics, bioglass, alumina, PSZ and zirconia, and calcium phosphate materials.

Choi, AH, Heness, G & Ben-Nissan, B 2018, 'Using finite element analysis to understand the mechanical properties of ceramic matrix composites' in Advances in Ceramic Matrix Composites, Elsevier, The Netherlands, pp. 375-400.
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© 2018 Elsevier Ltd. All rights reserved. Ceramic matrix composites (CMCs) are replacing other materials in applications where the higher costs are offset by improvements in performance. Due to their lack of toughness they are prone to catastrophic failure. To take advantage of the potential of CMCs and to minimize risks such as component failure, modeling and analysis tools such as finite element analysis (FEA) are essential for evaluating material performance nondestructively at the operating temperatures and conditions. FEA can determine mechanical properties such as interlaminar shear properties, cumulative damage failure, and crack deviation. This chapter introduces FEA and reviews the examination and validation of the design, mechanical properties, and failure modes of CMCs using FEA.

Christy, RD, Bernardo, JC, Hampel-Milagrosa, A & Fu, L 2018, 'Asian Agribusiness Management', WORLD SCIENTIFIC.
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Cranfield, CG, Kloda, A, Nikolaev, YA, Martinac, AD, Ridone, P, Bavi, N, Bavi, O, Petrov, E, Battle, AR, Nomura, T, Rohde, PR, Nakayama, Y, Rosholm, KR, Cox, CD, Baker, MA & Martinac, B 2018, 'Mechanosensitivity of Ion Channels' in Encyclopedia of Biophysics, Springer Berlin Heidelberg, pp. 1-11.
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Forbes, S & Ueland, M 2018, 'Time Since Death in Bioarchaeology and Human Osteology' in Smith, C (ed), Encyclopedia of Global Archaeology, Springer International Publishing, pp. 1-6.
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Time since death (TSD) is defined as the time frame between death and discovery of an organism. When estimated in an archaeological context, this time frame may be referred to as time since deposition and in a forensic context can be termed postmortem interval. Time since death cannot be established with certainty and for this reason is provided as an estimate of the range of time encompassing the period when death occurred. A shorter postmortem interval is typically associated with a narrower time range, while a longer postmortem interval has a broader time range and includes a wider margin of error. Presently, there is no single indicator which provides a reliable or accurate measure of the time since death of an organism.

Fu, S & Stojanovska, N 2018, 'Designer Drugs' in Forensic Toxicology, pp. 123-132.
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Designer drugs of abuse exist in a dynamic market with new drugs appearing all the time. Based on their chemical structures, designer drugs can be classified into amphetamine types, 2,5-dimethoxyamphetamines, 2,5-phenylamines (2C drugs), β-keto amphetamines (cathinones), phencyclidines, piperazines, pyrrolidinophenones, fentanyls, piperidines, tryptamine derivatives, synthetic steroids, and synthetic cannabinoids in “Spice” products, among other structural types. These designer drugs pose a serious health risk to consumers due to the limited toxicokinetic data available. Designer drugs also present an ongoing challenge to forensic chemists, forensic toxicologists, and law enforcement agencies due to their dynamic and changing markets. To effectively combat the problems associated with designer drugs, a collective effort needs to be in place from forensic scientists, health professionals, and law enforcement authorities. It is important to stay at the forefront of drug detection techniques and strategies to allow speedy identification of new substances as they emerge. Metabolism and toxicity data need to be collected to facilitate diagnosis and treatment of designer drug intoxication. At the same time, drug scheduling authorities need to schedule these drugs promptly to enable laws to be applied to the production, distribution, and consumption of these illicit substances to safeguard society.

Gupta, V & Reddy, CRK 2018, 'A simple protocol for a rapid and consistent production of a large number of viable protoplasts from the Ulvophycean species' in Protocols for Macroalgae Research, CRC Press, pp. 129-138.
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Haqqi, F, Heng, D, Joseph, L, Songsomboon, K, Christy, RD, Kudilok, K & Suchato, R 2018, 'CEO Agrifood Limited: Growing Through Value-Addition' in Asian Agribusiness Management, WORLD SCIENTIFIC, pp. 39-52.
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Huete, A, Koedsin, W & Wu, J 2018, 'Hyperspectral Applications to Landscape Phenology' in Advanced Applications in Remote Sensing of Agricultural Crops and Natural Vegetation, CRC Press, USA, pp. 131-144.
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Phenology is the study of annual recurring biological life cycle events and the drivers and controls of their periodicity. Shifts in phenology depict a plant's integrated response to climate and environmental changes and have become an important source of information on how plants are responding to climate change. Satellite data, with its synoptic views, repetitive sampling, and high spectral resolution offer numerous opportunities to advance the study of phenology. Thus far, satellite products have primarily contributed to coarse scale studies of “landscape phenology,” defined as the aggregate seasonal vegetation patterns sensed by satellites. Investigations of hyperspectral vegetation phenology are very limited and have yet to be exploited, yet phenologic life cycle events, such as flowering, leaf onset, and litterfall, can be quite dramatic visually, and will alter canopy optical properties. In this chapter, we review current knowledge of what is known about phenology optical signals at leaf, canopy, and landscape scales; we provide an overview of current and potential hyperspectral applications to assess life cycle events and determine phenophases; and we discuss the challenges and limitations of hyperspectral sensing in phenology applications. Hyperspectral applications covered include species detections based on unique phenology curves; optimal phenophases for species discrimination; and the spatiotemporal duality of phenological data, in which both climate as well as changes in species composition influence phenology. The key challenge is to integrate hyperspectral and finer spatial resolution data into phenology characterizations in order to resolve species phenology mixing. We conclude that hyperspectral data are key to advancing phenology science.

Johnson, A & Dubey, JP 2018, 'Foodborne Disease Handbook, Second Edition' in Foodborne Disease Handbook: Volume II: Viruses, Parasites, Pathogens, and HACCP, CRC Press, Boca Raton, pp. 389-405.
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The diagnosis of toxoplasmosis usually is based on one or more of the following: clinical signs, parasite isolation, antibody detection, cell-mediated responses, and antigen detection. However, the detection of Toxoplasma gondii DNA by polymerase chain reaction for diagnosis has become widespread. The clinical diagnosis of toxoplasmosis in humans is complicated due to the vast range and variation in degree of severity of symptoms. The most characteristic feature of acquired toxoplasmosis in the immunoincompetent host is central nervous system involvement. Along with the loss and reduction in quality of human life, toxoplasmosis causes great financial loss in the agricultural industry. Many serological tests have been used for the detection of immunoglobulin G T. gondii antibodies: Sabin-Feldman dye test, indirect hemagglutination, complement fixation, modified agglutination test, latex agglutination, indirect fluorescent antibody, and enzyme-linked immunosorbent assay. The diagnosis of toxoplasmosis has been confirmed by direct immunohistological detection of the parasite in tissue.

Kumar, M, Contreras-Porcia, L, Kumar, NM & Ralph, PJ 2018, 'Quantification and localization of reactive oxygen species in marine macrophytes' in Protocols for Macroalgae Research, CRC Press, pp. 267-277.
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Larkum, AWD, Kendrick, GA & Ralph, PJ 2018, 'Preface', pp. v-vii.
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Larkum, AWD, Pernice, M, Schliep, M, Davey, P, Szabo, M, Raven, JA, Lichtenberg, M, Brodersen, KE & Ralph, PJ 2018, 'Photosynthesis and Metabolism of Seagrasses' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 315-342.
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© Springer International Publishing AG, part of Springer Nature 2018. Seagrasses have a unique leaf morphology where the major site for chloroplasts is in the epidermal cells, stomata are absent and aerenchyma is present inside the epidermis. This means that the major site for photosynthesis is in the epidermis. Furthermore the lack of stomata means that the route for carbon uptake is via inorganic carbon (C i ) uptake across the vestigial cuticle and through the outer plasma membranes. Since the leaf may at times be in an unstirred situation diffusion through an unstirred layer outside the leaf may be a large obstacle to carbon uptake. The existence of a carbon concentrating mechanism is discussed, but its existence to date is not proven. Active bicarbonate uptake across the plasmalemma does not seem to operate; an external carbonic anhydrase and an extrusion of protons seem to play a role in enhancing CO 2 uptake. There is some evidence that a C4 mechanism plays a role in carbon fixation but more evidence from 'omics' is required. Photorespiration certainly occurs in seagrasses and an active xanthophyll cycle is present to cope with damaging high light, but both these biochemical mechanisms need further work. Finally, epiphytes pose a problem which impedes the uptake of C i and modifies the light environment inside the leaves.

Larkum, AWD, Waycott, M & Conran, JG 2018, 'Evolution and Biogeography of Seagrasses' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 3-29.
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© Springer International Publishing AG, part of Springer Nature 2018. Seagrasses are an organismal biological group united by their ability to grow in marine environments. As marine flowering plants they have evolved a combined suite of adaptations multiple times enabling the four known lineages containing species of seagrass to survive, and thrive, in the sea. Unlike many other biological groups of plants however, seagrasses are all derived from a single order of flowering plants, the Alismatales. This order, being derived early in the evolution of the monocotyledons, is comprised predominantly of aquatic plants, of all forms- emergent, submerged, freshwater, estuarine and marine. A review of seagrass fossils suggests that new discoveries of seagrass fossils along with confirmation of some earlier finds lead to a clear signal that some seagrass species had a wider distribution in the past compared with today. The discovery of new fossil sites should be encouraged as this will likely produce important valuable information on the evolution of this group. In general the biogeography of seagrasses suggests that these organisms evolved successfully in the Tethys Sea of the Late Cretaceous. However, the modern division into two groups, temperate and tropical tends to suggest that at some point an ecological separation occurred in both the Northern and Southern Hemispheres. There are a disproportionately large number of temperate seagrass species in southern Australia and there is significant endemism shown in Posidonia, Amphibolis and a unique species of Halophila (H. australis). The use of genetic and genomic techniques has begun to explain these distributions but we can expect a much bigger picture to emerge in the near future.

Morgan, RM, French, JC & Meakin, GE 2018, 'Understanding forensic trace evidence' in Routledge Handbook of Crime Science, Routledge, pp. 393-407.
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Mousley, JA & Matthews, C 2018, 'AUSTRALIA: Mathematics and its Teaching in Australia' in Series on Mathematics Education, WORLD SCIENTIFIC, pp. 113-155.
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Murray, S & Hallegraeff, G 2018, 'Harmful Algae Introductions: Vectors of Transfer, Mitigation, and Management' in Shumway, S, Burkholder, JA & Morton, S (eds), Harmful Algal Blooms A Compendium Desk Reference, Wiley, USA, pp. 493-506.
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Chapters in this volume will provide readers with information on causes of HAB, successful management and monitoring programs, control, prevention, and mitigation strategies, economic consequences of HAB, associated risks to human health, ...

Ralph, PJ, Crosswell, JR, Cannard, T & Steven, ADL 2018, 'Estimating Seagrass Blue Carbon and Policy Implications: The Australian Perspective' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 743-758.
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Rossy, Q, Décary-Hétu, D, Delémont, O & Mulone, M 2018, 'The Routledge International Handbook of Forensic Intelligence and Criminology' in Rossy, Q, Décary-Hétu, D, Delémont, O & Mulone, M (eds), The Routledge International Handbook of Forensic Intelligence and Criminology, Routledge, USA, pp. 65-76.
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© 2018 selection and editorial matter, Quentin Rossy, David Décary-Hétu, Olivier Delémont and Massimiliano Mulone; individual chapters, the contributors. The dominant conception of forensic sciences is as a patchwork of disciplines assisting the criminal justice system, but the 2009 NAS report questioned the robustness of the scientific foundations of essentially all the forensic science disciplines. Yet, solutions intended to counter this disturbing assessment have mainly focused on methodology upgrades epitomized by quality management strategies that are crowned by accreditation of laboratories and certification of individual forensic scientists.While a forensic science world without quality management is senseless, its reported and observed implementation begs the question whether it has developed from a necessary tool to a constraint contributing to frame a mistaken view of experimental sciences dedicated to responding to criminal and litigation matters. This article questions the adequacy of forensic-led regulation strategies for security problem-solving, calling fora better understanding of its original link with criminological concerns.

Schlögl, E 2018, 'Arbitrage-Free Interpolation in Models of Market Observable Interest Rates' in Sandmann, K & Schonbucher, PJ (eds), Advances in Finance and Stochastics: essays in honour of Dieter Sondermann, Springer-Verlag Berlin Heidelberg, Berlin, Germany, pp. 197-218.
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Models which postulate lognormal dynamics for interest rates which arecompounded according to market conventions, such as forward LIBOR or forwardswap rates, can be constructed initially in a discrete tenor framework.Interpolating interest rates between maturities in the discrete tenor structureis equivalent to extending the model to continuous tenor. The present papersets forth an alternative way of performing this extension; one which preservesthe Markovian properties of the discrete tenor models and guarantees thepositivity of all interpolated rates.

Scudder, N & Saw, B 2018, 'Health and Safety' in Behavioral Analysis, pp. 199-205.
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The health and safety of people at work are vitally important. The health and safety of forensic practitioners, who have to contend with a unique range of hazards, pose a challenge for both practitioners and management. While there are a myriad of hazards to deal with, effective controls of the risks can be undertaken, provided a systematic process is in place. Forensic practitioners work within the office and laboratory, as well as external environments outside of the control of management. Forensic practitioners can respond to major crime scenes in residential, corporate, industrial, and public places, ranging from a murder in a park to a postblast scene or an international deployment involving Disaster Victim Identification. The diverse role performed by forensic practitioners has challenged health and safety in this unique environment. This chapter discusses the value of documented risk assessments, introduces the concept of dynamic risk assessments and hierarchy of controls, besides providing specific information about a range of hazards identified in the laboratory and in the field.

Scudder, N & Saw, B 2018, 'Health and Safety' in Forensic Toxicology, pp. 347-354.
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The health and safety of people at work are vitally important. The health and safety of forensic practitioners, who have to contend with a unique range of hazards, pose a challenge for both practitioners and management. While there are a myriad of hazards to deal with, effective controls of the risks can be undertaken, provided a systematic process is in place. Forensic practitioners work within the office and laboratory, as well as external environments outside of the control of management. Forensic practitioners can respond to major crime scenes in residential, corporate, industrial, and public places, ranging from a murder in a park to a postblast scene or an international deployment involving Disaster Victim Identification. The diverse role performed by forensic practitioners has challenged health and safety in this unique environment. This chapter discusses the value of documented risk assessments, introduces the concept of dynamic risk assessments and hierarchy of controls, besides providing specific information about a range of hazards identified in the laboratory and in the field.

Seymour, JR, Laverock, B, Nielsen, DA, Trevathan-Tackett, SM & Macreadie, PI 2018, 'The Microbiology of Seagrasses' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 343-392.
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Like both terrestrial plants and other benthic marine organisms, seagrasses host abundant and diverse communities of microorganisms. These microbes fundamentally influence seagrass physiology and health, while also regulating the biogeochemical dynamics of entire seagrass meadows. Discrete populations of bacteria, fungi, microalgae, archaea and viruses inhabit seagrass leaves, roots and rhizomes and the surrounding sediments. The plethora of ecological interactions taking place between seagrasses and this microbiome span the continuum of symbiotic relationships from mutualism to parasitism. Indeed, the metabolic activities of some seagrass associated microbes, such as diazotrophic and sulphur oxidizing bacteria, govern the local chemical environment in ways that facilitate seagrass survival. On the other hand, pathogens, such as the protozoan parasite Labyrinthula cause disease outbreaks that can lead to mass seagrass die offs. While the role of the seagrass microbiome in defining the success of seagrass habitats is becoming increasingly apparent, there is still much to be learnt. For instance, the development of an understanding of how seagrass associated microbes may buffer or augment the negative impacts of growing environmental pressures will be valuable for informing decisions regarding the management and conservation of threatened seagrass habitats. In this chapter we will synthesise the current state of knowledge on the microbiology of seagrasses, with a goal of conveying the often overlooked importance of the seagrass microbiome in governing seagrass health and the biogeochemical stability of seagrass ecosystems.

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Advances in Hyperspectral Remote Sensing of Vegetation and Agricultural Crops' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 3-37.
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Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume II' in Hyperspectral Indices and Image Classifications for Agriculture and Vegetation, CRC Press, USA, pp. 251-286.
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This chapter provides a concise summary, insights, and highlights of the last 50 years of advances in hyperspectral remote sensing science pertaining to agriculture and vegetation. Topics covered in each of the 22 chapters of this Volume (Volume I: Hyperspectral Processes, Sensors, and Data Analysis) are discussed considering the strengths and limitations pertaining to specific topics. In a nutshell, this chapter provided here is the editor's view and guidance to readers on the essence of the volume. Readers can approach the summary chapter in two ways—either read it at the very beginning to get an overview of what to expect in various chapters, or read it at the very end to recall the main essence of the individual chapters and get the editor's perspective.

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume II: Hyperspectral Indices and Image Classifications for Agriculture and Vegetation' in Hyperspectral Indices and Image Classifications for Agriculture and Vegetation, pp. 251-286.
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This chapter provides a concise summary, insights, and highlights of the last 50 years of advances in hyperspectral remote sensing science pertaining to agriculture and vegetation. Topics covered in each of the 22 chapters of this Volume (Volume I: Hyperspectral Processes, Sensors, and Data Analysis) are discussed considering the strengths and limitations pertaining to specific topics. In a nutshell, this chapter provided here is the editor's view and guidance to readers on the essence of the volume. Readers can approach the summary chapter in two ways—either read it at the very beginning to get an overview of what to expect in various chapters, or read it at the very end to recall the main essence of the individual chapters and get the editor's perspective.

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume III' in Biophysical and Biochemical Characterization and Plant Species Studies, CRC Press, USA, pp. 303-341.
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The goal of this summary chapter is twofold. The first is to provide the reader an overview of the content of the preceding chapters. This they can read at the very beginning, before moving on to individual chapters in detail. Alternatively, they may read it at the very end to refresh their memory and to summarize the contents of the Volume. Second, this summary provides the editors’ perspective, bringing in their rich collective experience and expertise to guide the reader. We have kept the summaries brief and illustrative, so that the reader can quickly gather essential initial knowledge and guidance. The in-depth details can be found in the individual chapters.

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume IV' in Advanced Applications in Remote Sensing of Agricultural Crops and Natural Vegetation, CRC Press, USA, pp. 339-378.
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This conclusion presents some closing thoughts on the concepts covered in the preceding chapters of this book. The book focuses on precision farming applications using hyperspectral data. It highlights the need to have high spatial, high spectral, and frequent coverage resolutions of imagery for precision farming applications. The book also presents specific parameters modeled and mapped for precision farming applications and include: soil properties such as organic matter, electrical conductivity, potassium, manganese, pH, soil moisture, and soil salinity. It discusses the importance of flower mapping using the distinctive spectral characteristics of flowers, and studies the challenges and limitations of hyperspectral remote sensing in flower mapping. The book provides a fine synopsis of the existing state of knowledge in characterizing and mapping flowers using hyperspectral data in different environments using different sensors from various platforms. It suggests a clear methodology for modeling and mapping Crop water productivity using remote sensing.

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty-Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume I' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 395-436.
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Venkatesan, J, Anil, S, Singh, SK & Kim, S-K 2018, 'Recent Advances of Alginate Biomaterials in Tissue Engineering' in Marine Polysaccharides, Jenny Stanford Publishing, pp. 207-234.
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Wang, T, Liu, Y, Su, D & Wang, G 2018, '1D and 2D Flexible Carbon Matrix Materials for Lithium–Sulfur Batteries' in Flexible Energy Conversion and Storage Devices, Wiley, pp. 127-153.
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Wilkinson, S & Torpy, F 2018, 'Living Green Roofs' in Charlesworth, SM & Booth, CA (eds), Urban Pollution: Science and Management, Wiley, New York, pp. 131-145.
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© 2019 John Wiley & Sons Ltd. All rights reserved. There are increasing challenges for urban settlements in both developed and developing countries. This chapter explores the relationship between urban development, pollution, and green roofs as a valuable, contributory means of mitigating the effects of urban pollution using examples from two major Australian cities, Melbourne and Sydney. Pollution in urban environments can affect soil, water, and air, with the latter having the greatest effect on human health, well-being, and longevity. All cities are characterised by intense energy using activities and heat-retaining materials such as concrete and bitumen. These factors combine to create the ‘urban heat island effect’. Green roofs are versatile and can be used on flat and pitched roof designs. Green roofs have multiple benefits collectively or individually. Three different types of rooftop garden beds were used to provide three illustrative case studies.

Aaboud, M, Aad, G, Abbott, B, Abdinov, O, Abeloos, B, Abhayasinghe, DK, Abidi, SH, AbouZeid, OS, Abraham, NL, Abramowicz, H, Abreu, H, Abulaiti, Y, Acharya, BS, Adachi, S, Adamczyk, L, Adelman, J, Adersberger, M, Adiguzel, A, Adye, T, Affolder, AA, Afik, Y, Agheorghiesei, C, Aguilar-Saavedra, JA, Ahmadov, F, Aielli, G, Akatsuka, S, Åkesson, TPA, Akilli, E, Akimov, AV, Alberghi, GL, Albert, J, Albicocco, P, Alconada Verzini, MJ, Alderweireldt, S, Aleksa, M, Aleksandrov, IN, Alexa, C, Alexopoulos, T, Alhroob, M, Ali, B, Alimonti, G, Alison, J, Alkire, SP, Allaire, C, Allbrooke, BMM, Allen, BW, Allport, PP, Aloisio, A, Alonso, A, Alonso, F, Alpigiani, C, Alshehri, AA, Alstaty, MI, Alvarez Gonzalez, B, Álvarez Piqueras, D, Alviggi, MG, Amadio, BT, Amaral Coutinho, Y, Ambroz, L, Amelung, C, Amidei, D, Amor Dos Santos, SP, Amoroso, S, Amrouche, CS, Anastopoulos, C, Ancu, LS, Andari, N, Andeen, T, Anders, CF, Anders, JK, Anderson, KJ, Andreazza, A, Andrei, V, Anelli, CR, Angelidakis, S, Angelozzi, I, Angerami, A, Anisenkov, AV, Annovi, A, Antel, C, Anthony, MT, Antonelli, M, Antrim, DJA, Anulli, F, Aoki, M, Aparisi Pozo, JA, Aperio Bella, L, Arabidze, G, Araque, JP, Araujo Ferraz, V, Araujo Pereira, R, Arce, ATH, Ardell, RE, Arduh, FA, Arguin, J-F, Argyropoulos, S, Armbruster, AJ, Armitage, LJ, Armstrong, A, Arnaez, O, Arnold, H, Arratia, M, Arslan, O, Artamonov, A, Artoni, G, Artz, S, Asai, S, Asbah, N, Ashkenazi, A, Asimakopoulou, EM, Asquith, L, Assamagan, K, Astalos, R, Atkin, RJ, Atkinson, M, Atlay, NB, Augsten, K, Avolio, G, Avramidou, R, Ayoub, MK, Azuelos, G, Baas, AE, Baca, MJ, Bachacou, H, Bachas, K, Backes, M, Bagnaia, P, Bahmani, M, Bahrasemani, H, Bailey, AJ, Baines, JT, Bajic, M, Bakalis, C, Baker, OK, Bakker, PJ, Bakshi Gupta, D, Baldin, EM, Balek, P, Balli, F, Balunas, WK, Balz, J, Banas, E, Bandyopadhyay, A, Banerjee, S, Bannoura, AAE, Barak, L, Barbe, WM, Barberio, EL, Barberis, D, Barbero, M, Barillari, T, Barisits, M-S, Barkeloo, J, Barklow, T, Barlow, N, Barnea, R, Barnes, SL, Barnett, BM, Barnett, RM, Barnovska-Blenessy, Z, Baroncelli, A, Barone, G, Barr, AJ, Barranco Navarro, L, Barreiro, F, Barreiro Guimarães da Costa, J, Bartoldus, R, Barton, AE, Bartos, P, Basalaev, A, Bassalat, A, Bates, RL, Batista, SJ, Batlamous, S, Batley, JR, Battaglia, M, Bauce, M, Bauer, F, Bauer, KT, Bawa, HS & et al. 2018, 'Search for new phenomena in events with same-charge leptons and b-jets in pp collisions at $$ \sqrt{s}=13 $$ TeV with the ATLAS detector', Journal of High Energy Physics, vol. 2018, no. 12.
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Abstract A search for new phenomena in events with two same-charge leptons or three leptons and jets identified as originating from b-quarks in a data sample of 36.1 fb−1 of pp collisions at $$ \sqrt{s}=13 $$ s = 13 TeV recorded by the ATLAS detector at the Large Hadron Collider is reported. No significant excess is found and limits are set on vector-like quark, four-top-quark, and same-sign top-quark pair production. The observed (expected) 95% CL mass limits for a vector-like T- and B-quark singlet are m T > 0.98 (0.99) TeV and m B > 1.00 (1.01) TeV respectively. Limits on the production of the vector-like T 5/3-quark are also derived considering both pair and single production; in the former case the lower limit on the mass of the T 5/3-quark is (expected to be) 1.19 (1.21) TeV. The Standard Model four-top-quark production cross-section upper limit is (expected to be) 69 (29) fb. Constraints are also set on exotic four-top-quark production models. Finally, limits are s...

Abbasnejad, B, Thorby, W, Razmjou, A, Jin, D, Asadnia, M & Ebrahimi Warkiani, M 2018, 'MEMS piezoresistive flow sensors for sleep apnea therapy', Sensors and Actuators A: Physical, vol. 279, pp. 577-585.
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© 2018 Elsevier B.V. A MEMS liquid crystal polymer (LCP), used in the membrane-based pressure sensor, has been found highly useful as a flow sensor. Here we conducted a set of elaborate experiments using an air flow generator to investigate the potential of our LCP flow sensor for sleep apnea therapy. Critical properties of the LCP flow sensor, including flow range, resolution (sensitivity), accuracy, and response time, have been systematically characterized. As a result, LCP flow sensor achieves a limit of detection of 8 LPM to measure flow rate, better than the commercial flow sensor (>10 LPM). Our LCP flow sensor shows a favourable response in a large flow range (8–160 LPM) with a sensitivity of detecting a linear voltage response of 0.004 V per 1 LPM flow rate. With minimum detectable flow, high sensitivity and resolution, we further demonstrated our LCP flow sensor for detecting human respiration. Moreover, using a two- dimensional simulation in COMSOL Multiphysics, we demonstrated the deformation of LCP membrane in response to different flow velocities which leads to resistance change in sensor's strain gauge.

Abdul Halim, MF, Rodriguez, R, Stoltzfus, JD, Duggin, IG & Pohlschroder, M 2018, 'Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non‐homologous sortases from archaea and bacteria', Molecular Microbiology, vol. 108, no. 3, pp. 276-287.
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SummaryProper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C‐termini of substrates containing C‐terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid‐modified C‐terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram‐positive bacteria, which also process C‐termini of substrates whose C‐terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His‐Cys‐Arg residues of sortase catalytic sites. The study presented here shows that ArtAWT‐GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys173 (C173A), Arg214 (R214A) or Arg253 (R253A), and the serine substitution mutant for Cys173 (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtAC173A‐GFP, ArtAC173S‐GFP and ArtAR214A‐GFP cannot process substrates, while replacement of the third residue, ArtAR253A‐GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.

Achlatis, M, Pernice, M, Green, K, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2018, 'Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge', The ISME Journal, vol. 12, no. 5, pp. 1308-1318.
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Abstract Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of 15N-ammonium and 13C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially 13C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.

Afzal, I, Ahmad, MS, Malik, S, Ibrahim, M, Al Ayed, OS, Qadir, G, Al Doghaither, H & Gull, M 2018, 'Thermodynamics and Kinetics Parameters of Eichhornia crassipes Biomass for Bioenergy', Protein & Peptide Letters, vol. 25, no. 2, pp. 187-194.
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BACKGROUND: Eichhornia crassipes is an aquatic plant well known for its role in soil reclamation due to the containment of valuable nutrients. Moreover, its biomass is an abundant and low-cost biological resource. Pyrolysis of a biomass offers one of the cleanest methods to harness the bioenergy stored in the biomass. OBJECTIVE: The present study was focused on evaluating the bioenergy potential of Eichhornia crassipes via pyrolysis. METHODS: Biomass of E. crassipes was collected from a municipal wastewater pond. Oven dried powdered biomass of E. crassipes was subjected to pyrolysis at three heating rates including 10, 30 and 50 °C min-1 in a simultaneous Thermogravimetry-Differential Scanning Calorimetry analyzer under an inert environment containing nitrogen. Data obtained were subjected to isoconversional models of Kissenger-Akahira-Sunose (KSA) and Flynn-Wall-Ozawa (FWO) to understand the reaction chemistry. RESULTS: Kinetic parameters have shown that the pyrolysis followed first-order reaction kinetics. The average values of activation energies (129.71-133.03 kJ mol-1) and thermodynamic parameters including high heating values (18.12 MJ kg-1), Gibb's free energies (171-180 kJ mol-1) and enthalpy of reaction (124-127 kJ mol-1) have shown the remarkable bioenergy potential of this biomass. CONCLUSION: This low-cost biomass may be used to produce liquids, gases, and biochar in a costefficient and environmentally friendly way via pyrolysis or co-pyrolysis in the future.

Agbowuro, AA, Huston, WM, Gamble, AB & Tyndall, JDA 2018, 'Proteases and protease inhibitors in infectious diseases', Medicinal Research Reviews, vol. 38, no. 4, pp. 1295-1331.
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AbstractThere are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3‐4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti‐infective agents.

Agbowuro, AA, Mazraani, R, McCaughey, LC, Huston, WM, Gamble, AB & Tyndall, JDA 2018, 'Stereochemical basis for the anti-chlamydial activity of the phosphonate protease inhibitor JO146', Tetrahedron, vol. 74, no. 12, pp. 1184-1190.
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© 2017 Elsevier Ltd JO146, a mixture of two diastereomers of a peptidic phosphonate inhibitor for Chlamydial HtrA (CtHtrA), has reported activity against Chlamydia species in both human and koala. In this study we isolated the individual diastereomers JO146-D1 and JO146-D2 (in ≥90% purity) and assessed their individual inhibitory activity against the serine protease human neutrophil elastase (HNE) which is structurally and functionally related to CtHtrA, as well as in Chlamydia trachomatis cell culture. JO146-D2 [S,S,R-Boc-Val-Pro-Val P (OPh) 2 ], the isomer with the physiologically relevant valine at P1, had an approximate 2.5 – fold increase in in vitro HNE inhibition potency over JO146-D1 [S,S,S-Boc-Val-Pro-Val P (OPh) 2 ] and greater than 100 – fold increase in cellular anti-chlamydial activity compared to JO146-D1 which possesses the unnatural valine at P1. JO146 and the individual diastereomers had excellent selectivity for the serine protease HNE over the potential off-target serine proteases trypsin and chymotrypsin. Docking studies supported the biological data with a geometrically unfavoured interaction observed between the P1 valine residue of JO146-D1 and the enzyme S1 sub-pocket.

Agius, A, Morelato, M, Moret, S, Chadwick, S, Jones, K, Epple, R, Brown, J & Roux, C 2018, 'Dataset of coded handwriting features for use in statistical modelling', Data in Brief, vol. 16, pp. 1010-1024.
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© 2017 The Authors The data presented here is related to the article titled, “Using handwriting to infer a writer's country of origin for forensic intelligence purposes” (Agius et al., 2017) [1]. This article reports original writer, spatial and construction characteristic data for thirty-seven English Australian1 writers and thirty-seven Vietnamese writers. All of these characteristics were coded and recorded in Microsoft Excel 2013 (version 15.31). The construction characteristics coded were only extracted from seven characters, which were: ‘g’ ‘h’ ‘th’ ‘M’ ‘0’ ‘7’ and ‘9’. The coded format of the writer, spatial and construction characteristics is made available in this Data in Brief in order to allow others to perform statistical analyses and modelling to investigate whether there is a relationship between the handwriting features and the nationality of the writer, and whether the two nationalities can be differentiated. Furthermore, to employ mathematical techniques that are capable of characterising the extracted features from each participant.

Agius, A, Morelato, M, Moret, S, Chadwick, S, Jones, K, Epple, R, Brown, J & Roux, C 2018, 'Using handwriting to infer a writer’s country of origin for forensic intelligence purposes', Forensic Science International, vol. 282, pp. 144-156.
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© 2017 Elsevier B.V. Forensic science has traditionally focused the majority of its resources and objectives towards addressing Court-related questions. However, this view restricts the contribution of forensic science to one process and results in a loss of information as the investigative and intelligence roles are largely neglected. A forensic science discipline suffering from this imbalance is handwriting examination, which may be characterised as a time consuming and subjective process that is mostly carried out towards the end of the investigation for the purpose of judicial proceedings. Individual and habitual characteristics are the major handwriting features exploited, however alternate information concerning the author's native language could potentially be used as a key element in an intelligence framework. This research focussed on the detection of characteristics that differentiate Vietnamese and English Australian writers based on their English handwriting. The study began with the extraction of handwriting characteristics from the writing of people from the two populations. The data was analysed using a logistic regression model and a classification and regression tree (CRT). Each recognised four class characteristics that were capable of distinguishing between the two nationalities. The logistic regression and CRT models were both capable of correctly predicting 93% of cases. Their predictive capabilities were then tested and supported using blind exemplars in order to mirror casework settings. It appeared that when using their respective class characteristics, the two models were capable of differentiating English Australians from Vietnamese in the data set. This proof of concept research demonstrated the plausibility of exploiting this additional information from a handwriting trace and taking advantage of it in an intelligence-led framework.

Ahmed, Z, Pauszek, SJ, Ludi, A, LaRocco, M, Khan, E, Afzal, M, Arshed, MJ, Farooq, U, Arzt, J, Bertram, M, Brito, B, Naeem, K, Abubakar, M & Rodriguez, LL 2018, 'Genetic diversity and comparison of diagnostic tests for characterization of foot‐and‐mouth disease virus strains from Pakistan 2008–2012', Transboundary and Emerging Diseases, vol. 65, no. 2, pp. 534-546.
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We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.

Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, SA & Seymour, JR 2018, 'The Microbiome of the Cosmopolitan Diatom Leptocylindrus Reveals Significant Spatial and Temporal Variability', Frontiers in Microbiology, vol. 9, no. NOV.
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Copyright © 2018 Ajani, Kahlke, Siboni, Carney, Murray and Seymour. The ecological interactions between phytoplankton and marine bacteria have important implications for the productivity and biogeochemistry of ocean ecosystems. In this study we characterized the microbial assemblages associated with multiple isolates of the ecologically important diatom Leptocylindrus using amplicon sequencing of the 16S rRNA gene, to examine levels of conservation of the microbiome across closely related species or strains. We also assessed if the microbiome structure of a given diatom strain was dependent on the location from which it was isolated and if the microbiome of cultured isolates significantly changed overtime from the seawater in which they were isolated. The bacterial assemblages from 36 strains belonging to three species (Leptocylindrus danicus, Leptocylindrus convexus, and Leptocylindrus aporus) isolated from six locations spanning > 1000 km of south east Australian coastline over 1 year, were dominated by the Rhodobacteraceae (∼60%) and the Flavobacteriaceae (∼10%). Across all strains, only one 'core OTU' (Roseovarius sp.) was identified across all samples. We observed no significant differences in bacterial community composition between diatom species. Significant differences in microbiome structure were, however, observed between diatom strains collected at different sampling times and from differing locations, albeit these two factors were coupled. Moreover, while bacterial communities under domestication varied from the seawater in which they were isolated, they remained specific to the location/month of origin, i.e., different regions and time points harbored distinct bacterial communities. Our study delivers new knowledge in relation to diatom-bacterial associations, revealing that the location/time from which a diatom is isolated plays an important role in shaping its microbiome.

Ajani, PA, Larsson, ME, Woodcock, S, Rubio, A, Farrell, H, Brett, S & Murray, SA 2018, 'Bloom drivers of the potentially harmful dinoflagellate Prorocentrum minimum (Pavillard) Schiller in a south eastern temperate Australian estuary', Estuarine, Coastal and Shelf Science, vol. 215, pp. 161-171.
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© 2018 Elsevier Ltd Harmful algal blooms are an increasing concern in the estuarine reaches of the Hawkesbury-Nepean River, one of the largest coastal rivers systems in south eastern Australia. In the austral spring of 2016, an unprecedented bloom of the harmful mixotrophic dinoflagellate Prorocentrum minimum occurred in Berowra Creek (maximum cell abundance 1.9E+06 cells L−1, 89% of the total phytoplankton community), a major tributary of this river system. In response to this bloom, our study utilises an estuary-wide, thirteen-year time series of phytoplankton abundance and environmental data to examine the spatial and temporal patterns of this harmful alga and its potential bloom drivers in this system. P. minimum cell densities and environmental parameters varied over large spatial scales, with sites located in the main channel of the estuary significantly differing from those in the more urbanized tributary of Berowra Creek. Generalised additive modelling outputs suggested that blooms of P. minimum are complex, but generally corresponded to a spatial gradient of eutrophication and salinity, whereby P. minimum growth and concomitant high chlorophyll-a concentrations were enhanced at sites that were generally less saline and more eutrophic than others. Furthermore, temporal patterns suggested that blooms occurred abruptly and lasted up to three weeks, most often during the austral autumn to spring. While significant correlations were observed between rainfall and nutrients at all other sites, suggesting a pathway for nutrient availability, the association between rainfall and nutrient delivery was generally not observed in Berowra Creek (a 15-m deep site) suggesting that a continual supply of nutrients, coupled with unique bathymetry and water residence time at this site, are the most likely contributing factors to phytoplankton growth. This study presents the most comprehensive examination of P. minimum in any southern hemisphere estuary to date and...

Ajani, PA, McGinty, N, Finkel, ZV & Irwin, AJ 2018, 'Phytoplankton Realized Niches Track Changing Oceanic Conditions at a Long-Term Coastal Station off Sydney Australia', Frontiers in Marine Science, vol. 5, pp. 1-12.
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Ajani, PA, Verma, A, Lassudrie, M, Doblin, MA & Murray, SA 2018, 'A new diatom species P. hallegraeffii sp. nov. belonging to the toxic genus Pseudo-nitzschia (Bacillariophyceae) from the East Australian Current', PLOS ONE, vol. 13, no. 4, pp. e0195622-e0195622.
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© 2018 Ajani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. A new species belonging to the toxin producing diatom genus Pseudo-nitzschia, P. hallegraeffii sp. nov., is delineated and described from the East Australian Current (EAC). Clonal cultures were established by single cell isolation from phytoplankton net hauls collected as part of a research expedition in the EAC region in 2016 on the RV Investigator. Cultures were assessed for their morphological and genetic characteristics, their sexual compatibility with other Pseudo-nitzschia species, and their ability to produce domoic acid. Light and transmission electron microscopy revealed cells which differed from their closest relatives by their cell width, rows of poroids, girdle band structure and density of band straie. Phylogenetic analyses based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions showed this novel genotype clustered within the P. delicatissima complex, but formed a discrete clade from its closest relatives P. dolorosa, P. simulans, P. micropora and P. delicatissima. Complementary base changes (CBCs) were observed in the secondary structure of the 3’ nuclear ribosomal transcribed spacer sequence region (ITS2) between P. hallegraeffii sp. nov. and its closest related taxa, P. simulans and P. dolorosa. Under laboratory conditions, and in the absence of any zooplankton cues, strains of P. hallegraeffii sp. nov. did not produce domoic acid (DA) and were not sexually compatible with any other Pseudo-nitzschia clones tested. A total of 18 Pseudo-nitzschia species, including three confirmed toxigenic species (P. cuspidata, P. multistriata and P. australis) have now been unequivocally confirmed from eastern Australia.

Alabd, R, Safavi-Naeini, M, Wilson, KJ, Rosenfeld, AB & Franklin, DR 2018, 'A simulation study of BrachyShade, a shadow-based internal source tracking system for HDR prostate brachytherapy', Physics in Medicine & Biology, vol. 63, no. 20, pp. 205019-205019.
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This paper presents a simulation study of BrachyShade, a proposed internal source-tracking system for real time quality assurance in high dose rate prostate brachytherapy. BrachyShade consists of a set of spherical tungsten occluders located above a pixellated silicon photodetector. The source location is estimated by minimising the mean squared error between a parametric model of the shadow image and acquired images of the shadows projected on the detector plane. A novel algorithm is finally employed to correct the systemic error resulting from Compton scattering in the medium. The worst-case error obtained with BrachyShade for a 13.5 ms image acquisition is less than 1.3 mm in the most distant part of the treatment volume, while for 75% of source locations an error of less than 0.42 mm was achieved.

Al-Asfi, M, McNevin, D, Mehta, B, Power, D, Gahan, ME & Daniel, R 2018, 'Assessment of the Precision ID Ancestry panel', International Journal of Legal Medicine, vol. 132, no. 6, pp. 1581-1594.
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© 2018 Springer-Verlag GmbH Germany, part of Springer Nature Abstract The ability to provide accurate DNA-based forensic intelligence requires analysis of multiple DNA markers to predict the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of biological evidence. Massively parallel sequencing (MPS) enables the analysis of hundreds of DNA markers in multiple samples simultaneously, increasing the value of the intelligence provided to forensic investigators while reducing the depletion of evidential material resulting from multiple analyses. The Precision ID Ancestry Panel (formerly the HID Ion AmpliSeq™ Ancestry Panel) (Thermo Fisher Scientific) (TFS)) consists of 165 autosomal SNPs selected to infer BGA. Forensic validation criteria were applied to 95 samples using this panel to assess sensitivity (1 ng-15 pg), reproducibility (inter- and intra-run variability) and effects of compromised and forensic casework type samples (artificially degraded and inhibited, mixed source and aged blood and bone samples). BGA prediction accuracy was assessed using samples from individuals who self-declared their ancestry as being from single populations of origin (n = 36) or from multiple populations of origin (n = 14). Sequencing was conducted on Ion 318™ chips (TFS) on the Ion PGM™ System (TFS). HID SNP Genotyper v4.3.1 software (TFS) was used to perform BGA predictions based on admixture proportions (continental level) and likelihood estimates (sub-population level). BGA prediction was accurate at DNA template amounts of 125pg and 30pg using 21 and 25 PCR cycles respectively. HID SNP Genotyper continental level BGA assignments were concordant with BGAs for self-declared East Asian, African, European and South Asian individuals. Compromised, mixed source and admixed samples, in addition to sub-population level prediction, requires more extensive analysis.

Al-Badri, G & Castorina, A 2018, 'Insights into the Role of Neuroinflammation in the Pathogenesis of Multiple Sclerosis', Journal of Functional Morphology and Kinesiology, vol. 3, no. 1, pp. 13-13.
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Multiple sclerosis (MS) is a devastating disease, and with the increasing number of cases each year, it is becoming a significant socioeconomic burden for the affected people and the entire community. The aetiology of MS is largely unknown, but genetic susceptibility, exposure to infections and/or environmental toxicants are recognised as risk factors. MS is characterised by the appearance of lesions/plaques in the central nervous system, caused by destruction of the myelin sheet by auto-reactive T cells. Symptoms range from mild impairment of daily motor functions to severe sensory and cognitive disabilities necessitating mobility assistance, medical and support from caregivers. Due to the progressive nature of the disease, MS is gaining more attention and research to better understand its multifaceted pathogenesis. In the present review, we focus on some of the latest research related to the neuroinflammatory component of the disease, since it appears to play a critical role in MS pathogenesis. The goal is to shed more light on this specific domain of MS, in an attempt to assist in the identification of novel treatment trajectories and management plans.

Alfeus, M, Grasselli, M & Schlögl, E 2018, 'A Consistent Stochastic Model of the Term Structure of Interest Rates for Multiple Tenors', Journal of Economic Dynamics and Control, vol. 114.
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Explicitly taking into account the risk incurred when borrowing at a shortertenor versus lending at a longer tenor ('roll-over risk'), we construct astochastic model framework for the term structure of interest rates in which afrequency basis (i.e. a spread applied to one leg of a swap to exchange onefloating interest rate for another of a different tenor in the same currency)arises endogenously. This rollover risk consists of two components, a creditrisk component due to the possibility of being downgraded and thus facing ahigher credit spread when attempting to roll over short-term borrowing, and acomponent reflecting the (systemic) possibility of being unable to roll overshort-term borrowing at the reference rate (e.g., LIBOR) due to an absence ofliquidity in the market. The modelling framework is of 'reduced form' in thesense that (similar to the credit risk literature) the source of credit risk isnot modelled (nor is the source of liquidity risk). However, the framework hasmore structure than the literature seeking to simply model a different termstructure of interest rates for each tenor frequency, since relationshipsbetween rates for all tenor frequencies are established based on the modelledroll-over risk. We proceed to consider a specific case within this framework,where the dynamics of interest rate and roll-over risk are driven by amultifactor Cox/Ingersoll/Ross-type process, show how such model can becalibrated to market data, and used for relative pricing of interest ratederivatives, including bespoke tenor frequencies not liquidly traded in themarket.

Ali, H & Singh, SK 2018, 'Preparation and characterization of solid lipid nanoparticles of furosemide using quality by design', Particulate Science and Technology, vol. 36, no. 6, pp. 695-709.
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Alijani, H, Çetin, B, Akkuş, Y & Dursunkaya, Z 2018, 'Effect of design and operating parameters on the thermal performance of aluminum flat grooved heat pipes', Applied Thermal Engineering, vol. 132, pp. 174-187.
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Almohaywi, B, Taunk, A, Wenholz, DS, Nizalapur, S, Biswas, NN, Ho, KKK, Rice, SA, Iskander, G, Black, DS, Griffith, R & Kumar, N 2018, 'Design and Synthesis of Lactams Derived from Mucochloric and Mucobromic Acids as Pseudomonas aeruginosa Quorum Sensing Inhibitors', Molecules, vol. 23, no. 5, pp. 1106-1106.
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Bacterial infections, particularly hospital-acquired infections caused by Pseudomonas aeruginosa, have become a global threat with a high mortality rate. Gram-negative bacteria including P. aeruginosa employ N-acyl homoserine lactones (AHLs) as chemical signals to regulate the expression of pathogenic phenotypes through a mechanism called quorum sensing (QS). Recently, strategies targeting bacterial behaviour or QS have received great attention due to their ability to disarm rather than kill pathogenic bacteria, which lowers the evolutionary burden on bacteria and the risk of resistance development. In the present study, we report the design and synthesis of N-alkyl- and N-aryl 3,4 dichloro- and 3,4-dibromopyrrole-2-one derivatives through the reductive amination of mucochloric and mucobromic acid with aliphatic and aromatic amines. The quorum sensing inhibition (QSI) activity of the synthesized compounds was determined against a P. aeruginosa MH602 reporter strain. The phenolic compounds exhibited the best activity with 80% and 75% QSI at 250 µM and were comparable in activity to the positive control compound Fu-30. Computational docking studies performed using the LasR receptor protein of P. aeruginosa suggested the importance of hydrogen bonding and hydrophobic interactions for QSI.

Alqudah, A, McKinley, MC, McNally, R, Graham, U, Watson, CJ, Lyons, TJ & McClements, L 2018, 'Risk of pre‐eclampsia in women taking metformin: a systematic review and meta‐analysis', Diabetic Medicine, vol. 35, no. 2, pp. 160-172.
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AbstractAimsTo perform meta‐analyses of studies evaluating the risk of pre‐eclampsia in high‐risk insulin‐resistant women taking metformin prior to, or during pregnancy.MethodsA search was conducted of the Medline, EMBASE, Web of Science and Scopus databases. Both randomized controlled trials and prospective observational cohort studies of metformin treatment vs. placebo/control or insulin either prior to or during pregnancy were selected. The main outcome measure was the incidence of pre‐eclampsia in each treatment group.ResultsOverall, in five randomized controlled trials comparing metformin treatment (n = 611) with placebo/control (n = 609), no difference in the risk of pre‐eclampsia was found [combined/pooled risk ratio (RR), 0.86 (95% CI 0.33–2.26); P = 0.76; I2 = 66%]. Meta‐analysis of four cohort studies again showed no significant effect [RR, 1.21 (95% CI 0.56–2.61); P = 0.62; I2 = 30%]. A meta‐analysis of eight randomized controlled trials comparing metformin (n = 838) with insulin (n = 836), however, showed a reduced risk of pre‐eclampsia with metformin...

Alvarez, G, Schulte, J, Stockton, G & Wheeler, D 2018, 'A useful demonstration of calculus in a physics high school laboratory', Physics Education, vol. 53, no. 1, pp. 015006-015006.
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© 2017 IOP Publishing Ltd. The real power of calculus is revealed when it is applied to actual physical problems. In this paper, we present a calculus inspired physics experiment suitable for high school and undergraduate programs. A model for the theory of the terminal velocity of a falling body subject to a resistive force is developed and its validity tested in an experiment of a falling magnet in a column of self-induced eddy currents. The presented method combines multiple physics concepts such as 1D kinematics, classical mechanics, electromagnetism and non-trivial mathematics. It offers the opportunity for lateral as well as project-based learning.

Andersson, J, Fuller, MA, Wood, K, Holt, SA & Köper, I 2018, 'A tethered bilayer lipid membrane that mimics microbial membranes', Physical Chemistry Chemical Physics, vol. 20, no. 18, pp. 12958-12969.
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This work presents a self-assembled lipid bilayer architecture mimicking the outer membrane of Gram negative bacteria.

Angeloski, A, Gentle, AR, Scott, JA, Cortie, MB, Hook, JM, Westerhausen, MT, Bhadbhade, M, Baker, AT & McDonagh, AM 2018, 'From Lead(II) Dithiocarbamate Precursors to a Fast Response PbS Positive Temperature Coefficient Thermistor', Inorganic Chemistry, vol. 57, no. 4, pp. 2132-2140.
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© 2018 American Chemical Society. PbS submicron crystals were formed by thermolysis of two different lead dithiocarbamate complexes. These precursors were readily synthesized and fully characterized, and in situ synchrotron powder diffraction experiments were performed to characterize their decomposition. The structure and purity of resultant PbS was examined using scanning electron and transmission electron microscopies, powder X-ray diffraction, and infrared spectroscopy. Submicron crystalline PbS was used to create a new PbS thermistor with excellent sensitivity and an ultrarapid thermal response time.

Antonosyan, DA, Solntsev, AS & Sukhorukov, AA 2018, 'Photon-pair generation in a quadratically nonlinear parity-time symmetric coupler', Photonics Research, vol. 6, no. 4, pp. A6-A6.
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© 2018 Chinese Laser Press. Integrated nonlinear waveguide structures enable generation of quantum entangled photons. We describe theoretically the effects of spatially inhomogeneous loss on the creation of photon pairs through spontaneous parametric down-conversion in quadratically nonlinear directional couplers, where photons experience effective parity-time (PT) symmetric potential due to the presence of optical loss in one of the waveguides. We show that for losses below the PT-breaking threshold, the quantum photon states can be flexibly tuned similarly to conservative couplers, whereas for stronger losses, the correlations between two waveguide modes are suppressed. We also formulate a quantum-classical correspondence with sum-frequency generation for fast evaluation of device performance. These results can be applied for the design of quantum plasmonic circuits.

Archer, MS, Jones, SD & Wallman, JF 2018, 'Delayed reception of live blowfly (Calliphora vicina and Chrysomya rufifacies) larval samples: implications for minimum postmortem interval estimates', Forensic Sciences Research, vol. 3, no. 1, pp. 27-39.
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© 2017, © 2017 The Author(s). Published by Taylor & Francis Group on behalf of the Academy of Forensic Science. Forensic entomology evidence collected by police and mortuary staff may be delayed in getting to the entomologist. Live samples may continue developing and alter minimum postmortem interval (PMI min ) estimates. This study investigated development of simulated evidential samples of Calliphora vicina Robineau-Desvoidy and Chrysomya rufifacies (Macquart) (Diptera: Calliphoridae) maggots. Maggots of each species were studied in three developmental classes: “small” (late second/early third instar), “mid” (mid third instar) and “large” (late third instar). Seven replicates of 11 maggots in each class were assigned without food to four treatments: (1) 24 h at 20 °C; (2) 24 h at 4 °C; (3) 48 h at 20 °C and (4) 48 h at 4 °C. There was a significant difference in absolute length change across treatments, reflecting size for C. vicina, and interaction between size, time and temperature for Ch. rufifacies. Calliphora vicina maggots showed minimal mortality, and most second instar larvae moulted by the experiment's end. Chrysomya rufifacies showed heavy mortality and minimal moulting from the second to third instar. Only “large” Ch. rufifacies maggots kept at room temperature for 48 h pupariated. Since these results confirm that development can continue in live unfed maggot samples after their collection, it is not advisable to delay their preservation.

Asatryan, AA & Novikov, A 2018, 'Anderson localization of classical waves in weakly scattering one-dimensional Levy lattices', Physical Review B, vol. 98, no. 23, pp. 235144-1-235144-8.
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Assadi, MHN, Fronzi, M, Ford, M & Shigeta, Y 2018, 'High-performance Na ion cathodes based on the ubiquitous and reversible O redox reaction', Journal of Materials Chemistry A, vol. 6, no. 47, pp. 24120-24127.
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We identified high capacity, high voltage and low-strain Na cathode materials that rely on the reversible oxygen redox reaction.

Awasthi, R, Rathbone, MJ, Hansbro, PM, Bebawy, M & Dua, K 2018, 'Therapeutic prospects of microRNAs in cancer treatment through nanotechnology', Drug Delivery and Translational Research, vol. 8, no. 1, pp. 97-110.
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© 2017, Controlled Release Society. MicroRNAs (miRNAs) represent a new class of diagnostic and prognostic biomarker as well as new therapeutic targets in cancer therapy. miRNAs are gaining significant interest due to extensive advancements in knowledge since their discovery and, more recently, their translational application as therapeutic moieties and targets in the management of disease. miRNAs used in the treatment of cancer would position them as a new class of emerging therapeutic agents. Indeed, numerous candidate miRNAs have been identified as having therapeutic application in the treatment of cancer, but there is still much to learn about how to transform these into effective, patient-compliant, and targeted drug delivery systems. In this mini review, we discuss the utility and potential of nanotechnology in miRNA formulation and delivery with particular emphasis on cancer, including their role in conferring multidrug resistance and metastatic capacity. This review benefits both the formulation and biological scientists in understanding and exploring the new vistas of miRNA delivery using nanotechnology in the cancer clinically.

Awasthi, R, Roseblade, A, Hansbro, PM, Rathbone, MJ, Dua, K & Bebawy, M 2018, 'Nanoparticles in Cancer Treatment: Opportunities and Obstacles', Current Drug Targets, vol. 19, no. 14, pp. 1696-1709.
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In the United States, the estimated number of new cancer cases in 2018 will be approx. 1.7 million. Historically, combination chemotherapy has been the primary choice of treatment. However, chemotherapeutics have pharmaceutical limitations, among which include problems with stability and aqueous solubility. Likewise, dose limiting toxicity is significant with nonspecific toxicity to healthy cells, hair loss, loss of appetite, peripheral neuropathy and diarrhea being typical side effects. The emergence of Multidrug resistance (MDR) also presents s a significant challenge for the successful treatment of cancer whereby cancer cells become cross resistant to many of the chemotherapeutic agents used. Nanotechnology presents a new frontier for cancer treatment. It holds potential in minimizing systemic toxicity through the development of functionalized particles for targeted treatment. They also provide an alternative strategy to circumvent multidrug resistance as they have a capacity to by-pass the drug efflux mechanism associated with this phenotype. Aside from the advantages they offer in treatment, nanoparticles are also emerging to be valuable diagnostic entities. This article highlights the various ways nanotechnology is being used to improve the treatment and management of cancer. We also discuss the opportunities and obstacles in this area and provide an up to date review of progress in the treatment of cancer.

Baek, J-S, Tan, CH, Ng, NKJ, Yeo, YP, Rice, SA & Loo, SCJ 2018, 'A programmable lipid-polymer hybrid nanoparticle system for localized, sustained antibiotic delivery to Gram-positive and Gram-negative bacterial biofilms', Nanoscale Horizons, vol. 3, no. 3, pp. 305-311.
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Lipid-polymer hybrid nanoparticle enhances antibiotic efficacy through localised, sustained delivery to bacterial biofilms.

Baffour, B, Silva, D, Veiga, A, Sexton, C & Brown, JJ 2018, 'Small area estimation strategy for the 2011 Census in England and Wales', Statistical Journal of the IAOS, vol. 34, no. 3, pp. 395-407.
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© 2018-IOS Press and the authors. All rights reserved. The use of model-based small area estimation for adjusting census results in the UK was first introduced in the 2001 Census. The aim was to obtain local level population estimates by age-sex groups, adjusted for the level of undercount that combined results from the Census and the Census Coverage Survey. A similar approach was adopted for the 2011 Census but with new features and this paper describes the work carried out to arrive at the chosen small area strategy. Simulation studies are used to investigate three proposed small area estimation methods: a local fixed effects model (the 2001 Census approach), a direct estimator and a synthetic estimator. The results indicate that both the synthetic and the local fixed effect models constitute good options to produce accurate and reliable local authority population estimates. A proposal is made to implement a small area estimation procedure that accommodates both the synthetic and local fixed models, as in some selected areas with differing local authority under-coverage rates a local fixed effects model may perform best. We examine this strategy under real census conditions based on the final results from the 2011 census.

Baines, KJ, Wright, TK, Gibson, PG, Powell, H, Hansbro, PM & Simpson, JL 2018, 'Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD', ERJ Open Research, vol. 4, no. 4, pp. 00031-2018.
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Long-term, low-dose azithromycin reduces exacerbation frequency in chronic obstructive pulmonary disease (COPD), yet the mechanism remains unclear. This study characterised genome-wide gene expression changes in patients with neutrophilic COPD following long-term, low-dose azithromycin treatment.Patients with neutrophilic COPD (>61% or >162×104cells per mL sputum neutrophils) were randomised to receive either azithromycin or placebo for 12 weeks. Sputum and blood were obtained before and after 12 weeks of treatment. Gene expression was defined using microarrays. Networks were analysed using the Search Tool for the Retrieval of Interacting Gene database.In sputum, 403 genes were differentially expressed following azithromycin treatment (171 downregulated and 232 upregulated), and three following placebo treatment (one downregulated and two upregulated) compared to baseline (adjusted p<0.05 by paired t-test, fold-change >1.5). In blood, 138 genes were differentially expressed with azithromycin (121 downregulated and 17 upregulated), and zero with placebo compared to baseline (adjusted p<0.05 by paired t-test, fold-change >1.3). Network analysis revealed one key network in both sputum (14 genes) and blood (46 genes), involving interferon-stimulated genes, human leukocyte antigens and genes regulating T-cell responses.Long-term, low-dose azithromycin is associated with downregulation of genes regulating antigen presentation, interferon and T-cell responses, and numerous inflammatory pathways in the airways and blood of neutrophilic COPD patients.

Baker, KG, Radford, DT, Evenhuis, C, Kuzhiumparam, U, Ralph, PJ & Doblin, MA 2018, 'Thermal niche evolution of functional traits in a tropical marine phototroph', Journal of Phycology, vol. 54, no. 6, pp. 799-810.
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Land‐based plants and ocean‐dwelling microbial phototrophs known as phytoplankton, are together responsible for almost all global primary production. Habitat warming associated with anthropogenic climate change has detrimentally impacted marine primary production, with the effects observed on regional and global scales. In contrast to slower‐growing higher plants, there is considerable potential for phytoplankton to evolve rapidly with changing environmental conditions. The energetic constraints associated with adaptation in phytoplankton are not yet understood, but are central to forecasting how global biogeochemical cycles respond to contemporary ocean change. Here, we demonstrate a number of potential trade‐offs associated with high‐temperature adaptation in a tropical microbial eukaryote, Amphidinium massartii (dinoflagellate). Most notably, the population became high‐temperature specialized (higher fitness within a narrower thermal envelope and higher thermal optimum), and had a greater nutrient requirement for carbon, nitrogen and phosphorus. Evidently, the energetic constraints associated with living at elevated temperature alter competiveness along other environmental gradients. While high‐temperature adaptation led to an irreversible change in biochemical composition (i.e., an increase in fatty acid saturation), the mechanisms underpinning thermal evolution in phytoplankton remain unclear, and will be crucial to understanding whether the trade‐offs observed here are species‐specific or are representative of the evolutionary constraints in all phytoplankton.

Baldeaux, J, Ignatieva, K & Platen, E 2018, 'Detecting money market bubbles', Journal of Banking & Finance, vol. 87, pp. 369-379.
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Bao, G, Wong, K-L, Jin, D & Tanner, PA 2018, 'A stoichiometric terbium-europium dyad molecular thermometer: energy transfer properties', Light: Science & Applications, vol. 7, no. 1, pp. 1-10.
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AbstractThe optical thermometer has shown great promise for use in the fields of aeronautical engineering, environmental monitoring and medical diagnosis. Self-referencing lanthanide thermo-probes distinguish themselves because of their accuracy, calibration, photostability, and temporal dimension of signal. However, the use of conventional lanthanide-doped materials is limited by their poor reproducibility, random distance between energy transfer pairs and interference by energy migration, thereby restricting their utility. Herein, a strategy for synthesizing hetero-dinuclear complexes that comprise chemically similar lanthanides is introduced in which a pair of thermosensitive dinuclear complexes, cycTb-phEu and cycEu-phTb, were synthesized. Their structures were geometrically optimized with an internuclear distance of approximately 10.6Å. The sensitive linear temperature-dependent luminescent intensity ratios of europium and terbium emission over a wide temperature range (50–298K and 10–200K, respectively) and their temporal dimension responses indicate that both dinuclear complexes can act as excellent self-referencing thermometers. The energy transfer from Tb3+ to Eu3+ is thermally activated, with the most important pathway involving the 7F1 Eu3+J-multiplet at room temperature. The energy transfer from the antenna to Eu3+ was simulated, and it was found that the most important ligand contributions to the rate come from transfers to the Eu3+ upper states rather than direct ligand–metal transfer to 5D1 or 5D0. As the first molecular-based thermometer with clear validation of the metal ratio and a fixed distance between the metal pairs, these dinuclear complexes can...

Bao, G, Zha, S, Liu, Z, Fung, Y-H, Chan, C-F, Li, H, Chu, P-H, Jin, D, Tanner, PA & Wong, K-L 2018, 'Reversible and Sensitive Hg²⁺ Detection by a Cell-Permeable Ytterbium Complex', Inorganic Chemistry, vol. 57, no. 1, pp. 120-128.
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© 2017 American Chemical Society. A cell-permeable ytterbium complex shows reversible binding with Hg2+ in aqueous solution and in vitroby off-on visible and NIR emission. The fast response and 150 nM sensitivity of Hg2+ detection is based upon FRET and the lanthanide antenna effect. The reversible Hg2+ detection can be performed in vitro, and the binding mechanism is suggested by NMR employing the motif structure in a La complex and by DFT calculations.

Bao, W, Liu, L, Wang, C, Choi, S, Wang, D & Wang, G 2018, 'Facile Synthesis of Crumpled Nitrogen‐Doped MXene Nanosheets as a New Sulfur Host for Lithium–Sulfur Batteries', Advanced Energy Materials, vol. 8, no. 13, pp. 1702485-1702485.
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AbstractCrumpled nitrogen‐doped MXene nanosheets with strong physical and chemical coadsorption of polysulfides are synthesized by a novel one‐step approach and then utilized as a new sulfur host for lithium–sulfur batteries. The nitrogen‐doping strategy enables introduction of heteroatoms into MXene nanosheets and simultaneously induces a well‐defined porous structure, high surface area, and large pore volume. The as‐prepared nitrogen‐doped MXene nanosheets have a strong capability of physical and chemical dual‐adsorption for polysulfides and achieve a high areal sulfur loading of 5.1 mg cm–2. Lithium–sulfur batteries, based on crumpled nitrogen‐doped MXene nanosheets/sulfur composites, demonstrate outstanding electrochemical performances, including a high reversible capacity (1144 mA h g–1 at 0.2C rate) and an extended cycling stability (610 mA h g–1 at 2C after 1000 cycles).

Bao, W, Liu, L, Wang, C, Choi, S, Wang, D & Wang, G 2018, 'Solar Cells: Facile Synthesis of Crumpled Nitrogen‐Doped MXene Nanosheets as a New Sulfur Host for Lithium–Sulfur Batteries (Adv. Energy Mater. 13/2018)', Advanced Energy Materials, vol. 8, no. 13, pp. 1870060-1870060.
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Bao, W, Tang, X, Guo, X, Choi, S, Wang, C, Gogotsi, Y & Wang, G 2018, 'Porous Cryo-Dried MXene for Efficient Capacitive Deionization', Joule, vol. 2, no. 4, pp. 778-787.
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© 2018 Elsevier Inc. Aerogel-like, porous Ti3C2Tx MXene architecture electrode displayed a high electroadsorption capacity for capacitive deionization of saline water. A vacuum freeze-drying process was employed to prevent the restacking of MXene nanosheets due to van der Waals forces, leading to the formation of a porous structure with a large specific surface area. When applied as electrode materials for capacitive deionization, porous MXene demonstrated a high specific capacitance of 156 F/g and a volumetric capacitance of 410 F/cm3 in 1 M sodium chloride (NaCl) electrolyte. The porous Ti3C2Tx MXene electrodes can deliver a high electroadsorption capacity of 118 mg/cm3 (45 mg/g) in 10,000 mg/L NaCl solution (applied voltage: 1.2 V) and excellent cycling stability (up to 60 cycles) in comparison with the restacked MXene and activated carbon electrodes, indicating its promising potential for desalination applications. We report a rationally designed process to produce an aerogel-like porous MXene electrode material for capacitive deionization. The intercalation-delamination of organic compounds and a vacuum freeze-drying technique were employed to prevent the restacking of MXene nanosheets due to van der Waals forces. The porous Ti3C2Tx is hydrophilic and has a well-defined porous structure with a high surface area and high electrical conductivity. When applied as electrodes in a capacitive deionization cell, porous Ti3C2Tx MXene electrodes exhibited an impressively high ion adsorption capacity of 118 mg/cm3 in a salt solution with the concentration of 10,000 mg/L, which is more than 12 times higher than previously reported carbon-based electrode materials. The porous MXene materials may open a new avenue for high-performance capacitive desalination. Porous Ti3C2Tx MXene architectures were prepared and used as electrode materials with a high electrosorption capacity for capacitive deionization of saline or brackish water. The porous Ti3C2Tx MXene elect...

Barraza Bernadas, V, Grings, F, Restrepo-Coupe, N & Huete, A 2018, 'Comparison of the performance of latent heat flux products over southern hemisphere forest ecosystems: estimating latent heat flux error structure using in situ measurements and the triple collocation method', International Journal of Remote Sensing, vol. 39, no. 19, pp. 6300-6315.
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© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group. In this study, we compared different remote-sensing (RS)-based land surface models (LSM) and reanalysis latent heat flux (LE) products over different forest ecosystems. We analysed the performance of three RS products, the MOD16A2, the Breathing Earth System Simulator (BESS) model, and a combined optical-microwave model (COM) in their ability to replicate eddy covariance (EC) flux observations of LE at eight southern hemisphere forest ecosystems and compared their results to simulated LE from the offline LSM (GLDAS/NOAH) and a reanalysis LE dataset (MERRA). To determine spatial uncertainties, we used the triple collocation (TC) method, which does not require a priori knowledge of the true LE value, at selected Australian EC locations and over an area without in situ measurement (the Dry Chaco Forest (DCF), Argentina). The spatial pattern of the TC results was commensurable with uncertainties calculated using EC observations, indicating that the TC method is a robust technique to estimate spatial uncertainties. As global products have been validated with EC measurement from Ozflux stations, we hypothesized and found, using the TC model, that LE products achieve a better performance over areas with EC from networks than over sites without ground-based measurements and may reflect over-calibration of models or a need for a more diverse representation of ecosystems at flux tower networks.

Barry, SE, Ellis, M, Yang, Y, Guan, G, Wang, X, Britton, WJ & Saunders, BM 2018, 'Identification of a plasma microRNA profile in untreated pulmonary tuberculosis patients that is modulated by anti-mycobacterial therapy', Journal of Infection, vol. 77, no. 4, pp. 341-348.
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© 2018 The British Infection Association Objective: microRNA expression profiles are of interest as a biomarker of tuberculosis (TB). How anti-TB therapy effects miRNA profiles is unknown and was examined. Methods: We identified 87 plasma miRNAs that were significantly modified in an exploratory group of 19 Chinese pulmonary TB (PTB) patients compared to 14 healthy controls. We selected 10 of these miRNAs for analysis in a cohort of 100 PTB patients prior to, and at one, two and six months during treatment. Results: Five miRNAs were differentially expressed in PTB patients compared to controls at diagnosis; miRs −29a and −99b were up-regulated, whilst miRs −21, −146a and −652 were down-regulated. A combination of 5 miRNA distinguished TB from healthy controls with a sensitivity of 94%, a specificity of 88%, and an AUC of 0.976. Within one month of treatment, significant changes in miRs −29a, −99b, −26a and 146a levels occurred in successfully treated patients, although not all miRNAs returned to baseline by treatment completion. Conclusion: A 5-miRNA signature shows potential for development as a novel biomarker for TB disease with potential to predict response to treatment. The failure of all miRNA to return to baseline levels may reflect ongoing remodelling in the lung parenchyma that continues after completion of anti-TB therapy.

Batmunkh, M, Shrestha, A, Bat‐Erdene, M, Nine, MJ, Shearer, CJ, Gibson, CT, Slattery, AD, Tawfik, SA, Ford, MJ, Dai, S, Qiao, S & Shapter, JG 2018, 'Electrocatalytic Activity of a 2D Phosphorene‐Based Heteroelectrocatalyst for Photoelectrochemical Cells', Angewandte Chemie International Edition, vol. 57, no. 10, pp. 2644-2647.
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AbstractResearch into efficient synthesis, fundamental properties, and potential applications of phosphorene is currently the subject of intense investigation. Herein, solution‐processed phosphorene or few‐layer black phosphorus (FL‐BP) sheets are prepared using a microwave exfoliation method and used in photoelectrochemical cells. Based on experimental and theoretical (DFT) studies, the FL‐BP sheets are found to act as catalytically active sites and show excellent electrocatalytic activity for triiodide reduction in dye‐sensitized solar cells. Importantly, the device fabricated based on the newly designed cobalt sulfide (CoSx) decorated nitrogen and sulfur co‐doped carbon nanotube heteroelectrocatalyst coated with FL‐BP (FL‐BP@N,S‐doped CNTs‐CoSx) displayed an impressive photovoltaic efficiency of 8.31 %, outperforming expensive platinum based cells. This work paves the way for using phosphorene‐based electrocatalysts for next‐generation energy‐storage systems.

Batmunkh, M, Shrestha, A, Bat‐Erdene, M, Nine, MJ, Shearer, CJ, Gibson, CT, Slattery, AD, Tawfik, SA, Ford, MJ, Dai, S, Qiao, S & Shapter, JG 2018, 'Electrocatalytic Activity of a 2D Phosphorene‐Based Heteroelectrocatalyst for Photoelectrochemical Cells', Angewandte Chemie, vol. 130, no. 10, pp. 2674-2677.
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AbstractResearch into efficient synthesis, fundamental properties, and potential applications of phosphorene is currently the subject of intense investigation. Herein, solution‐processed phosphorene or few‐layer black phosphorus (FL‐BP) sheets are prepared using a microwave exfoliation method and used in photoelectrochemical cells. Based on experimental and theoretical (DFT) studies, the FL‐BP sheets are found to act as catalytically active sites and show excellent electrocatalytic activity for triiodide reduction in dye‐sensitized solar cells. Importantly, the device fabricated based on the newly designed cobalt sulfide (CoSx) decorated nitrogen and sulfur co‐doped carbon nanotube heteroelectrocatalyst coated with FL‐BP (FL‐BP@N,S‐doped CNTs‐CoSx) displayed an impressive photovoltaic efficiency of 8.31 %, outperforming expensive platinum based cells. This work paves the way for using phosphorene‐based electrocatalysts for next‐generation energy‐storage systems.

Been, F, O'Brien, J, Lai, FY, Morelato, M, Vallely, P, McGowan, J, van Nuijs, ALN, Covaci, A & Mueller, JF 2018, 'Analysis of N,N‐dimethylamphetamine in wastewater – a pyrolysis marker and synthesis impurity of methamphetamine', Drug Testing and Analysis, vol. 10, no. 10, pp. 1590-1598.
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AbstractThe increased availability of high purity crystalline methamphetamine (MA) in Australia raised concerns because of high dosages and its potential consumption through inhalation. The present work investigates the possibility of using wastewater levels of N,N‐dimethylamphetamine (DMA), a pyrolysis by‐product, as an indirect indicator of MA smoking. A dedicated liquid chromatography quadrupole‐time‐of‐flight mass spectrometry (LC–QToF–MS) method was set up to detect and quantify DMA in wastewater samples. Wastewater samples were collected from 8 locations across Australia during the period 2011–2016. Data about the abundance of DMA in MA seizures as well as in residues from drug paraphernalia were obtained from forensic laboratories in Australia. DMA/MA ratios measured in wastewater ranged from 0.0001 to 0.09 (median 0.007). DMA/MA ratios in bulk seizures are generally below 0.0025, with a median value of 0.0004, whilst residues in paraphernalia ranged from 0.031 to 3.37. DMA/MA ratios in wastewater decreased between 2011 and 2016, in parallel to an increase in MA loads. Furthermore, wastewater analyses highlighted a strong positive correlation between DMA/MA ratios and per capita MA use (Pearson's correlation ρ= 0.61, p‐value <0.001). Nonetheless, geographical specificities could be highlighted between the investigated locations. The obtained data could help authorities detect hot spots of drug use as well as to plan specific intervention campaigns to tackle the issue. In future, simultaneous analysis of DMA and MA in both wastewater and seizures could improve our understanding about MA use and its consumption patterns.

Behrendt, L, Raina, J-B, Lutz, A, Kot, W, Albertsen, M, Halkjær-Nielsen, P, Sørensen, SJ, Larkum, AWD & Kühl, M 2018, 'In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina', The ISME Journal, vol. 12, no. 2, pp. 556-567.
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Abstract The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.

Bekendam, RH, Iyu, D, Passam, F, Stopa, JD, De Ceunynck, K, Muse, O, Bendapudi, PK, Garnier, CL, Gopal, S, Crescence, L, Chiu, J, Furie, B, Panicot‐Dubois, L, Hogg, PJ, Dubois, C & Flaumenhaft, R 2018, 'Protein disulfide isomerase regulation by nitric oxide maintains vascular quiescence and controls thrombus formation', Journal of Thrombosis and Haemostasis, vol. 16, no. 11, pp. 2322-2335.
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Benson, N, Oliveria Dos Santos, R, Griffiths, K, Cole, N, Doble, P, Roux, C & Blanes, L 2018, 'Erratum to “The development of a stabbing machine for forensic textile damage analysis” [FSI (2017) 132–139]>', Forensic Science International, vol. 285, pp. 161-161.
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Berger, B, Berger, C, Heinrich, J, Niederstätter, H, Hecht, W, Hellmann, A, Rohleder, U, Schleenbecker, U, Morf, N, Freire-Aradas, A, McNevin, D, Phillips, C & Parson, W 2018, 'Dog breed affiliation with a forensically validated canine STR set', Forensic Science International: Genetics, vol. 37, pp. 126-134.
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We tested a panel of 13 highly polymorphic canine short tandem repeat (STR) markers for dog breed assignment using 392 dog samples from the 23 most popular breeds in Austria, Germany, and Switzerland. This STR panel had originally been selected for canine identification. The dog breeds sampled in this study featured a population frequency ≥1% and accounted for nearly 57% of the entire pedigree dog population in these three countries. Breed selection was based on a survey comprising records for nearly 1.9 million purebred dogs belonging to more than 500 different breeds. To derive breed membership from STR genotypes, a range of algorithms were used. These methods included discriminant analysis of principal components (DAPC), STRUCTURE, GeneClass2, and the adegenet package for R. STRUCTURE analyses suggested 21 distinct genetic clusters. Differentiation between most breeds was clearly discernable. Fourteen of 23 breeds (61%) exhibited maximum mean cluster membership proportions of more than 0.70 with a highest value of 0.90 found for Cavalier King Charles Spaniels. Dogs of only 6 breeds (26%) failed to consistently show only one major cluster. The DAPC method yielded the best assignment results in all 23 declared breeds with 97.5% assignment success. The frequency-based assignment test also provided a high success rate of 87%. These results indicate the potential viability of dog breed prediction using a well-established and sensitive set of 13 canine STR markers intended for forensic routine use.

Berhane, AM, Jeong, K-Y, Bradac, C, Walsh, M, Englund, D, Toth, M & Aharonovich, I 2018, 'Photophysics of GaN single-photon emitters in the visible spectral range', Physical Review B, vol. 97, no. 16.
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© 2018 American Physical Society. In this work, we present a detailed photophysical analysis of recently discovered, optically stable single-photon emitters (SPEs) in gallium nitride (GaN). Temperature-resolved photoluminescence measurements reveal that the emission lines at 4 K are three orders of magnitude broader than the transform-limited width expected from excited-state lifetime measurements. The broadening is ascribed to ultrafast spectral diffusion. The photophysical study on several emitters at room temperature (RT) reveals an average brightness of (427±215)kCounts/s. Finally, polarization measurements from 14 emitters are used to determine visibility as well as dipole orientation of defect systems within the GaN crystal. Our results underpin some of the fundamental properties of SPEs in GaN both at cryogenic and RT, and define the benchmark for future work in GaN-based single-photon technologies.

Berry, T, Dutta, D, Chen, R, Leong, A, Wang, H, Donald, WA, Parviz, M, Cornell, B, Willcox, M, Kumar, N & Cranfield, CG 2018, 'Lipid Membrane Interactions of the Cationic Antimicrobial Peptide Chimeras Melimine and Cys-Melimine', Langmuir, vol. 34, no. 38, pp. 11586-11592.
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Copyright © 2018 American Chemical Society. Melimine and its derivatives are synthetic chimeric antimicrobial agents based on protamine and melittin. The binding of solubilized melimine and its derivative, with a cysteine on N-terminus, (cys-melimine) on tethered bilayer lipid membranes (tBLMs) was examined using ac electrical impedance spectroscopy. The addition of melimine and cys-melimine initially increased membrane conduction, which subsequently falls over time. The results were obtained for tBLMs comprising zwitterionic phosphatidylcholine, anionic phosphatidylglycerol, or tBLMs made using purified lipids from Escherichia coli. The effect on conduction is more marked with the cysteine variant than the noncysteine variant. The variation in membrane conduction most probably arises from individual melimines inducing increased ionic permeability, which is then reduced as the melimines aggregate and phase-separate within the membrane. The actions of these antimicrobials are modeled in terms of altering the critical packing parameter (CPP) of the membranes. The variations in the peptide length of cys-melimine were compared with a truncated version of the peptide, cys-mel4. The results suggest that the smaller molecule impacts the membrane by a mechanism that increases the average CPP, reducing membrane conduction. Alternatively, an uncharged alanine-replacement version of melimine still produced an increase in membrane conduction, further supporting the CPP model of geometry-induced toroidal pore alterations. All the data were then compared to their antimicrobial effectiveness for the Gram-positive and Gram-negative strains of bacteria, and their fusogenic properties were examined using dynamic light scattering in 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine lipid spheroids. We conclude that a degree of correlation exists between the antimicrobial effectiveness of the peptides studied here and their modulation of membrane conductivity.

Bertram, MR, Delgado, A, Pauszek, SJ, Smoliga, GR, Brito, B, Stenfeldt, C, Hartwig, EJ, Jumbo, SD, Abdoulmoumini, M, Oliva Marie, AA, Salhine, R, Rodriguez, LL, Garabed, R & Arzt, J 2018, 'Effect of vaccination on cattle subclinically infected with foot-and-mouth disease virus in Cameroon', Preventive Veterinary Medicine, vol. 155, pp. 1-10.
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Foot-and-mouth disease (FMD) is one of the most contagious and economically important livestock diseases worldwide. Four serotypes of FMD virus (FMDV; O, A, SAT1, SAT2) circulate in Cameroon, and a trivalent inactivated vaccine against the three most common serotypes (O, A, SAT2) was recently introduced in 2014. The objective of this study was to characterize vaccine performance in cattle under natural hyperendemic conditions in the Adamawa region of Cameroon. Vaccinated cattle (n = 50) and non-vaccinated controls (n = 100) were monitored by serum and oropharyngeal fluid (OPF) sample collection through a 12-month period. Anti-FMDV non-structural protein (anti-NSP) seroprevalence increased from 59.3% (89/150) at the beginning of the study to 85.8% (103/120) at the end of the study, and FMDV RNA was found in 28% (42/150) of animals overall, despite detection of clinical signs of FMD in only 6 non-vaccinated animals. Viral sequence analysis indicated that subclinical infections of FMDV serotypes O and A were present within the study herds during the study period, which was reflected by an overall increase of anti-NSP seroprevalence during the study. There was no association between vaccination status and seroconversion or prevalence of FMDV RNA in OPF. Younger cattle had higher odds of detection of FMDV RNA in OPF, but older animals were more likely to be seropositive. This study suggests vaccination of herds previously exposed to FMDV may help to limit clinical signs and reduce economic losses caused by FMDV. These findings also suggest that subclinical circulation of FMDV occurs in hyperendemic regions regardless of vaccination.

Bertram, MR, Vu, LT, Pauszek, SJ, Brito, BP, Hartwig, EJ, Smoliga, GR, Hoang, BH, Phuong, NT, Stenfeldt, C, Fish, IH, Hung, VV, Delgado, A, VanderWaal, K, Rodriguez, LL, Long, NT, Dung, DH & Arzt, J 2018, 'Lack of Transmission of Foot-and-Mouth Disease Virus From Persistently Infected Cattle to Naïve Cattle Under Field Conditions in Vietnam', Frontiers in Veterinary Science, vol. 5.
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Bharatula, LD, Marsili, E, Rice, S & Kwan, JJ 2018, 'The effects of high intensity focused ultrasound on biofilms formed by Pseudomonas aeruginosa', The Journal of the Acoustical Society of America, vol. 143, no. 3_Supplement, pp. 1928-1928.
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Bacterial infections are increasingly difficult to treat due to their growing resistance to antibiotics. Most of these bacterial infections form a biofilm that limits the effectiveness of the antibiotic. Biofilms are microbial cells that are protected by a self-generated matrix of extracellular polymeric substances. In addition to their intrinsic antibiotic resistance, these biofilms are able to respond to the stresses from the antibiotic by inducing drug resistance mechanisms. Currently, the strategy to combat drug resistance is to develop novel drugs, however, the rate of drug development is being surpassed by the rate of drug resistance. There is therefore a need for alternative means in enhancing the efficacy of current drug therapeutics. We propose to use of high intensity focused ultrasound (HIFU) to disrupt the biofilm and promote drug penetration. However, the effects of HIFU on these bacterial communities remain unknown. Here we report on microstructural changes within biofilms formed by Pseudomonas aeruginosa due to exposure to HIFU at 500 kHz center frequency. Changes to the biofilm were nondestructively measured through impedance spectroscopy and confocal microscopy. Biofilms were shown to induce cavitation (as measured by a passive cavitation detector) at relatively low pressure amplitudes suggesting the presence of cavitation nuclei within the extracellular matrix.

Bhullar, KS, Lagarón, NO, McGowan, EM, Parmar, I, Jha, A, Hubbard, BP & Rupasinghe, HPV 2018, 'Kinase-targeted cancer therapies: progress, challenges and future directions', Molecular Cancer, vol. 17, no. 1.
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© 2018 The Author(s). The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.

Bihana, S, Dhiman, A, Singh, G & Satija, S 2018, 'Gas chromatography-mass spectroscopy analysis of bioactive compounds in the whole plant parts of ethanolic extract of Asclepias Curassavica L.', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 107-114.
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Objective: The present study was carried out to cultivate Asclepias curassavica and explore the phytoconstituents of ethanolic extract of A. curassavica whole part using gas chromatography-mass spectroscopy (GC-MS). This research may be useful for constituent(s)-based pharmacological activity. Materials and Methods: 5 g of powdered plant material was taken in a spotless, level container and soaked in 80 ml of ethanol, and extraction was done by hot extraction method. The glass container with extract was sealed and kept aside for few hours. It was then filtered through Whatman filter paper No.42. Ethanolic extract of A. curassavica was further undertaken for GC-MS analysis. Result: The ethanolic extract of the whole plant of A. curassavica revealed the presence of 49 diverse phytochemical compounds. Several of these phytoconstituents are reported to possess pharmacological potential. Conclusion: A. curassavica L. has been successfully cultivated, authenticated, and used for the identification of its organic chemical components by GC-MS. Pesticide residues may have an adverse effect on the food chain, and the concentration should be within permissible range for safe human consumption of any herbal drug product. A. curassavica has been observed as a tremendous source of many important phytochemicals, especially glycosidal, alkaloids, steroidal, and terpenoidal compounds. There were no pesticidal residues found in the tested plant drug. Therefore, it may be explored for the production of natural medicinal formulations in pharmaceutical drug industries including anticancer drugs, antibacterial, antimicrobial, antiasthmatics, urine acidifiers, and antimicrobial on account of its potential antioxidant activity.

Billatos, E, Faiz, A, Gesthalter, Y, LeClerc, A, Alekseyev, YO, Xiao, X, Liu, G, ten Hacken, NHT, Heijink, IH, Timens, W, Brandsma, CA, Postma, DS, van den Berge, M, Spira, A & Lenburg, ME 2018, 'Impact of acute exposure to cigarette smoke on airway gene expression', Physiological Genomics, vol. 50, no. 9, pp. 705-713.
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Background: Understanding effects of acute smoke exposure (ASE) on airway epithelial gene expression and their relationship with the effects of chronic smoke exposure may provide biological insights into the development of smoking-related respiratory diseases. Methods: Bronchial airway epithelial cell brushings were collected from 63 individuals without recent cigarette smoke exposure and before and 24 h after smoking three cigarettes. RNA from these samples was profiled on Affymetrix Human Gene 1.0 ST microarrays. Results: We identified 91 genes differentially expressed 24 h after ASE (false discovery rate < 0.25). ASE induced genes involved in xenobiotic metabolism, oxidative stress, and inflammation and repressed genes related to cilium morphogenesis and cell cycle. While many genes altered by ASE are altered similarly in chronic smokers, metallothionein genes are induced by ASE and suppressed in chronic smokers. Metallothioneins are also suppressed in current and former smokers with lung cancer relative to those without lung cancer. Conclusions: Acute exposure to as little as three cigarettes and chronic smoking induce largely concordant changes in airway epithelial gene expression. Differences in short-term and long-term effects of smoking on metallothionein expression and their relationship to lung cancer requires further study given these enzymes’ role in the oxidative stress response.

Bishop, DP, Cole, N, Zhang, T, Doble, PA & Hare, DJ 2018, 'A guide to integrating immunohistochemistry and chemical imaging', Chemical Society Reviews, vol. 47, no. 11, pp. 3770-3787.
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A ‘how-to’ guide for designing chemical imaging experiments using antibodies and immunohistochemistry.

Bishop, DP, Grossgarten, M, Dietrich, D, Vennemann, A, Cole, N, Sperling, M, Wiemann, M, Doble, PA & Karst, U 2018, 'Correction: Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry', Analytical Methods, vol. 10, no. 8, pp. 926-926.
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Correction for ‘Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry’ by David P. Bishop et al., Anal. Methods, 2018, DOI: 10.1039/c7ay02294h.

Bishop, DP, Grossgarten, M, Dietrich, D, Vennemann, A, Cole, N, Sperling, M, Wiemann, M, Doble, PA & Karst, U 2018, 'Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry', Analytical Methods, vol. 10, no. 8, pp. 836-840.
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We demonstrate the use of LA-ICP-MS for determining the location and quantification of silver in a rat spleen following nanoparticle exposure.

Bishop, DP, Hare, DJ, Clases, D & Doble, PA 2018, 'Applications of liquid chromatography-inductively coupled plasma-mass spectrometry in the biosciences: A tutorial review and recent developments', TrAC Trends in Analytical Chemistry, vol. 104, pp. 11-21.
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© 2017 The biological function of minor and trace elements is ordinarily determined by their association with specific proteins, peptides and other biomolecules. Therefore, measuring the total elemental content of a biological sample provides limited information, particularly when a specific effect is due to an individual metal-protein complex. Speciation of metalloproteins, heteroatom-containing molecules or other compounds tagged with an exogenous metal can be used to overcome this limitation. A range of chromatographic separation techniques with on-line elemental detection using inductively coupled plasma-mass spectrometry (ICP-MS) have been applied to the biosciences, and each technique has intrinsic features that must be considered when designing speciation experiments. This tutorial review provides an overview of speciation in the biosciences, highlighting the unique abilities and limitations encountered. A selection of recent technical advances and new applications, the challenges of sample preparation and implementation of new technical developments are discussed, as well as the future directions of technology that is rapidly gaining a foothold in the contemporary biochemistry laboratory.

Bishop, J, Fronzi, M, Elbadawi, C, Nikam, V, Pritchard, J, Fröch, JE, Duong, NMH, Ford, MJ, Aharonovich, I, Lobo, CJ & Toth, M 2018, 'Deterministic Nanopatterning of Diamond Using Electron Beams', ACS Nano, vol. 12, no. 3, pp. 2873-2882.
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© 2018 American Chemical Society. Diamond is an ideal material for a broad range of current and emerging applications in tribology, quantum photonics, high-power electronics, and sensing. However, top-down processing is very challenging due to its extreme chemical and physical properties. Gas-mediated electron beam-induced etching (EBIE) has recently emerged as a minimally invasive, facile means to dry etch and pattern diamond at the nanoscale using oxidizing precursor gases such as O2 and H2O. Here we explain the roles of oxygen and hydrogen in the etch process and show that oxygen gives rise to rapid, isotropic etching, while the addition of hydrogen gives rise to anisotropic etching and the formation of topographic surface patterns. We identify the etch reaction pathways and show that the anisotropy is caused by preferential passivation of specific crystal planes. The anisotropy can be controlled by the partial pressure of hydrogen and by using a remote RF plasma source to radicalize the precursor gas. It can be used to manipulate the geometries of topographic surface patterns as well as nano- and microstructures fabricated by EBIE. Our findings constitute a comprehensive explanation of the anisotropic etch process and advance present understanding of electron-surface interactions.

Blackman, CJ, Gleason, SM, Cook, AM, Chang, Y, Laws, CA & Westoby, M 2018, 'The links between leaf hydraulic vulnerability to drought and key aspects of leaf venation and xylem anatomy among 26 Australian woody angiosperms from contrasting climates', Annals of Botany, vol. 122, no. 1, pp. 59-67.
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Blas Achic, BG, Wang, T, Su, Y, Kipnis, V, Dodd, K & Carroll, RJ 2018, 'Categorizing a continuous predictor subject to measurement error', Electronic Journal of Statistics, vol. 12, no. 2, pp. 4032-4056.
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© 2018, Institute of Mathematical Statistics. All rights reserved. Epidemiologists often categorize a continuous risk predictor, even when the true risk model is not a categorical one. Nonetheless, such categorization is thought to be more robust and interpretable, and thus their goal is to fit the categorical model and interpret the categorical parameters. We address the question: with measurement error and categorization, how can we do what epidemiologists want, namely to estimate the parameters of the categorical model that would have been estimated if the true predictor was observed? We develop a general methodology for such an analysis, and illustrate it in linear and logistic regression. Simulation studies are presented and the methodology is applied to a nutrition data set. Discussion of alternative approaches is also included.

Blaskovich, MAT, Pitt, ME, Elliott, AG & Cooper, MA 2018, 'Can octapeptin antibiotics combat extensively drug-resistant (XDR) bacteria?', Expert Review of Anti-infective Therapy, vol. 16, no. 6, pp. 485-499.
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Bloomfield, KJ, Cernusak, LA, Eamus, D, Ellsworth, DS, Colin Prentice, I, Wright, IJ, Boer, MM, Bradford, MG, Cale, P, Cleverly, J, Egerton, JJG, Evans, BJ, Hayes, LS, Hutchinson, MF, Liddell, MJ, Macfarlane, C, Meyer, WS, Prober, SM, Togashi, HF, Wardlaw, T, Zhu, L & Atkin, OK 2018, 'A continental‐scale assessment of variability in leaf traits: Within species, across sites and between seasons', Functional Ecology, vol. 32, no. 6, pp. 1492-1506.
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AbstractPlant species show considerable leaf trait variability that should be accounted for in dynamic global vegetation models (DGVMs). In particular, differences in the acclimation of leaf traits during periods more and less favourable to growth have rarely been examined.We conducted a field study of leaf trait variation at seven sites spanning a range of climates and latitudes across the Australian continent; 80 native plant species were included. We measured key traits associated with leaf structure, chemistry and metabolism during the favourable and unfavourable growing seasons.Leaf traits differed widely in the degree of seasonal variation displayed. Leaf mass per unit area (Ma) showed none. At the other extreme, seasonal variation accounted for nearly a third of total variability in dark respiration (Rdark).At the non‐tropical sites, carboxylation capacity (Vcmax) at the prevailing growth temperature was typically higher in summer than in winter. When Vcmax was normalized to a common reference temperature (25°C), however, the opposite pattern was observed for about 30% of the species. This suggests that metabolic acclimation is possible, but far from universal.Intraspecific variation—combining measurements of individual plants repeated at contrasting seasons, different leaves from the same individual, and multiple conspecific plants at a given site—dominated total variation for leaf metabolic traits V

Boakes, RA, Kendig, MD, Martire, SI & Rooney, KB 2018, 'Giving up sugary drinks: is switching to diet beverages a good move?', Appetite, vol. 123, pp. 454-454.
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Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2018, 'Acid‐Catalyzed Conversion of Carbohydrates into Value‐Added Small Molecules in Aqueous Media and Ionic Liquids', ChemSusChem, vol. 11, no. 4, pp. 642-660.
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AbstractBiomass is the only realistic major alternative source (to crude oil) of hydrocarbon substrates for the commercial synthesis of bulk and fine chemicals. Within biomass, terrestrial sources are the most accessible, and therein lignocellulosic materials are most abundant. Although lignin shows promise for the delivery of certain types of organic molecules, cellulose is a biopolymer with significant potential for conversion into high‐volume and high‐value chemicals. This review covers the acid‐catalyzed conversion of lower value (poly)carbohydrates into valorized organic building‐block chemicals (platform molecules). It focuses on those conversions performed in aqueous media or ionic liquids to provide the reader with a perspective on what can be considered a best case scenario, that is, that the overall process is as sustainable as possible.

Bogema, DR, Micallef, ML, Liu, M, Padula, MP, Djordjevic, SP, Darling, AE & Jenkins, C 2018, 'Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes', BMC Genomics, vol. 19, no. 1, pp. 298-298.
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© 2018 The Author(s). Background: Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T. orientalis sourced from Australian herds. Results: Using de novo assembled sequences and a single nucleotide variant (SNV) analysis pipeline, we found extensive genetic divergence between the T. orientalis genotypes. A genome-wide phylogeny reconstructed to address continued confusion over nomenclature of this species displayed concordance with prior phylogenetic studies based on the major piroplasm surface protein (MPSP) gene. However, average nucleotide identity (ANI) values revealed that the divergence between isolates is comparable to that observed between other theilerias which represent distinct species. Analysis of SNVs revealed putative recombination between the Chitose and Buffeli genotypes and also between Australian and Japanese Ikeda isolates. Finally, to inform future vaccine studies, dN/dS ratios and surface location predictions were analysed. Six predicted surface protein targets were confirmed to be expressed during the piroplasm phase of the parasite by mass spectrometry. Conclusions: We used whole genome sequencing to demonstrate that the T. orientalis Ikeda, Chitose and Buffeli variants show substantial genetic divergence. Our data indicates that future researchers could potentially consider disease-associated Ikeda and closely related genotypes as a separate species from non-pathogenic Chitose and Buffeli.

Boonyaratanakornkit, V, Hamilton, N, Márquez-Garbán, DC, Pateetin, P, McGowan, EM & Pietras, RJ 2018, 'Extranuclear signaling by sex steroid receptors and clinical implications in breast cancer', Molecular and Cellular Endocrinology, vol. 466, pp. 51-72.
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© 2017 Elsevier B.V. Estrogen and progesterone play essential roles in the development and progression of breast cancer. Over 70% of breast cancers express estrogen receptors (ER) and progesterone receptors (PR), emphasizing the need for better understanding of ER and PR signaling. ER and PR are traditionally viewed as transcription factors that directly bind DNA to regulate gene networks. In addition to nuclear signaling, ER and PR mediate hormone-induced, rapid extranuclear signaling at the cell membrane or in the cytoplasm which triggers downstream signaling to regulate rapid or extended cellular responses. Specialized membrane and cytoplasmic proteins may also initiate hormone-induced extranuclear signaling. Rapid extranuclear signaling converges with its nuclear counterpart to amplify ER/PR transcription and specify gene regulatory networks. This review summarizes current understanding and updates on ER and PR extranuclear signaling. Further investigation of ER/PR extranuclear signaling may lead to development of novel targeted therapeutics for breast cancer management.

Booth, DJ & Sear, J 2018, 'Coral expansion in Sydney and associated coral-reef fishes', Coral Reefs, vol. 37, no. 4, pp. 995-995.
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Booth, DJ, Beretta, GA, Brown, L & Figueira, WF 2018, 'Predicting Success of Range-Expanding Coral Reef Fish in Temperate Habitats Using Temperature-Abundance Relationships', Frontiers in Marine Science, vol. 5, no. FEB.
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© 2018 Booth, Beretta, Brown and Figueira. An 18-year database of coral reef fish expatriation poleward in South East Australia was used to estimate persistence of coal reef fish recruits on temperate reefs. Surveys have identified over 150 coral reef fish species recruiting to temperate reefs at latitudes of 34°S (Sydney) and 60 species to 37°S (Merimbula) with 20 and 5 species respectively overwintering in at least 1 year over the study duration. We developed indices of vulnerability of key species to drops in water temperatures, by relating drops in abundances of species to temperature drops. Twenty species were ranked according to their temperature vulnerability. Overall, the families Chaetodontidae (butterflyfishes), Acanthuridae (surgeonfishes), Labridae (wrasses) and Pomacetnridae (damselfishes) had similar cold-water tolerance. However, there was considerable variability within families, for instance in the Pomacentridae, species from the genus Abudefduf appeared to have better cold-temperature tolerance than the other species. Predicted minimum overwintering temperature varied from 15.6°C to 19.8°C, with some species showing lower Tzero at Merimbula, the more poleward location. There was general concordance between a species' tolerance to cold-water and its tendency to occur as an overwinter but also notable exceptions. So while this work demonstrates the potential utility of tolerance to seasonal temperature drops as a means to predict range expansion capacity of vagrant species, the exceptional cases serve to highlight alternative factors. Specifically, tolerance to seasonal cooling of water is not the only important factor when predicting the range expansion capacity of a species. Factors affecting the general abundance of the vagrants, such as habitat suitability and competitor/predator environments will also be critical where overwinter survival becomes a lottery.

Borovkov, K, Mishura, Y, Novikov, A & Zhitlukhin, M 2018, 'New and refined bounds for expected maxima of fractional Brownian motion', Statistics & Probability Letters, vol. 137, pp. 142-147.
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© 2018 Elsevier B.V. For the fractional Brownian motion BH with the Hurst parameter value H in (0,1∕2), we derive new upper and lower bounds for the difference between the expectations of the maximum of BH over [0,1] and the maximum of BH over the discrete set of values in−1, i=1,…,n. We use these results to improve our earlier upper bounds for the expectation of the maximum of BH over [0,1] and derive new upper bounds for Pickands’ constant.

Bosman, KJ, Wensing, AMJ, Pijning, AE, van Snippenberg, WJ, van Ham, PM, de Jong, DMC, Hoepelman, AIM & Nijhuis, M 2018, 'Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms', Journal of the International AIDS Society, vol. 21, no. 9.
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AbstractIntroductionThe latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype‐tolerance using digital PCR.MethodsA subtype‐B‐specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype‐tolerance in digital PCR (Bio‐Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE

Bouman, HA, Platt, T, Doblin, M, Figueiras, FG, Gudmundsson, K, Gudfinnsson, HG, Huang, B, Hickman, A, Hiscock, M, Jackson, T, Lutz, VA, Mélin, F, Rey, F, Pepin, P, Segura, V, Tilstone, GH, van Dongen-Vogels, V & Sathyendranath, S 2018, 'Photosynthesis–irradiance parameters of marine phytoplankton: synthesis of a global data set', Earth System Science Data, vol. 10, no. 1, pp. 251-266.
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Abstract. The photosynthetic performance of marine phytoplankton varies in response to a variety of factors, environmental and taxonomic. One of the aims of the MArine primary Production: model Parameters from Space (MAPPS) project of the European Space Agency is to assemble a global database of photosynthesis–irradiance (P-E) parameters from a range of oceanographic regimes as an aid to examining the basin-scale variability in the photophysiological response of marine phytoplankton and to use this information to improve the assignment of P-E parameters in the estimation of global marine primary production using satellite data. The MAPPS P-E database, which consists of over 5000 P-E experiments, provides information on the spatio-temporal variability in the two P-E parameters (the assimilation number, PmB, and the initial slope, αB, where the superscripts B indicate normalisation to concentration of chlorophyll) that are fundamental inputs for models (satellite-based and otherwise) of marine primary production that use chlorophyll as the state variable. Quality-control measures consisted of removing samples with abnormally high parameter values and flags were added to denote whether the spectral quality of the incubator lamp was used to calculate a broad-band value of αB. The MAPPS database provides a photophysiological data set that is unprecedented in number of observations and in spatial coverage. The database will be useful to a variety of research communities, including marine ecologists, biogeochemical modellers, remote-sensing scientists and algal physiologists. The compiled data are available at https://doi.org/10.1594/PANGAEA.874087 (Bouman et al., 2017).

Bradbury, P, Traini, D, Ammit, AJ, Young, PM & Ong, HX 2018, 'Repurposing of statins via inhalation to treat lung inflammatory conditions', Advanced Drug Delivery Reviews, vol. 133, pp. 93-106.
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© 2018 Elsevier B.V. Despite many therapeutic advancements over the past decade, the continued rise in chronic inflammatory lung diseases incidence has driven the need to identify and develop new therapeutic strategies, with superior efficacy to treat these diseases. Statins are one class of drug that could potentially be repurposed as an alternative treatment for chronic lung diseases. They are currently used to treat hypercholesterolemia by inhibiting the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, that catalyses the rate limiting step in the mevalonate biosynthesis pathway, a key intermediate in cholesterol metabolism. Recent research has identified statins to have other protective pleiotropic properties including anti-inflammatory, anti-oxidant, muco-inhibitory effects that may be beneficial for the treatment of chronic inflammatory lung diseases. However, clinical studies have yielded conflicting results. This review will summarise some of the current evidences for statins pleiotropic effects that could be applied for the treatment of chronic inflammatory lung diseases, their mechanisms of actions, and the potential to repurpose statins as an inhaled therapy, including a detailed discussion on their different physical-chemical properties and how these characteristics could ultimately affect treatment efficacies. The repurposing of statins from conventional anti-cholesterol oral therapy to inhaled anti-inflammatory formulation is promising, as it provides direct delivery to the airways, reduced risk of side effects, increased bioavailability and tailored physical-chemical properties for enhanced efficacy.

Bradfield, LA, Hart, G & Balleine, BW 2018, 'Inferring action-dependent outcome representations depends on anterior but not posterior medial orbitofrontal cortex', Neurobiology of Learning and Memory, vol. 155, pp. 463-473.
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© 2018 Elsevier Inc. Although studies examining orbitofrontal cortex (OFC) often treat it as though it were functionally homogeneous, recent evidence has questioned this assumption. Not only are the various subregions of OFC (lateral, ventral, and medial) hetereogeneous, but there is further evidence of heterogeneity within those subregions. For example, several studies in both humans and monkeys have revealed a functional subdivision along the anterior-posterior gradient of the medial OFC (mOFC). Given our previous findings suggesting that, in rats, the mOFC is responsible for inferring the likelihood of unobservable action outcomes (Bradfield, Dezfouli, van Holstein, Chieng, & Balleine, 2015), and given the anterior nature of the placements of our prior manipulations, we decided to assess whether the rat mOFC also differs in connection and function along its anteroposterior axis. We first used retrograde tracing to compare the density of efferents from mOFC to several structures known to contribute to goal-directed action: the mediodorsal thalamus, basolateral amygdala, posterior dorsomedial striatum, nucleus accumbens core and ventral tegmental area. We then compared the functional effects of anterior versus posterior mOFC excitotoxic lesions on tests of Pavlovian-instrumental transfer, instrumental outcome devaluation and outcome-specific reinstatement. We found evidence that the anterior mOFC had greater connectivity with the accumbens core and greater functional involvement in goal-directed action than the posterior mOFC. Consistent with previous findings across species, therefore, these results suggest that the anterior and posterior mOFC of the rat are indeed functionally distinct, and that it is the anterior mOFC that is particularly critical for inferring unobservable action outcomes.

Bradfield, LA, Matamales, M & Bertran-Gonzalez, J 2018, 'The Thalamostriatal Pathway and the Hierarchical Control of Action', Neuron, vol. 100, no. 3, pp. 521-523.
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Bradley, DJ, Gladstone, W & Gribben, PE 2018, 'Relationships between the spread of Caulerpa filiformis and fish communities on temperate rocky reefs', Journal of Fish Biology, vol. 93, no. 1, pp. 12-20.
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The previously sub‐dominant native marine macrophyte Caulerpa filiformis is now dominant on many sub‐tidal rocky reefs in New South Wales (NSW), Australia and is expanding its distribution. As C. filiformis is highly chemically defended and structurally different to co‐occurring habitat‐forming macrophytes, two key attributes that govern fish assemblages, we hypothesized that fish assemblages, particularly herbivorous fishes, would be different at sites where C. filiformis occurred from where it was previously absent and within sites, fish community structure would be correlated to the cover of C. filiformis. We investigated these hypotheses by determining reef‐associated fish assemblage attributes (assemblage structure, species richness, total abundance, Shannon‐Weiner diversity, abundance of herbivorous species) along transects within sites where C. filiformis was present and absent. Surprisingly, despite large patches and very high densities of C. filiformis on the reefs we sampled, at larger spatial scales (i.e., among sites) no fish assemblage metrics differed between sites with large stands of C. filiformis and sites without the alga. Moreover the abundance of one dominant herbivore, the rock cale Aplodactylus lophodon, was greater at sites within large beds of C. filiformis....

Braun, M, Kirkup, L & Chadwick, S 2018, 'The impact of inquiry orientation and other elements of cultural framework on student engagement in first year laboratory programs', International Journal of Innovation in Science and Mathematics Education, vol. 26, no. 4, pp. 30-48.
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Inquiry-oriented approaches to learning have gradually entered science laboratory programs, aiming to deliver an authentic experience of doing science, enhance student engagement with the material, and bring greater emphasis on generic skills underpinning graduate attributes. Although such approaches have demonstrated pedagogical advantages and improved student engagement, it is not clear how the advantages should be weighted against other elements of what may be regarded as the laboratory program's cultural framework. We analysed two large-enrolment introductory tertiary programs: physics and chemistry at the University of Technology Sydney. The programs differed in the level of inquiry orientation but also in approaches to design, logistics and relevancy. We found that, based on student survey responses, the putative advantages of a deeper inquiry orientation in the physics laboratory were insufficient to compensate for the apparent advantages arising from the other elements of the cultural framework in the chemistry laboratory.

Bray, K, Cheung, L, Hossain, KR, Aharonovich, I, Valenzuela, SM & Shimoni, O 2018, 'Versatile multicolor nanodiamond probes for intracellular imaging and targeted labeling', Journal of Materials Chemistry B, vol. 6, no. 19, pp. 3078-3084.
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We report on the first demonstration of FNDs containing either silicon or nitrogen vacancy color centers for multi-color bio-imaging.

Bray, K, Kato, H, Previdi, R, Sandstrom, R, Ganesan, K, Ogura, M, Makino, T, Yamasaki, S, Magyar, AP, Toth, M & Aharonovich, I 2018, 'Single crystal diamond membranes for nanoelectronics', Nanoscale, vol. 10, no. 8, pp. 4028-4035.
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Single crystal, nanoscale diamond membranes are highly sought after for a variety of applications including nanophotonics, nanoelectronics and quantum information science.

Bray, K, Regan, B, Trycz, A, Previdi, R, Seniutinas, G, Ganesan, K, Kianinia, M, Kim, S & Aharonovich, I 2018, 'Single Crystal Diamond Membranes and Photonic Resonators Containing Germanium Vacancy Color Centers', ACS Photonics, vol. 5, no. 12, pp. 4817-4822.
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Copyright © 2018 American Chemical Society. Single crystal diamond membranes that host optically active emitters are highly attractive components for integrated quantum nanophotonics. In this work we demonstrate bottom-up synthesis of single crystal diamond membranes containing germanium vacancy (GeV) color centers. We employ a lift-off technique to generate the membranes and perform chemical vapor deposition in the presence of a germanium source to realize the in situ doping. Finally, we show that these membranes are suitable for engineering of photonic resonators such as microdisk cavities with quality factors of ∼1500. The robust and scalable approach to engineer single crystal diamond membranes containing emerging color centers is a promising pathway for the realization of diamond integrated quantum nanophotonic circuits on a chip.

Brito, B, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Dong, PV, Stenfeldt, C, Rodriguez, LL, King, DP, Knowles, NJ, Bachanek-Bankowska, K, Long, NT, Dung, DH & Arzt, J 2018, 'A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences', Scientific Reports, vol. 8, no. 1, pp. 6472-6472.
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AbstractRecombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

Brito, BP, Mohapatra, JK, Subramaniam, S, Pattnaik, B, Rodriguez, LL, Moore, BR & Perez, AM 2018, 'Dynamics of widespread foot‐and‐mouth disease virus serotypes A, O and Asia‐1 in southern Asia: A Bayesian phylogenetic perspective', Transboundary and Emerging Diseases, vol. 65, no. 3, pp. 696-710.
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Foot-and-mouth disease (FMD) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV) have emerged. Here, we performed an integrative phylogenetic analysis of all FMDV serotypes (A, O and Asia-1) circulating in southern Asia, including viral sequences collected until 2013. Our results describe the occurrence of FMD caused by different serotypes and lineages, focusing in the cycles where a specific lineage predominates within a region for a protracted period and then are rapidly or progressively replaced by an emergent or re-emergent strain that is introduced from an adjacent region. Transmission between the two main regions in southern Asia (the Indian subcontinent and the region comprised by Afghanistan, Iran and Pakistan) has been limited. Results of time divergence estimation of lineages that currently circulate in this region indicate that the most recent common ancestor of endemic lineages are: 1992 [1989-1995] for lineage O/PanAsia; 1997 [1995-1999] for PanAsia2; 2001 [1998-2004] for O/Ind2001; 2001 [2000-2002] for A/Iran-05; 1990 [1988-1991] for A/G-18 (G-VII); 2003 [2000-2006] for Asia-1 Sindh08 and 2002 [1999-2004] for Asia-1 G-VIII. We estimated the mean of the overall substitution rate of the VP1 coding region (substitution/site/year) for serotype O (5.95 × 10-3 ), serotype A (1.19 × 10-2 ) and serotype Asia-1 (3.08 × 10-3 ). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV.

Brodersen, KE, Siboni, N, Nielsen, DA, Pernice, M, Ralph, PJ, Seymour, J & Kühl, M 2018, 'Seagrass rhizosphere microenvironment alters plant‐associated microbial community composition', Environmental Microbiology, vol. 20, no. 8, pp. 2854-2864.
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SummaryThe seagrass rhizosphere harbors dynamic microenvironments, where plant‐driven gradients of O2and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass‐mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrassZostera muelleritogether with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2S and pH occurred. Significantly higher relative abundances of sulphate‐reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide‐oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2S re‐oxidation here were similar to those observed in a pre‐sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant‐microbe interactions potentially affecting seagrass health.

Brown, A, Foss, A, Miller, MA & Gibson, Q 2018, 'Detection of cyanotoxins (microcystins/nodularins) in livers from estuarine and coastal bottlenose dolphins (Tursiops truncatus) from Northeast Florida', Harmful Algae, vol. 76, pp. 22-34.
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Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative', Scientific Data, vol. 5, no. 1, pp. 180130-180130.
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AbstractSustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

Buchmann, JP, Fourment, M & Holmes, EC 2018, 'The Biological Object Notation (BON): a structured file format for biological data', Scientific Reports, vol. 8, no. 1.
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AbstractThe large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between computers and applications. There has also been a substantial increase in the amount of metadata associated with biological data sets, which is being increasingly incorporated into existing data formats. Despite the existence of structured formats based on XML, biological data sets are mainly formatted using unstructured file formats, and the incorporation of metadata results in increasingly complex parsing routines such that they become more error prone. To overcome these problems, we present the “biological object notation” (BON) format, a new way to exchange and parse nearly all biological data sets more efficiently and with less error than other currently available formats. Based on JavaScript Object Notation (JSON), BON simplifies parsing by clearly separating the biological data from its metadata and reduces complexity compared to XML based formats. The ability to selectively compress data up to 87% compared to other file formats and the reduced complexity results in improved transfer times and less error prone applications.

Burgess, JK, Ketheson, A, Faiz, A, Limbert Rempel, KA, Oliver, BG, Ward, JPT & Halayko, AJ 2018, 'Phenotype and Functional Features of Human Telomerase Reverse Transcriptase Immortalized Human Airway Smooth Muscle Cells from Asthmatic and Non-Asthmatic Donors', Scientific Reports, vol. 8, no. 1, pp. 805-805.
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AbstractAsthma is an obstructive respiratory disease characterised by chronic inflammation with airway hyperresponsiveness. In asthmatic airways, there is an increase in airway smooth muscle (ASM) cell bulk, which differs from non-asthmatic ASM in characteristics. This study aimed to assess the usefulness of hTERT immortalisation of human ASM cells as a research tool. Specifically we compared proliferative capacity, inflammatory mediator release and extracellular matrix (ECM) production in hTERT immortalised and parent primary ASM cells from asthmatic and non-asthmatic donors. Our studies revealed no significant differences in proliferation, IL-6 and eotaxin-1 production, or CTGF synthesis between donor-matched parent and hTERT immortalised ASM cell lines. However, deposition of ECM proteins fibronectin and fibulin-1 was significantly lower in immortalised ASM cells compared to corresponding primary cells. Notably, previously reported differences in proliferation and inflammatory mediator release between asthmatic and non-asthmatic ASM cells were retained, but excessive ECM protein deposition in asthmatic ASM cells was lost in hTERT ASM cells. This study shows that hTERT immortalised ASM cells mirror primary ASM cells in proliferation and inflammatory profile characteristics. Moreover, we demonstrate both strengths and weaknesses of this immortalised cell model as a representation of primary ASM cells for future asthma pathophysiological research.

Burke, C, Burnard, D, Polkinghorne, A, Webb, J & Huston, WM 2018, 'Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll', Microorganisms, vol. 6, no. 3, pp. 68-68.
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The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.

Butera, D, Passam, F, Ju, L, Cook, KM, Woon, H, Aponte-Santamaría, C, Gardiner, E, Davis, AK, Murphy, DA, Bronowska, A, Luken, BM, Baldauf, C, Jackson, S, Andrews, R, Gräter, F & Hogg, PJ 2018, 'Autoregulation of von Willebrand factor function by a disulfide bond switch', Science Advances, vol. 4, no. 2.
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We demonstrate mechanochemical regulation of platelet adhesion to von Willebrand factor in thrombosis and hemostasis.

Butterworth, NJ, Byrne, PG, Keller, PA & Wallman, JF 2018, 'Body Odor and Sex: Do Cuticular Hydrocarbons Facilitate Sexual Attraction in the Small Hairy Maggot Blowfly?', Journal of Chemical Ecology, vol. 44, no. 3, pp. 248-256.
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Calarco, L, Barratt, J & Ellis, J 2018, 'Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence', Genome Biology and Evolution, vol. 10, no. 9, pp. 2417-2431.
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© The Author(s) 2018. Neospora caninum is an apicomplexan parasite responsible for neosporosis, a disease causing hind limb paralysis in dogs and abortion in cattle, resulting in substantial economic losses to beef and dairy industries. Marked differences in pathogenicity exist between N. caninum strains suggesting that intrinsic genetic differences exist between them. These differences likely exist in genes expressed during the tachyzoite lifecycle stage which is responsible for the pathogenesis of neosporosis. An improved understanding of these genetic differences is essential to understanding N. caninum virulence, though such knowledge is scarce. Using a variant detection workflow we compared the tachyzoite transcriptomes of two N. caninum strains with different virulence properties: NC-Liverpool (virulent) and NC-Nowra (avirulent). This workflow identified 3130 SNPs and 6123 indels between the strains, and nine markers capturing 30 variants were Sanger sequenced for both strains. Sequencing of these loci was extended to an additional eight strains and subsequent phylogenetic analysis supported a genetic population structure comprised of two major clades with no geographical segregation. Sequence polymorphisms within coding regions of tachyzoiteassociated genes were concentrated on chromosomes XI and XII, with 19 distinct tachyzoite-associated SNP hotspot regions identified within coding regions of the N. caninum nuclear genome. The variants were predominantly located in loci associated with protein binding, protein-protein interactions, transcription, and translation. Furthermore, 468 nonsynonymous SNPs identified within protein-coding genes were associated with protein kinase activity, protein binding, protein phosphorylation, and proteolysis. This work may implicate these processes and the specific proteins involved as novel effectors of N. caninum tachyzoite virulence.

Camp, EF, Schoepf, V & Suggett, DJ 2018, 'How can “Super Corals” facilitate global coral reef survival under rapid environmental and climatic change?', Global Change Biology, vol. 24, no. 7, pp. 2755-2757.
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AbstractCoral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term “Super Coral” in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. “How Super is Super”? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how “Super Corals” can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.

Camp, EF, Schoepf, V, Mumby, PJ & Suggett, DJ 2018, 'Editorial: The Future of Coral Reefs Subject to Rapid Climate Change: Lessons From Natural Extreme Environments', Frontiers in Marine Science, vol. 5, no. NOV.
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Camp, EF, Schoepf, V, Mumby, PJ, Hardtke, LA, Rodolfo-Metalpa, R, Smith, DJ & Suggett, DJ 2018, 'The Future of Coral Reefs Subject to Rapid Climate Change: Lessons from Natural Extreme Environments', Frontiers in Marine Science, vol. 5, no. FEB.
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© 2018 Camp, Schoepf, Mumby, Hardtke, Rodolfo-Metalpa, Smith and Suggett. Global climate change and localized anthropogenic stressors are driving rapid declines in coral reef health. In vitro experiments have been fundamental in providing insight into how reef organisms will potentially respond to future climates. However, such experiments are inevitably limited in their ability to reproduce the complex interactions that govern reef systems. Studies examining coral communities that already persist under naturally-occurring extreme and marginal physicochemical conditions have therefore become increasingly popular to advance ecosystem scale predictions of future reef form and function, although no single site provides a perfect analog to future reefs. Here we review the current state of knowledge that exists on the distribution of corals in marginal and extreme environments, and geographic sites at the latitudinal extremes of reef growth, as well as a variety of shallow reef systems and reef-neighboring environments (including upwelling and CO2 vent sites). We also conduct a synthesis of the abiotic data that have been collected at these systems, to provide the first collective assessment on the range of extreme conditions under which corals currently persist. We use the review and data synthesis to increase our understanding of the biological and ecological mechanisms that facilitate survival and success under sub-optimal physicochemical conditions. This comprehensive assessment can begin to: (i) highlight the extent of extreme abiotic scenarios under which corals can persist, (ii) explore whether there are commonalities in coral taxa able to persist in such extremes, (iii) provide evidence for key mechanisms required to support survival and/or persistence under sub-optimal environmental conditions, and (iv) evaluate the potential of current sub-optimal coral environments to act as potential refugia under changing environmental conditions. Such a collect...

Canfield, PJ, Blake, IM, Cai, Z-L, Luck, IJ, Krausz, E, Kobayashi, R, Reimers, JR & Crossley, MJ 2018, 'A new fundamental type of conformational isomerism', Nature Chemistry, vol. 10, no. 6, pp. 615-624.
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© 2018 The Author(s). Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Canfield, PJ, Blake, IM, Cai, Z-L, Luck, IJ, Krausz, E, Kobayashi, R, Reimers, JR & Crossley, MJ 2018, 'Publisher Correction: A new fundamental type of conformational isomerism', Nature Chemistry, vol. 10, no. 9, pp. 989-989.
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Cao, L, Wen, Q, Feng, Y, Ji, D, Li, H, Li, N, Jiang, L & Guo, W 2018, 'On the Origin of Ion Selectivity in Ultrathin Nanopores: Insights for Membrane‐Scale Osmotic Energy Conversion', Advanced Functional Materials, vol. 28, no. 39.
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AbstractNanopores in ultrathin or atomically thin membranes attract broad interest because the infinitesimal pore depth allows selective transport of ions and molecules with ultimate permeability. Toward large‐scale osmotic energy conversion, great challenges remain in extrapolating the promising single‐pore demonstration to really powerful macroscopic applications. Herein, the origin of the selective ion transport in ultrathin nanopores is systematically investigated. Based on a precise Poisson and Nernst–Planck model calculation, it is found that the generation of net diffusion current and membrane potential stems from the charge separation within the electric double layer on the outer membrane surface, rather than that on the inner pore wall. To keep the charge selectivity of the entire membrane, a critical surface charged area surrounding each pore orifice is therefore highly demanded. Otherwise, at high pore density, the membrane selectivity and the overall power density would fall down instead, which explains the giant gap between the actual experimental achievements and the single‐pore estimation. To maximize the power generation, smaller nanopores (pore diameter ≈1–2 nm) are appropriate for large‐scale osmotic energy conversion. With a porosity of ≈10%, the total power density approaches more than 200 W m‐2, anticipating a substantial advance toward high‐performance large‐scale nanofluidic power sources.

Carroll, R, Su, Y & Reedy, J 2018, 'Clustering in General Measurement Error Models', Statistica Sinica, vol. 28, no. 4, pp. 2337-2351.
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© Institute of Statistical Science. All rights reserved. This paper is dedicated to the memory of Peter G. Hall. It concerns a deceptively simple question: if one observes variables corrupted with measurement error of possibly very complex form, can one recreate asymptotically the clusters that would have been found had there been no measurement error? We show that the answer is yes, and that the solution is surprisingly simple and general. The method itself is to simulate, by computer, realizations with the same distribution as that of the true variables, and then to apply clustering to these realizations. Technically, we show that if one uses K-means clustering or any other risk minimizing clustering, and a multivariate deconvolution device with certain smoothness and convergence properties, then, in the limit, the cluster means based on our method converge to the same cluster means as if there were no measurement error. Along with the method and its technical justification, we analyze two important nutrition data sets, finding patterns that make sense nutritionally.

Carstensen, A, Herdean, A, Schmidt, SB, Sharma, A, Spetea, C, Pribil, M & Husted, S 2018, 'The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain', Plant Physiology, vol. 177, no. 1, pp. 271-284.
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Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley (Hordeum vulgare). P deficiency reduces the orthophosphate concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol oxidation retards electron transport to the cytochrome b6f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high-light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and, hence, reduces CO2 fixation. In parallel, lumen acidification activates the energy-dependent quenching component of the nonphotochemical quenching mechanism and prevents the overexcitation of photosystem II and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of orthophosphate to the leaf tissue.

Carter, DJ, Brown, J & Saunders, C 2018, 'The Patient’s Voice: Australian Health Care Quality and Safety Regulation From the Perspective of the Public', Journal of Law and Medicine, vol. 25, no. 2, pp. 408-428.
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The quality and safety of health care is a topic of permanent debate in the field of health services policy and regulation. Often absent from this debate, however, are the views and values of the public. These are excluded by a dominant narrative of health care regulation which understands the regulation of quality and safety in health care as principally a technical and instrumental undertaking. This approach constrains the application of law and legal regulation, devaluing their normative and expressive function in this field. In-part as a form of corrective, we offer an analysis based on recent survey data, of the attitudes and perceptions held by the Australian public towards stakeholder responsibility for, and the regulation of, health care quality and safety.

Casey, E, Ribaux, O & Roux, C 2018, 'Digital transformations and the viability of forensic science laboratories: Crisis-opportunity through decentralisation', Forensic Science International, vol. 289, pp. e24-e25.
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Castorina, A, Al-Badri, G, Leggio, G, Musumeci, G, Marzagalli, R & Drago, F 2018, 'Tackling dipeptidyl peptidase IV in neurological disorders', Neural Regeneration Research, vol. 13, no. 1, pp. 26-26.
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Dipeptidyl peptidase IV (DPP-IV) is a serine protease best known for its role in inactivating glucagon-like peptide-1 (GLP-1), pituitary adenylate cyclase-activating polypeptide (PACAP) and glucose-dependent insulinotropic peptide (GIP), three stimulators of pancreatic insulin secretion with beneficial effects on glucose disposal. Owing to the relationship between DPP-IV and these peptides, inhibition of DPP-IV enzyme activity is considered as an attractive treatment option for diabetic patients. Nonetheless, increasing studies support the idea that DPP-IV might also be involved in the development of neurological disorders with a neuroinflammatory component, potentially through its non-incretin activities on immune cells. In this review article, we aim at highlighting recent literature describing the therapeutic value of DPP-IV inhibitors for the treatment of such neurological conditions. Finally, we will illustrate some of the promising results obtained using berberine, a plant extract with potent inhibitory activity on DPP-IV.

Chadwick, S, de la Hunty, M & Baker, A 2018, 'Developing Awareness of Professional Behaviors and Skills in the First-Year Chemistry Laboratory', Journal of Chemical Education, vol. 95, no. 6, pp. 947-953.
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Copyright © 2018 American Chemical Society and Division of Chemical Education, Inc. Students in first-year chemistry classes come from a variety of backgrounds, with many students unaware of the qualities and behaviors of a professional scientist. Throughout their degree, students will gradually develop their cognitive skills, but they may not be adequately taught or assessed on their professional behavioral skills as a scientist until late in the undergraduate course. By assessing the professional skills of students in first-year chemistry practical classes, this innovation commenced the development of students' professional identity from the beginning of their university experience. The skills that were assessed included preparedness, cooperation in the group activities, working safely in the laboratory, and time management. By engaging students with professional behaviors and what it means to be a scientist during their first semester, students can potentially carry this through their whole undergraduate degree. This task was received positively by students and staff with over 50% of students believing it increased their confidence in the laboratory. Staff also saw a significant improvement in student behavior and engagement because of this task.

Chadwick, S, Moret, S, Jayashanka, N, Lennard, C, Spindler, X & Roux, C 2018, 'Investigation of some of the factors influencing fingermark detection', Forensic Science International, vol. 289, pp. 381-389.
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© 2018 Elsevier B.V. The primary aims of fingermark detection research are to improve the quality and increase the rate of detection of identifiable impressions. This is usually performed through the development of new methods and technologies to provide alternatives to or improve current procedures. While research of this nature is important to pursue, it fails to address the underlying question related to the factors that affect the detection of a latent fingermark. There has been significant research that has examined the differences between techniques, donors and fingermark age, as well as the composition of latent fingermarks. However, they tend not to focus on determining how these factors influence the quality of the developed mark. This study involved the development and evaluation of over 14,000 natural fingermarks deposited on a variety of surfaces to examine the effect of substrate, age, donor variability (both inter- and intra-), depletions and type of finger on fingermark development. Fingermarks were deposited on four substrates (two non-porous and two porous) and developed with either indanedione-zinc (IND-Zn) or cyanoacrylate followed by rhodamine 6G staining (CA + R6G). Three independent assessors graded each mark on the quality of development using an absolute scale proposed by the UK Centre for Applied Science and Technology (CAST). The data generated from these assessments were then analysed for trends or other useful insights. The results from this work reaffirm that individual substrate characteristics (and the choice of development technique) play a significant role in determining the number and quality of marks developed. It was found that fingermarks were more likely to be detected on porous substrates and to also be of a higher quality than on non-porous. The effect of fingermark donor variability was also explored, with significant differences observed between donors and within donors. This research shows that current detectio...

Chartrand, KM, Szabó, M, Sinutok, S, Rasheed, MA & Ralph, PJ 2018, 'Living at the margins – The response of deep-water seagrasses to light and temperature renders them susceptible to acute impacts', Marine Environmental Research, vol. 136, pp. 126-138.
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© 2018 Elsevier Ltd Seagrasses inhabit environments where light varies at different timescales, nonetheless are acutely sensitive to reductions in light beyond some conditional bounds. Two tropical deep-water seagrasses, Halophila decipiens and Halophila spinulosa, from the Great Barrier Reef were tested for their response to defined light and temperature regimes to identify their growth requirements and potential thresholds of mortality. Species were exposed to two light intensities, saturating (75 μmol photons m−2 s−1) and limiting (25 μmol photons m−2 s−1) light and two temperature treatments (26 °C and 30 °C) over a four-week period. Wavelength-specific parameters of PSII photochemistry were evaluated for seagrass leaves, as well as shoot density, gas exchange, and pigment content. Both species were sustained under saturating light levels (3.2 mol photons m−2 d−1) while limiting light led to decreased shoot density for H. decipiens and H. spinulosa after two and four weeks, respectively. Wavelength-specific photochemistry was also affected under light-limiting treatments for both species while the functional absorption cross section was highly conserved. Photoacclimation and physiological adjustments by either species was not adequate to compensate for reduced irradiance suggesting these plants reside at the margins of their functional limits. As such, relatively short periods of light attenuating events, like dredging or flood plumes, may be detrimental to deep-water seagrass populations.

Chellappan, DK, Hansbro, PM, Dua, K, Hsu, A, Gupta, G, Ng, ZY, Wong, J-Y, Chellian, J & Panneerselvam, J 2018, 'Vesicular Systems Containing Curcumin and Their Applications in Respiratory Disorders – A Mini Review', Pharmaceutical Nanotechnology, vol. 5, no. 4, pp. 250-254.
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Vesicular systems like nanotechnology and liposomes are gaining tremendous attention lately in the field of respiratory diseases. These formulations enhance bioavailability of the drug candidate, which could be achieved through a novel drug delivery mechanism. Moreover, the therapeutic potential achieved through these systems is highly controllable over long durations of time providing better efficacy and patient compliance.The objective of this paper is to review the recent literature on vesicular drug delivery systems containing curcumin.We have collated and summarized various recent attempts made to develop different controlled release drug delivery systems containing curcumin which would be of great interest for herbal, formulation and biological scientists. There are several vesicular nanotechnological techniques involving curcumin which have been studied recently, targeting pulmonary diseases.Different vesicular systems containing curcumin are being studied for their therapeutic potential in different respiratory diseases. There has been a renewed interest in formulations containing curcumin recently, primarily owing to the broad spectrum therapeutic potential of this miracle substance. Various types of formulations, containing curcumin, targeting different bodily systems have recently emerged and, nevertheless, the search for newer frontiers with this drug goes on.This mini review, in this direction, tries to highlight the key research interventions employing vesicular systems of drug delivery with curcumin.

Chellappan, DK, Ng, ZY, Wong, J-Y, Hsu, A, Wark, P, Hansbro, N, Taylor, J, Panneerselvam, J, Madheswaran, T, Gupta, G, Bebawy, M, Hansbro, PM & Dua, K 2018, 'Immunological Axis of Curcumin-Loaded Vesicular Drug Delivery Systems', Future Medicinal Chemistry, vol. 10, no. 8, pp. 839-844.
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Several vesicular systems loaded with curcumin have found their way in the therapeutic applications of several diseases, primarily acting through their immunological pathways. Such systems use particles at a nanoscale range, bringing about their intended use through a range of complex mechanisms. Apart from delivering drug substances into target tissues, these vesicular systems also effectively overcome problems like insolubility and unequal drug distribution. Several mechanisms are explored lately by different workers, and interest over vesicular curcumin has been renewed in the past decade. This commentary discusses several immunological targets in which curcumin is employed in a vesicular form.

Chellappan, DK, Sivam, NS, Teoh, KX, Leong, WP, Fui, TZ, Chooi, K, Khoo, N, Yi, FJ, Chellian, J, Cheng, LL, Dahiya, R, Gupta, G, Singhvi, G, Nammi, S, Hansbro, PM & Dua, K 2018, 'Gene therapy and type 1 diabetes mellitus', Biomedicine & Pharmacotherapy, vol. 108, pp. 1188-1200.
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© 2018 Elsevier Masson SAS Background: Type 1 diabetes mellitus (T1DM) is an autoimmune disorder characterized by T cell-mediated self-destruction of insulin-secreting islet β cells. Management of T1DM is challenging and complicated especially with conventional medications. Gene therapy has emerged as one of the potential therapeutic alternatives to treat T1DM. This review primarily focuses on the current status and the future perspectives of gene therapy in the management of T1DM. A vast number of the studies which are reported on gene therapy for the management of T1DM are done in animal models and in preclinical studies. In addition, the safety of such therapies is yet to be established in humans. Currently, there are several gene level interventions that are being investigated, notably, overexpression of genes and proteins needed against T1DM, transplantation of cells that express the genes against T1DM, stem-cells mediated gene therapy, genetic vaccination, immunological precursor cell-mediated gene therapy and vectors. Methods: We searched the current literature through searchable online databases, journals and other library sources using relevant keywords and search parameters. Only relevant publications in English, between the years 2000 and 2018, with evidences and proper citations, were considered. The publications were then analyzed and segregated into several subtopics based on common words and content. A total of 126 studies were found suitable for this review. Findings: Generally, the pros and cons of each of the gene-based therapies have been discussed based on the results collected from the literature. However, there are certain interventions that require further detailed studies to ensure their effectiveness. We have also highlighted the future direction and perspectives in gene therapy, which, researchers could benefit from.

Chen, C, Wang, F, Wen, S, Su, QP, Wu, MCL, Liu, Y, Wang, B, Li, D, Shan, X, Kianinia, M, Aharonovich, I, Toth, M, Jackson, SP, Xi, P & Jin, D 2018, 'Multi-photon near-infrared emission saturation nanoscopy using upconversion nanoparticles', Nature Communications, vol. 9, no. 1.
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AbstractMultiphoton fluorescence microscopy (MPM), using near infrared excitation light, provides increased penetration depth, decreased detection background, and reduced phototoxicity. Using stimulated emission depletion (STED) approach, MPM can bypass the diffraction limitation, but it requires both spatial alignment and temporal synchronization of high power (femtosecond) lasers, which is limited by the inefficiency of the probes. Here, we report that upconversion nanoparticles (UCNPs) can unlock a new mode of near-infrared emission saturation (NIRES) nanoscopy for deep tissue super-resolution imaging with excitation intensity several orders of magnitude lower than that required by conventional MPM dyes. Using a doughnut beam excitation from a 980 nm diode laser and detecting at 800 nm, we achieve a resolution of sub 50 nm, 1/20th of the excitation wavelength, in imaging of single UCNP through 93 μm thick liver tissue. This method offers a simple solution for deep tissue super resolution imaging and single molecule tracking.

Chen, F, Ji, S, Liu, Q, Wang, H, Liu, H, Brett, DJL, Wang, G & Wang, R 2018, 'Rational Design of Hierarchically Core–Shell Structured Ni₃S₂@NiMoO₄ Nanowires for Electrochemical Energy Storage', Small, vol. 14, no. 27, pp. 1800791-1800791.
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AbstractRational design and controllable synthesis of nanostructured materials with unique microstructure and excellent electrochemical performance for energy storage are crucially desired. In this paper, a facile method is reported for general synthesis of hierarchically core–shell structured Ni3S2@NiMoO4 nanowires (NWs) as a binder‐free electrode for asymmetric supercapacitors. Due to the intimate contact between Ni3S2 and NiMoO4, the hierarchical structured electrodes provide a promising unique structure for asymmetric supercapacitors. The as‐prepared binder‐free Ni3S2@NiMoO4 electrode can significantly improve the electrical conductivity between Ni3S2 and NiMoO4, and effectively avoid the aggregation of NiMoO4 nanosheets, which provide more active space for storing charge. The Ni3S2@NiMoO4 electrode presents a high areal capacity of 1327.3 µAh cm−2 and 67.8% retention of its initial capacity when current density increases from 2 to 40 mA cm−2. In a two‐electrode Ni3S2@NiMoO4//active carbon cell, the active materials deliver a high energy density of 121.5 Wh kg−1 at a power density of 2.285 kW kg−1 with excellent cycling stability.

Chen, H 2018, 'Gold nanoparticles improve metabolic profile of mice fed a high-fat diet', J Nanobiotechnology, vol. 16.
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BACKGROUND:Obesity is a high risk for multiple metabolic disorders due to excessive influx of energy, glucose and lipid, often from a western based diet. Low-grade inflammation plays a key role in the progression of such metabolic disorders. The anti-inflammatory property of gold compounds has been used in treating rheumatoid arthritis in the clinic. Previously we found that pure gold nanoparticles (AuNPs, 21 nm) also possess anti-inflammatory effects on the retroperitoneal fat tissue following intraperitoneal injection, by downregulating tumor necrosis factor (TNF) α. However, whether such an effect can change the risk of metabolic disorders in the obese has not been well studied. The study employed C57BL/6 mice fed a pellet high fat diet (HFD, 43% as fat) that were treated daily with AuNPs [low (HFD-LAu) or high (HFD-HAu) dose] via intraperitoneal injection for 9 weeks. In the in vitro study, RAW264.7 macrophages and 3T3-L1 adipocytes were cultured with low and high concentrations of AuNPs alone or together.RESULTS:The HFD-fed mice showed a significant increase in fat mass, glucose intolerance, dyslipidemia, and liver steatosis. The HFD-LAu group showed an 8% reduction in body weight, ameliorated hyperlipidemia, and normal glucose tolerance; while the HFD-HAu group had a 5% reduction in body weight with significant improvement in their glucose intolerance and hyperlipidemia. The underlying mechanism may be attributed to a reduction in adipose and hepatic local proinflammatory cytokine production, e.g. TNFα. In vitro studies of co-cultured murine RAW264.7 macrophage and 3T3-L1 adipocytes supported this proposed mechanism.CONCLUSION:AuNPs demonstrate a promising profile for potential management of obesity related glucose and lipid disorders and are useful as a research tool for the study of biological mechanisms.

Chen, H, Chan, YL, Linnane, C, Mao, Y, Anwer, AG, Sapkota, A, Annissa, TF, Herok, G, Vissel, B, Oliver, BG, Saad, S & Gorrie, CA 2018, 'L-Carnitine and extendin-4 improve outcomes following moderate brain contusion injury', Scientific Reports, vol. 8, no. 1.
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AbstractThere is a need for pharmaceutical agents that can reduce neuronal loss and improve functional deficits following traumatic brain injury (TBI). Previous research suggests that oxidative stress and mitochondrial dysfunction play a major role in neuronal damage after TBI. Therefore, this study aimed to investigate two drugs known to have antioxidant effects, L-carnitine and exendin-4, in rats with moderate contusive TBI. L-carnitine (1.5 mM in drinking water) or exendin-4 (15 µg/kg/day, ip) were given immediately after the injury for 2 weeks. Neurological function and brain histology were examined (24 h and 6 weeks post injury). The rats with TBI showed slight sensory, motor and memory functional deficits at 24 h, but recovered by 6 weeks. Both treatments improved sensory and motor functions at 24 h, while only exendin-4 improved memory. Both treatments reduced cortical contusion at 24 h and 6 weeks, however neither affected gliosis and inflammatory cell activation. Oxidative stress was alleviated and mitochondrial reactive oxygen species was reduced by both treatments, however only mitochondrial functional marker protein transporter translocase of outer membrane 20 was increased at 24 h post injury. In conclusion, L-carnitine and exendin-4 treatments immediately after TBI can improve neurological functional outcome and tissue integrity by reducing oxidative stress.

Chen, H, Li, G, Chan, YL, Chapman, DG, Sukjamnong, S, Nguyen, T, Annissa, T, McGrath, KC, Sharma, P & Oliver, BG 2018, 'Maternal E-Cigarette Exposure in Mice Alters DNA Methylation and Lung Cytokine Expression in Offspring', American Journal of Respiratory Cell and Molecular Biology, vol. 58, no. 3, pp. 366-377.
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Copyright © 2018 by the American Thoracic Society E-cigarette usage is increasing, especially among the young, with both the general population and physicians perceiving them as a safe alternative to tobacco smoking. Worryingly, e-cigarettes are commonly used by pregnant women. As nicotine is known to adversely affect children in utero, we hypothesized that nicotine delivered via e-cigarettes would negatively affect lung development. To test this, we developed a mouse model of maternal e-vapor (nicotine and nicotine-free) exposure and investigated the impact on the growth and lung inflammation in both offspring and mothers. Female Balb/c mice were exposed to e-fluid vapor containing nicotine (18 mg/ml nicotine E-cigarette [E-cig18], equivalent to two cigarettes per treatment, twice daily,) or nicotine free (E-cig0 mg/ml) from 6 weeks before mating until pups weaned. Male offspring were studied at Postnatal Day (P) 1, P20, and at 13 weeks. The mothers were studied when the pups weaned. In the mothers' lungs, e-cigarette exposure with and without nicotine increased the proinflammatory cytokines IL-1b, IL-6, and TNF-a. In adult offspring, TNF-a protein levels were increased in both E-cig18 and E-cig0 groups, whereas IL-1b was suppressed. This was accompanied by global changes in DNA methylation. In this study, we found that e-cigarette exposure during pregnancy adversely affected maternal and offspring lung health. As this occurred with both nicotine-free and nicotine-containing e-vapor, the effects are likely due to by-products of vaporization rather than nicotine.

Chen, H, Li, G, Chan, YL, Nguyen, T, van Reyk, D, Saad, S & Oliver, BG 2018, 'Modulation of neural regulators of energy homeostasis, and of inflammation, in the pups of mice exposed to e-cigarettes', Neuroscience Letters, vol. 684, pp. 61-66.
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© 2018 Background: Maternal smoking can lead to perturbations in central metabolic regulators such as neuropeptide Y (NPY) and pro-opiomelanocortin (POMC) signalling components in offspring. With the growing interest in e-cigarettes as a tobacco replacement, this short report assessed central metabolic regulation in offspring of mouse dams exposed to e-cigarettes. We examined the impact of continuous use of e-cigarettes, and e-cigarette replacement of tobacco cigarettes during pregnancy. Supplementation of an antioxidant L-carnitine was also co-used with tobacco cigarette in the mother to determine whether the impact of maternal tobacco smoking was oxidative stress driven. Methods: Balb/c mice were exposed to either nicotine-containing (E-cig18) or nicotine-free (E-cig0) e-cigarette aerosols or tobacco smoke (SE) prior to mating and until their pups were weaned. After mating, two SE sub-groups were changed to E-cig18 exposure (Replacement), or supplementation L-carnitine while SE was continued. Male offspring were studied at weaning age. Results: The offspring of E-cig0 dams were the heaviest with the most body fat. Replacing SE with E-cig18 during pregnancy resulted in offspring with significantly less body fat. E-cig0 offspring had significantly increased mRNA expression of brain NPY and iNOS. Maternal SE upregulated mRNA expression of NPY, NPY Y1 receptor, POMC downstream components, and iNOS expression, which were normalised in Replacement offspring, but only partially normalised with maternal L-carnitine supplementation during gestation and lactation. Conclusions: Maternal exposure to either tobacco and nicotine-free e-cigarettes lead to disturbances in the level of central homeostatic control markers in offspring, suggesting that maternal exposure to e-cigarettes is not without risks.

Chen, H, McGowan, EM, Ren, N, Lal, S, Nassif, N, Shad-Kaneez, F, Qu, X & Lin, Y 2018, 'Nattokinase: A Promising Alternative in Prevention and Treatment of Cardiovascular Diseases', Biomarker Insights, vol. 13, pp. 117727191878513-117727191878513.
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Cardiovascular disease (CVD) is the leading cause of death in the world and our approach to the control and management of CVD mortality is limited. Nattokinase (NK), the most active ingredient of natto, possesses a variety of favourable cardiovascular effects and the consumption of Natto has been linked to a reduction in CVD mortality. Recent research has demonstrated that NK has potent fibrinolytic activity, antihypertensive, anti-atherosclerotic, and lipid-lowering, antiplatelet, and neuroprotective effects. This review covers the major pharmacologic effects of NK with a focus on its clinical relevance to CVD. It outlines the advantages of NK and the outstanding issues pertaining to NK pharmacokinetics. Available evidence suggests that NK is a unique natural compound that possesses several key cardiovascular beneficial effects for patients with CVD and is therefore an ideal drug candidate for the prevention and treatment of CVD. Nattokinase is a promising alternative in the management of CVD.

Chen, H, Ng, JPM, Bishop, DP, Milthorpe, BK & Valenzuela, SM 2018, 'Gold nanoparticles as cell regulators: beneficial effects of gold nanoparticles on the metabolic profile of mice with pre-existing obesity', Journal of Nanobiotechnology, vol. 16, no. 1.
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Chen, H, Ng, JPM, Tan, Y, McGrath, K, Bishop, DP, Oliver, B, Chan, YL, Cortie, MB, Milthorpe, BK & Valenzuela, SM 2018, 'Gold nanoparticles improve metabolic profile of mice fed a high-fat diet', Journal of Nanobiotechnology, vol. 16, no. 1.
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© 2018 The Author(s). Background: Obesity is a high risk for multiple metabolic disorders due to excessive influx of energy, glucose and lipid, often from a western based diet. Low-grade inflammation plays a key role in the progression of such metabolic disorders. The anti-inflammatory property of gold compounds has been used in treating rheumatoid arthritis in the clinic. Previously we found that pure gold nanoparticles (AuNPs, 21 nm) also possess anti-inflammatory effects on the retroperitoneal fat tissue following intraperitoneal injection, by downregulating tumor necrosis factor (TNF) α. However, whether such an effect can change the risk of metabolic disorders in the obese has not been well studied. The study employed C57BL/6 mice fed a pellet high fat diet (HFD, 43% as fat) that were treated daily with AuNPs [low (HFD-LAu) or high (HFD-HAu) dose] via intraperitoneal injection for 9 weeks. In the in vitro study, RAW264.7 macrophages and 3T3-L1 adipocytes were cultured with low and high concentrations of AuNPs alone or together. Results: The HFD-fed mice showed a significant increase in fat mass, glucose intolerance, dyslipidemia, and liver steatosis. The HFD-LAu group showed an 8% reduction in body weight, ameliorated hyperlipidemia, and normal glucose tolerance; while the HFD-HAu group had a 5% reduction in body weight with significant improvement in their glucose intolerance and hyperlipidemia. The underlying mechanism may be attributed to a reduction in adipose and hepatic local proinflammatory cytokine production, e.g. TNFα. In vitro studies of co-cultured murine RAW264.7 macrophage and 3T3-L1 adipocytes supported this proposed mechanism. Conclusion: AuNPs demonstrate a promising profile for potential management of obesity related glucose and lipid disorders and are useful as a research tool for the study of biological mechanisms.

Chen, WY & Wand, MP 2018, 'Factor graph fragmentization of expectation propagation', Journal of the Korean Statistical Society, vol. 49, no. 3, pp. 722-756.
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Expectation propagation is a general approach to fast approximate inferencefor graphical models. The existing literature treats models separately when itcomes to deriving and coding expectation propagation inference algorithms. Thiscomes at the cost of similar, long-winded algebraic steps being repeated andslowing down algorithmic development. We demonstrate how factor graphfragmentization can overcome this impediment. This involves adoption of themessage passing on a factor graph approach to expectation propagation andidentification of factor graph sub-graphs, which we call fragments, that arecommon to wide classes of models. Key fragments and their correspondingmessages are catalogued which means that their algebra does not need to berepeated. This allows compartmentalization of coding and efficient softwaredevelopment.

Chen, X, Ren, B, Yu, D, Xu, B, Zhang, Z & Chen, G 2018, 'Uniaxial low cycle fatigue behavior for pre-corroded 16MND5 bainitic steel in simulated pressurized water reactor environment', Journal of Nuclear Materials, vol. 504, pp. 267-276.
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Chen, Y, Choi, S, Su, D, Gao, X & Wang, G 2018, 'Self-standing sulfur cathodes enabled by 3D hierarchically porous titanium monoxide-graphene composite film for high-performance lithium-sulfur batteries', Nano Energy, vol. 47, pp. 331-339.
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© 2018 Elsevier Ltd Although lithium-sulfur batteries show great promise for next-generation energy storage due to their high energy density, the practical implementation of lithium-sulfur batteries has been largely impeded by the shuttle effect of lithium polysulfides and low areal capacity (< 2 mAh cm−2). Here we rationally design a new self-standing host enabled by a 3D hierarchically-porous titanium monoxide-graphene composite film to overcome the two issues at once. The hierarchically porous graphene scaffold not only can facilitate rapid lithium ion and electron transport, but also provide sufficient spaces to accommodate sulfur and buffer the volume expansion during the lithiation process. In addition, the ultrafine and polar titanium monoxide nanoparticles embedded in the three-dimensional graphene networks show strong chemical anchoring for polysulfides as evidenced by ex-situ X-ray photoelectron spectroscopy analysis, and their inherent metallic conductivity accelerates the redox reaction kinetics. Benefiting from this attractive architecture, the freestanding titanium monoxide-graphene/sulfur cathode delivered a high initial capacity of 1350 mAh g−1 at 0.1 C, a Coulombic efficiency approaching 100%, and a high-rate capacity of 832 mAh g−1 at 2 C. Moreover, when the areal sulfur loading was increased to 5.2 mg cm−2, the titanium monoxide-graphene/sulfur electrode delivered a high areal capacity of 3.2 mAh cm−2 after 300 cycles at 0.2 C, demonstrating excellent cycling performance compared with other recently reported sulfur cathodes with high areal sulfur loadings.

Chen, Y, Duong, HTT, Wen, S, Mi, C, Zhou, Y, Shimoni, O, Valenzuela, SM & Jin, D 2018, 'Exonuclease III-Assisted Upconversion Resonance Energy Transfer in a Wash-Free Suspension DNA Assay', Analytical Chemistry, vol. 90, no. 1, pp. 663-668.
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© 2017 American Chemical Society. Sensitivity is the key in optical detection of low-abundant analytes, such as circulating RNA or DNA. The enzyme Exonuclease III (Exo III) is a useful tool in this regard; its ability to recycle target DNA molecules results in markedly improved detection sensitivity. Lower limits of detection may be further achieved if the detection background of autofluorescence can be removed. Here we report an ultrasensitive and specific method to quantify trace amounts of DNA analytes in a wash-free suspension assay. In the presence of target DNA, the Exo III recycles the target DNA by selectively digesting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed from the probe DNA is proportional to the number of target DNAs. Remaining intact probe DNAs are then bound onto upconversion nanoparticles (energy donor), which allows for upconversion luminescence resonance energy transfer (LRET) that can be used to quantify the difference between the free dye and tagged dye (energy acceptor). This scheme simply avoids both autofluorescence under infrared excitation and many tedious washing steps, as the free dye molecules are physically located away from the nanoparticle surface, and as such they remain 'dark' in suspension. Compared to alternative approaches requiring enzyme-assisted amplification on the nanoparticle surface, introduction of probe DNAs onto nanoparticles only after DNA hybridization and signal amplification steps effectively avoids steric hindrance. Via this approach, we have achieved a detection limit of 15 pM in LRET assays of human immunodeficiency viral DNA.

Cheng, A, Zhao, T, Tse, K-H, Chow, H-M, Cui, Y, Jiang, L, Du, S, Loy, MMT & Herrup, K 2018, 'ATM and ATR play complementary roles in the behavior of excitatory and inhibitory vesicle populations', Proceedings of the National Academy of Sciences, vol. 115, no. 2.
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Significance The symptoms of neurological diseases such as autism and schizophrenia are often attributed to a loss of excitatory/inhibitory balance of neural network function. By showing that ATR and ATM impact inhibitory and excitatory vesicle trafficking differently, our work expands the known repertoire of cytoplasmic functions for the two kinases and provides a new perspective on the origins of the symptoms of ataxia-telangiectasia (A-T) and Seckel syndrome (ATM and ATR deficiency, respectively). While these findings have their most immediate implications for the neurologic and cognitive symptoms of A-T and Seckel syndrome, they have potential relevance to a much broader range of neurologic conditions.

Cheng, B, Nikitopoulos, CS & Schlögl, E 2018, 'Pricing of long-dated commodity derivatives: Do stochastic interest rates matter?', Journal of Banking & Finance, vol. 95, pp. 148-166.
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© 2017 Elsevier B.V. Does modelling stochastic interest rates, beyond stochastic volatility, improve pricing performance on long-dated commodity derivatives? To answer this question, we consider futures price models for commodity derivatives that allow for stochastic volatility and stochastic interest rates and a correlation structure between the underlying variables. We examine the empirical pricing performance of these models on pricing long-dated crude oil derivatives. Estimating the model parameters from historical crude oil futures prices and option prices, we find that stochastic interest rate models improve pricing performance on long-dated crude oil derivatives, when the interest rate volatility is relatively high. Furthermore, increasing the model dimensionality does not tend to improve the pricing performance on long-dated crude oil option prices, but it matters for long-dated futures prices. We also find empirical evidence for a negative correlation between crude oil futures prices and interest rates that contributes to improving fit to long-dated crude oil option prices.

Cheng, YY, Jin, HC, Chan, MWY, Chu, WK & Grusch, M 2018, 'Epigenetic Biomarkers in Cancer', Disease Markers, vol. 2018, pp. 1-2.
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Cheng, YY, Sarun, K, Lee, K, Clarke, C, Cheng, N & Takahashi, K 2018, 'P2.06-07 Genomic Deletion of BAP1 and CDKN2A are Better MM Diagnostic Biomarkers.', Journal of Thoracic Oncology, vol. 13, no. 10, pp. S744-S745.
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Cheung, EYY, Gahan, ME & McNevin, D 2018, 'Prediction of biogeographical ancestry in admixed individuals', Forensic Science International: Genetics, vol. 36, pp. 104-111.
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Cheung, EYY, Gahan, ME & McNevin, D 2018, 'Predictive DNA analysis for biogeographical ancestry', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-8.
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© 2018, © 2018 Australian Academy of Forensic Sciences. Establishment of national DNA databases in Australia and overseas has increased the number of criminal convictions, yet a high volume of serious crime cases remain with no suspect profile nor any DNA database matches. In these circumstances prediction of biogeographical ancestry (BGA) and externally visible characteristics can assist by providing forensic intelligence in conjunction with, or in place of, eyewitness testimonies. To predict the BGA of an individual requires: genetic markers selected for their ability to differentiate between BGAs; representative BGA reference populations; and a prediction algorithm (‘classifier’) that predicts the BGA of an unknown individual based on genetic markers in the reference populations. The human genome contains autosomal ancestry informative markers that are easily harvested from publicly accessible collections of genotypes with associated ancestry information. A number of classification methods are available including Bayesian approaches and distance-based algorithms. BGA is likely to be continuous rather than discrete and some methods are inappropriate for the prediction of admixed BGA. As predictive services become available to the public and private sectors, there is a risk of results being misinterpreted if an inappropriate tool is applied. Understanding the underlying marker sets, reference populations and classification algorithms is required to prevent ill-informed predictions.

Cheung, S, Wu, D, Daly, HC, Busschaert, N, Morgunova, M, Simpson, JC, Scholz, D, Gale, PA & O'Shea, DF 2018, 'Real-Time Recording of the Cellular Effects of the Anion Transporter Prodigiosin', Chem, vol. 4, no. 4, pp. 879-895.
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Chew, SC, Yam, JKH, Matysik, A, Seng, ZJ, Klebensberger, J, Givskov, M, Doyle, P, Rice, SA, Yang, L & Kjelleberg, S 2018, 'Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus', mBio, vol. 9, no. 6.
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Bacteria in natural and engineered environments form biofilms that include many different species. Microorganisms rely on a number of different strategies to manage social interactions with other species and to access resources, build biofilm consortia, and optimize growth. For example, Pseudomonas aeruginosa and Staphylococcus aureus are biofilm-forming bacteria that coinfect the lungs of cystic fibrosis patients and diabetic and chronic wounds. P. aeruginosa is known to antagonize S. aureus growth. However, many of the factors responsible for mixed-species interactions and outcomes such as infections are poorly understood. Biofilm bacteria are encased in a self-produced extracellular matrix that facilitates interspecies behavior and biofilm development. In this study, we examined the poorly understood roles of the major matrix biopolymers and their regulators in mixed-species biofilm interactions and development.

Chilambi, GS, Gao, IH, Yoon, BK, Park, S, Kawakami, LM, Ravikumar, V, Chan-Park, MB, Cho, N-J, Bazan, GC, Kline, KA, Rice, SA & Hinks, J 2018, 'Membrane adaptation limitations inEnterococcus faecalisunderlie sensitivity and the inability to develop significant resistance to conjugated oligoelectrolytes', RSC Advances, vol. 8, no. 19, pp. 10284-10293.
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COEs are emerging antimicrobials to combat drug resistant infections and to which bacteria develop only limited resistance.

Choi, S & Wang, G 2018, 'Advanced Lithium‐Ion Batteries for Practical Applications: Technology, Development, and Future Perspectives', Advanced Materials Technologies, vol. 3, no. 9, pp. 1700376-1700376.
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AbstractLithium‐ion batteries have been used to operate various electric devices over the last decade. Electronic devices have been developed rapidly to achieve a high level of performance and enter into new markets. However, lithium‐ion batteries face limitations as a result of the low theoretical energy density of existing materials. Thus, many researchers have sought to investigate different ways to enhance the performance of batteries when used for practical applications. This review revisits the literature related to the development of high performance lithium‐ion batteries, which have been shown to have achieved outstanding results in a full cell test. In particular, the full cell test is critically important when seeking to develop materials that are appropriate for use in practical applications, and it also helps meet the increasing demands of new lithium‐ion batteries that are a result of emerging technology. This review article aims to provide information about the development of lithium‐ion batteries and the latest developments in new materials and nanotechnology. Furthermore, it will outline the challenges faced by the research community in developing advanced batteries and the outlook for the next generation of lithium‐ion batteries.

Choi, S, Su, D, Shin, M, Park, S & Wang, G 2018, 'Pomegranate‐Structured Silica/Sulfur Composite Cathodes for High‐Performance Lithium–Sulfur Batteries', Chemistry – An Asian Journal, vol. 13, no. 5, pp. 568-576.
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AbstractPorous materials have many structural advantages for energy storage and conversion devices such as rechargeable batteries, supercapacitors, and fuel cells. When applied as a host material in lithium‐sulfur batteries, porous silica materials with a pomegranate‐like architecture can not only act as a buffer matrix for accommodating a large volume change of sulfur, but also suppress the polysulfide shuttle effect. The porous silica/sulfur composite cathodes exhibit excellent electrochemical performances including a high specific capacity of 1450 mA h g−1, a reversible capacity of 82.9 % after 100 cycles at a rate of C/2 (1 C=1672 mA g−1) and an extended cyclability over 300 cycles at 1 C‐rate. Furthermore, the high polysulfide adsorption property of porous silica has been proven by ex‐situ analyses, showing a relationship between the surface area of silica and polysulfide adsorption ability. In particular, the modified porous silica/sulfur composite cathode, which is treated by a deep‐lithiation process in the first discharge step, exhibits a highly reversible capacity of 94.5 % at 1C‐rate after 300 cycles owing to a formation of lithiated‐silica frames and stable solid‐electrolyte‐interphase layers.

Choi, V, Cobbin, D & Walsh, S 2018, 'Does Modern Research Concerning Chinese Medicine Acupoints Relate to Original Prescriptions? If Not, Why Not?', Medical Acupuncture, vol. 30, no. 6, pp. 336-347.
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© 2018, Mary Ann Liebert, Inc., publishers 2018. Objective: Huang Fu Mi's Zhen Jiu Jia Yi Jing (ZJJYJ) is regarded as the earliest text (282 ce) on differential diagnosis and clinical acumoxa therapy in Chinese Medicine. Are contemporary manual acupuncture practices consistent with those reported in the ZJJYJ? The aim of this research was to investigate if modern manual acupuncture uses reported in research are consistent with classical practices reported in the ZJJYJ. Materials and Methods: A database search of human research studies from 1995 to 2016 was performed for all 270 acupoints for all 8 leg/body channels. The clinical foci of these modern publications were compared with acupoint clinical indications documented in the Song Dynasty Chinese edition (1077) of the ZJJYJ and the sole English translation (translated and compiled by Yang and Chace in 1994) of The Systematic Classic of Acupuncture and Moxibustion. Results: Of 2149 articles in English, 63 met the search criteria. These articles predominately reported acupoints on the lower leg, back, chest, and head. Correlations between the acupoints used in modern research and those used in the ZJJYJ were minimal. Clinical indications from the ZJJYJ typically involved symptoms relating to pain, swelling, fever, seizures, hallucinatory states, dysentery, malaria, and tuberculosis, which are now treated pharmacologically. However, one-third of modern studies were functional magnetic resonance imaging (fMRI) investigations of neurophysiologic effects of manual acupuncture on the human brain. Conclusions: While, superficially, the ZJJYJ might seem irrelevant in modern manual acupuncture practices, well-documented physical effects (e.g., pain relief) of manual acupuncture do provide measurable outcomes for use in fMRI research. Therefore, the classical text does provide a guide for future research on influential acupoints on the leg and body channels.

Christenson, SA, van den Berge, M, Faiz, A, Inkamp, K, Bhakta, N, Bonser, LR, Zlock, LT, Barjaktarevic, IZ, Barr, RG, Bleecker, ER, Boucher, RC, Bowler, RP, Comellas, AP, Curtis, JL, Han, MK, Hansel, NN, Hiemstra, PS, Kaner, RJ, Krishnanm, JA, Martinez, FJ, O’Neal, WK, Paine, R, Timens, W, Wells, JM, Spira, A, Erle, DJ & Woodruff, PG 2018, 'An airway epithelial IL-17A response signature identifies a steroid-unresponsive COPD patient subgroup', Journal of Clinical Investigation, vol. 129, no. 1, pp. 169-181.
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BACKGROUND:Chronic obstructive pulmonary disease (COPD) is a heterogeneous smoking-related disease characterized by airway obstruction and inflammation. This inflammation may persist even after smoking cessation and responds variably to corticosteroids. Personalizing treatment to biologically similar "molecular phenotypes" may improve therapeutic efficacy in COPD. IL-17A is involved in neutrophilic inflammation and corticosteroid resistance, and thus may be particularly important in a COPD molecular phenotype. METHODS:We generated a gene expression signature of IL-17A response in bronchial airway epithelial brushings from smokers with and without COPD (n = 238), and validated it using data from 2 randomized trials of IL-17 blockade in psoriasis. This IL-17 signature was related to clinical and pathologic characteristics in 2 additional human studies of COPD: (a) SPIROMICS (n = 47), which included former and current smokers with COPD, and (b) GLUCOLD (n = 79), in which COPD participants were randomized to placebo or corticosteroids. RESULTS:The IL-17 signature was associated with an inflammatory profile characteristic of an IL-17 response, including increased airway neutrophils and macrophages. In SPIROMICS the signature was associated with increased airway obstruction and functional small airways disease on quantitative chest CT. In GLUCOLD the signature was associated with decreased response to corticosteroids, irrespective of airway eosinophilic or type 2 inflammation. CONCLUSION:These data suggest that a gene signature of IL-17 airway epithelial response distinguishes a biologically, radiographically, and clinically distinct COPD subgroup that may benefit from personalized therapy. TRIAL REGISTRATION:ClinicalTrials.gov NCT01969344. FUNDING:Primary support from the NIH, grants K23HL123778, K12HL11999, U19AI077439, DK072517, U01HL137880, K24HL137013 and R01HL121774 and contracts HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN2682...

Cinner, JE, Maire, E, Huchery, C, MacNeil, MA, Graham, NAJ, Mora, C, McClanahan, TR, Barnes, ML, Kittinger, JN, Hicks, CC, D’Agata, S, Hoey, AS, Gurney, GG, Feary, DA, Williams, ID, Kulbicki, M, Vigliola, L, Wantiez, L, Edgar, GJ, Stuart-Smith, RD, Sandin, SA, Green, A, Hardt, MJ, Beger, M, Friedlander, AM, Wilson, SK, Brokovich, E, Brooks, AJ, Cruz-Motta, JJ, Booth, DJ, Chabanet, P, Gough, C, Tupper, M, Ferse, SCA, Sumaila, UR, Pardede, S & Mouillot, D 2018, 'Gravity of human impacts mediates coral reef conservation gains', Proceedings of the National Academy of Sciences, vol. 115, no. 27, pp. E6116-E6125.
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Significance Marine reserves that prohibit fishing are a critical tool for sustaining coral reef ecosystems, yet it remains unclear how human impacts in surrounding areas affect the capacity of marine reserves to deliver key conservation benefits. Our global study found that only marine reserves in areas of low human impact consistently sustained top predators. Fish biomass inside marine reserves declined along a gradient of human impacts in surrounding areas; however, reserves located where human impacts are moderate had the greatest difference in fish biomass compared with openly fished areas. Reserves in low human-impact areas are required for sustaining ecological functions like high-order predation, but reserves in high-impact areas can provide substantial conservation gains in fish biomass.

Clark, JS, Poore, AGB & Doblin, MA 2018, 'Shaping up for stress: Physiological flexibility is key to survivorship in a habitat-forming macroalga', Journal of Plant Physiology, vol. 231, pp. 346-355.
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Organisms from all domains of life can have highly variable morphologies, with this plasticity suggested to increase fitness and survivability under stressful conditions. Predicting how organisms will adapt to environmental change requires an understanding of how variable morphologies perform under environmental stress. Morphological plasticity has been documented within marine macroalgae inhabiting environmental gradients, however the functional consequences of this variation has been rarely tested. In this study, form-function was assessed in the habitat-forming, intertidal macroalga Hormosira banksii. Morphological variation was quantified on two spatial scales (tidal gradient versus latitudinal gradient) and the performance tested (relative water content and photosynthetic efficiency) of morphological variants during heat and desiccation stress. At regional scales, individuals at the warm distributional edge were overall smaller in size, and had smaller vesicles (higher surface area to volume ratio; SA:VOL) than those from central populations. At local scales, individuals high on the shore were generally shorter and had larger vesicles than those low on the shore. Vesicle morphology (SA:VOL) was found to predict relative water content and photosynthetic performance during desiccation and rehydration. Differences in SA:VOL of vesicles between heights on the shore may reflect water requirements needed to maintain tissue hydration for photosynthesis during low tide. Warm-edge populations showed increased thermal sensitivity as indicated by decreased photosynthetic yield of PSII and delays in recovery after desiccation. Sensitivities to higher temperatures amongst warm-edge populations are potentially due to smaller fluctuations in regional temperatures as well as their morphology. This study provides a mechanistic understanding of the morphological variation among H. banksii populations. It suggests that H. banksii has a high degree of morphological plasticity r...

Clarke, C, Liu, D, Wang, F, Liu, Y, Chen, C, Ton-That, C, Xu, X & Jin, D 2018, 'Large-scale dewetting assembly of gold nanoparticles for plasmonic enhanced upconversion nanoparticles', Nanoscale, vol. 10, no. 14, pp. 6270-6276.
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The integrated methods of core shell upconversion nanoparticle synthesis, thermal annealing and gold dewetting produce gold-decorated upconversion nanoparticles with enhanced emission.

Claywell, BC, Dinh, V, Fourment, M, McCoy, CO & Matsen IV, FA 2018, 'A Surrogate Function for One-Dimensional Phylogenetic Likelihoods', Molecular Biology and Evolution, vol. 35, no. 1, pp. 242-246.
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© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. Phylogenetics has seen a steady increase in data set size and substitution model complexity, which require increasing amounts of computational power to compute likelihoods. This motivates strategies to approximate the likelihood functions for branch length optimization and Bayesian sampling. In this article, we develop an approximation to the 1D likelihood function as parametrized by a single branch length. Our method uses a four-parameter surrogate function abstracted from the simplest phylogenetic likelihood function, the binary symmetric model. We show that it offers a surrogate that can be fit over a variety of branch lengths, that it is applicable to a wide variety of models and trees, and that it can be used effectively as a proposal mechanism for Bayesian sampling. The method is implemented as a stand-Alone open-source C library for calling from phylogenetics algorithms; it has proven essential for good performance of our online phylogenetic algorithm sts.

Cohen, A, Zinger, A, Tiberti, N, Grau, GER & Combes, V 2018, 'Differential plasma microvesicle and brain profiles of microRNA in experimental cerebral malaria', Malaria Journal, vol. 17, no. 1, pp. 192-192.
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© 2018 The Author(s). Background: Cerebral malaria (CM) is a fatal complication of Plasmodium infection, mostly affecting children under the age of five in the sub-Saharan African region. CM pathogenesis remains incompletely understood, although sequestered infected red blood cells, inflammatory cells aggregating in the cerebral blood vessels, and the microvesicles (MV) that they release in the circulation, have been implicated. Plasma MV numbers increase in CM patients and in the murine model, where blocking their release, genetically or pharmacologically, protects against brain pathology, suggesting a role of MV in CM neuropathogenesis. In this work, the microRNA (miRNA) cargo of MV is defined for the first time during experimental CM with the overarching hypothesis that this characterization could help understand CM pathogenesis. Results: The change in abundance of miRNA was studied following infection of CBA mice with Plasmodium berghei ANKA strain (causing experimental CM), and Plasmodium yoelii, which causes severe malaria without cerebral complications, termed non-CM (NCM). miRNA expression was analyzed using microarrays to compare MV from healthy (NI) and CM mice, yielding several miRNA of interest. The differential expression profiles of these selected miRNA (miR-146a, miR-150, miR-193b, miR-205, miR-215, miR-467a, and miR-486) were analyzed in mouse MV, MV-free plasma, and brain tissue by quantitative reverse transcription PCR (RT-qPCR). Two miRNA - miR-146a and miR-193b - were confirmed as differentially abundant in MV from CM mice, compared with NCM and NI mice. These miRNA have been shown to play various roles in inflammation, and their dysregulation during CM may be critical for triggering the neurological syndrome via regulation of their potential downstream targets. Conclusions: These data suggest that, in the mouse model at least, miRNA may have a regulatory role in the pathogenesis of severe malaria.

Cole, JM, Gong, Y, McCree-Grey, J, Evans, PJ & Holt, SA 2018, 'Modulation of N3 and N719 dye···TiO₂ Interfacial Structures in Dye-Sensitized Solar Cells As Influenced by Dye Counter Ions, Dye Deprotonation Levels, and Sensitizing Solvent', ACS Applied Energy Materials, vol. 1, no. 6, pp. 2821-2831.
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Colusso, AV, McDonagh, A & Cortie, MB 2018, 'X‐ray‐induced reduction of a surfactant/polyoxotungstate hybrid compound', Surface and Interface Analysis, vol. 50, no. 12-13, pp. 1384-1388.
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We investigate the spontaneous reduction of a photochromic surfactant/polyoxotungstate hybrid during repeated X‐ray photoelectron spectroscopy (XPS) scans and show how this effect may confound attempts to use soft X‐rays to characterise materials of this nature. The W4f core‐level spectra revealed a progressive increase of W5+ and W4+ species at the expense of W6+ as irradiation time increased. The samples developed a blue colour attributed to the presence of W4+ and/or W5+. The progressive photoreduction is also associated with a shift of the W6+ peak within the W4f spectrum to lower binding energies. This work highlights the need to consider inadvertent changes in oxidation state during X‐ray photoelectron spectroscopy characterisation of samples containing photoreducible transition metals.

Colusso, AV, McDonagh, AM, Gentle, A & Cortie, MB 2018, 'Photomechanical photochromism in a cetyltrimethylammonium isopolytungstate', RSC Advances, vol. 8, no. 34, pp. 18776-18783.
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The photochromic properties of a hybrid compound comprised of the surfactant cation cetyltrimethylammonium [(C₁₆H₃₃)N(CH₃)₃]⁺ and the isopolytungstate anion [H₂W₁₂O₄₀]⁶⁻ is investigated.

Cooper, ER, McGrath, KCY, Li, X & Heather, AK 2018, 'Androgen Bioassay for the Detection of Nonlabeled Androgenic Compounds in Nutritional Supplements', International Journal of Sport Nutrition and Exercise Metabolism, vol. 28, no. 1, pp. 10-18.
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Both athletes and the general population use nutritional supplements. Athletes often turn to supplements hoping that consuming the supplement will help them be more competitive and healthy, while the general population hopes to improve body image or vitality. While many supplements contain ingredients that may have useful properties, there are supplements that are contaminated with compounds that are banned for use in sport or have been deliberately adulterated to fortify a supplement with an ingredient that will produce the advertised effect. In the present study, we have used yeast cell and mammalian cell androgen bioassays to characterize the androgenic bioactivity of 112 sports supplements available from the Australian market, either over the counter or via the Internet. All 112 products did not declare an androgen on the label as an included ingredient. Our findings show that six out of 112 supplements had strong androgenic bioactivity in the yeast cell bioassay, indicating products spiked or contaminated with androgens. The mammalian cell bioassay confirmed the strong androgenic bioactivity of five out of six positive supplements. Supplement 6 was metabolized to weaker androgenic bioactivity in the mammalian cells. Further to this, Supplement 6 was positive in a yeast cell progestin bioassay. Together, these findings highlight that nutritional supplements, taken without medical supervision, could expose or predispose users to the adverse consequences of androgen abuse. The findings reinforce the need to increase awareness of the dangers of nutritional supplements and highlight the challenges that clinicians face in the fast-growing market of nutritional supplements.

Copeland, E, Leonard, K, Carney, R, Kong, J, Forer, M, Naidoo, Y, Oliver, BGG, Seymour, JR, Woodcock, S, Burke, CM & Stow, NW 2018, 'Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites', Frontiers in Cellular and Infection Microbiology, vol. 8, no. FEB, pp. 1-14.
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© 2018 Copeland, Leonard, Carney, Kong, Forer, Naidoo, Oliver, Seymour, Woodcock, Burke and Stow. Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site.

Cortie, MB, Cortie, DL & Timchenko, V 2018, 'Heat transfer from nanoparticles for targeted destruction of infectious organisms', International Journal of Hyperthermia, vol. 34, no. 2, pp. 157-167.
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Whereas the application of optically or magnetically heated nanoparticles to destroy tumours is now well established, the extension of this concept to target pathogens has barely begun. Here we examine the challenge of targeting pathogens by this means and, in particular, explore the issues of power density and heat transfer. Depending on the rate of heating, either hyperthermia or thermoablation may occur. This division of the field is fundamental and implies very different sources of excitation and heat transfer for the two modes, and different strategies for their clinical application. Heating by isolated nanoparticles and by agglomerates of nanoparticles is compared: hyperthermia is much more readily achieved with agglomerates and for large target volumes, a factor which favours magnetic excitation and moderate power densities. In contrast, destruction of planktonic pathogens is best achieved by localised thermoablation and very high power density, a scenario that is best delivered by pulsed optical excitation.

Curson, ARJ, Williams, BT, Pinchbeck, BJ, Sims, LP, Martínez, AB, Rivera, PPL, Kumaresan, D, Mercadé, E, Spurgin, LG, Carrión, O, Moxon, S, Cattolico, RA, Kuzhiumparambil, U, Guagliardo, P, Clode, PL, Raina, J-B & Todd, JD 2018, 'DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton', Nature Microbiology, vol. 3, no. 4, pp. 430-439.
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© 2018 The Author(s). Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton4, and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified5. However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.

Cwiklinski, K, Jewhurst, H, McVeigh, P, Barbour, T, Maule, AG, Tort, J, O'Neill, SM, Robinson, MW, Donnelly, S & Dalton, JP 2018, 'Infection by the Helminth Parasite Fasciola hepatica Requires Rapid Regulation of Metabolic, Virulence, and Invasive Factors to Adjust to Its Mammalian Host', Molecular & Cellular Proteomics, vol. 17, no. 4, pp. 792-809.
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© 2018 by The American Society for Biochemistry and Molecular Biology, Inc. The parasite Fasciola hepatica infects a broad range of mammals with impunity. Following ingestion of parasites (metacercariae) by the host, newly excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall and migrate to the liver. Successful infection takes just a few hours and involves negotiating hurdles presented by host macromolecules, tissues and micro-environments, as well as the immune system. Here, transcriptome and proteome analysis of ex vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude of metabolic and developmental alterations that take place in order for the parasite to establish infection. We found that metacercariae despite being encased in a cyst are metabolically active, and primed for infection. Following excystment, NEJ expend vital energy stores and rapidly adjust their metabolic pathways to cope with their new and increasingly anaerobic environment. Temperature increases induce neoblast proliferation and the remarkable up-regulation of genes associated with growth and development. Cysteine proteases synthesized by gastrodermal cells are secreted to facilitate invasion and tissue degradation, and tegumental transporters, such as aquaporins, are varied to deal with osmotic/salinity changes. Major proteins of the total NEJ secretome include proteases, protease inhibitors and anti-oxidants, and an array of immunomodulators that likely disarm host innate immune effector cells. Thus, the challenges of infection by F. hepatica parasites are met by rapid metabolic and physiological adjustments that expedite tissue invasion and immune evasion; these changes facilitate parasite growth, development and maturation. Our molecular analysis of the critical processes involved in host invasion has identified key targets for future drug and vaccine strategies directed at preventing parasite infection.

Czibula, OG, Gu, H & Zinder, Y 2018, 'Lagrangian relaxation versus genetic algorithm based metaheuristic for a large partitioning problem', Theoretical Computer Science, vol. 718, pp. 24-36.
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© 2017 Elsevier B.V. This paper is concerned with a partitioning problem. One of the applications, and the motivation for this research, is the problem of class formation for training and retraining sessions at large electricity distributors. Two different approaches are developed. One is based on the Quadratic Multiple Knapsack formulation and Lagrangian relaxation. The other is a matheuristic developed as an amalgamation of Genetic Algorithms and Integer Programming. The approaches are tested by means of computational experiments. Both heuristics outperformed the direct application of quadratic programming, with the Lagrangian relaxation based approach performing the best on average, and the Genetic Algorithm based approach performing the best on the larger test cases.

Czibula, OG, Gu, H & Zinder, Y 2018, 'Planning personnel retraining: column generation heuristics', Journal of Combinatorial Optimization, vol. 36, no. 3, pp. 896-915.
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Dachian, S, Kordzakhia, N, Kutoyants, YA & Novikov, A 2018, 'Estimation of cusp location of stochastic processes: a survey', Statistical Inference for Stochastic Processes, vol. 21, no. 2, pp. 345-362.
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© 2018, Springer Science+Business Media B.V., part of Springer Nature. We present a review of some recent results on estimation of location parameter for several models of observations with cusp-type singularity at the change point. We suppose that the cusp-type models fit better to the real phenomena described usually by change point models. The list of models includes Gaussian, inhomogeneous Poisson, ergodic diffusion processes, time series and the classical case of i.i.d. observations. We describe the properties of the maximum likelihood and Bayes estimators under some asymptotic assumptions. The asymptotic efficiency of estimators are discussed as well and the results of some numerical simulations are presented. We provide some heuristic arguments which demonstrate the convergence of log-likelihood ratios in the models under consideration to the fractional Brownian motion.

Dai, S, Tymchenko, M, Xu, Z-Q, Tran, TT, Yang, Y, Ma, Q, Watanabe, K, Taniguchi, T, Jarillo-Herrero, P, Aharonovich, I, Basov, DN, Tao, TH & Alù, A 2018, 'Internal Nanostructure Diagnosis with Hyperbolic Phonon Polaritons in Hexagonal Boron Nitride', Nano Letters, vol. 18, no. 8, pp. 5205-5210.
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Copyright © 2018 American Chemical Society. Imaging materials and inner structures with resolution below the diffraction limit has become of fundamental importance in recent years for a wide variety of applications. We report subdiffractive internal structure diagnosis of hexagonal boron nitride by exciting and imaging hyperbolic phonon polaritons. On the basis of their unique propagation properties, we are able to accurately locate defects in the crystal interior with nanometer resolution. The precise location, size, and geometry of the concealed defects are reconstructed by analyzing the polariton wavelength, reflection coefficient, and their dispersion. We have also studied the evolution of polariton reflection, transmission, and scattering as a function of defect size and photon frequency. The nondestructive high-precision polaritonic structure diagnosis technique introduced here can be also applied to other hyperbolic or waveguide systems and may be deployed in the next-generation biomedical imaging, sensing, and fine structure analysis.

Daines, AM, Robinson, H, Glenny, M, Williams, DBG & Hinkley, SFR 2018, 'Linear and macrocyclic water soluble polyacylhydrazones and their utilisation in coatings', Progress in Organic Coatings, vol. 121, pp. 38-44.
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© 2018 Elsevier B.V. Water soluble polyacylhydrazones have been generated that contain a high proportion of renewable materials. The polyacylhydrazones were found to be present simultaneously as linear and macrocyclic species, the latter being favoured at higher concentrations and in certain combinations of levulinoyl ester/acyldihydrazide. Levulinoyl esters with multiple ketone reactive sites were targeted as building blocks for the backbone. Reaction of these species in aqueous media with commercially available acyldihydrazides afforded a series of high solids-content water soluble polyacylhydrazone solutions. Evaporation of the water from the solutions reproducibly generated films with differing and useful characteristics. One of the polyhydrazones was successfully formulated into two different types of resin bases of commercial coating systems, producing paint products with renewable content.

Dann, LM, McKerral, JC, Smith, RJ, Tobe, SS, Paterson, JS, Seymour, JR, Oliver, RL & Mitchell, JG 2018, 'Microbial micropatches within microbial hotspots', PLOS ONE, vol. 13, no. 5, pp. e0197224-e0197224.
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© 2018 Dann et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

Davey, PA, Pernice, M, Ashworth, J, Kuzhiumparambil, U, Szabó, M, Dolferus, R & Ralph, PJ 2018, 'A new mechanistic understanding of light-limitation in the seagrass Zostera muelleri', Marine Environmental Research, vol. 134, pp. 55-67.
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© 2018 Elsevier Ltd In this study we investigated the effect of light-limitation (∼20 μmol photons m−2 s−1) on the southern hemisphere seagrass, Zostera muelleri. RNA sequencing, chlorophyll fluorometry and HPLC techniques were used to investigate how the leaf-specific transcriptome drives changes in photosynthesis and photo-pigments in Z. muelleri over 6 days. 1593 (7.51%) genes were differentially expressed on day 2 and 1481 (6.98%) genes were differentially expressed on day 6 of the experiment. Differential gene expression correlated with significant decreases in rETRMax, Ik, an increase in Yi (initial photosynthetic quantum yield of photosystem II), and significant changes in pigment composition. Regulation of carbohydrate metabolism was observed along with evidence that abscisic acid may serve a role in the low-light response of this seagrass. This study provides a novel understanding of how Z. muelleri responds to light-limitation in the marine water column and provides potential molecular markers for future conservation monitoring efforts.

Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, van Ruth, P, Waite, AM, Wright, S & Richardson, AJ 2018, 'A database of chlorophyll a in Australian waters', Scientific Data, vol. 5, no. 1.
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AbstractChlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

Dawson, A, Huston, W, Kawaguchi, S, King, C, Cropp, R, Wild, S, Eisenmann, P, Townsend, K & Bengtson Nash, S 2018, 'Uptake and Depuration Kinetics Influence Microplastic Bioaccumulation and Toxicity in Antarctic Krill (Euphausia superba)', Environmental Science & Technology, vol. 52, no. 5, pp. 3195-3201.
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© 2018 American Chemical Society. The discarding of plastic products has led to the ubiquitous occurrence of microplastic particles in the marine environment. The uptake and depuration kinetics of ingested microplastics for many marine species still remain unknown despite its importance for understanding bioaccumulation potential to higher trophic level consumers. In this study, Antarctic krill (Euphausia superba) were exposed to polyethylene microplastics to quantify acute toxicity and ingestion kinetics, providing insight into the bioaccumulation potential of microplastics at the first-order consumer level. In the 10 day acute toxicity assay, no mortality or dose-dependent weight loss occurred in exposed krill, at any of the exposure concentrations (0, 10, 20, 40, or 80% plastic diet). Krill exposed to a 20% plastic diet for 24 h displayed fast uptake (22 ng mg-1 h-1) and depuration (0.22 h-1) rates, but plastic uptake did not reach steady state. Efficient elimination also resulted in no bioaccumulation over an extended 25 day assay, with most individuals completely eliminating their microplastic burden in less than 5 days post exposure. Our results support recent findings of limited acute toxicity of ingested microplastics at this trophic level, and suggest sublethal chronic end points should be the focus of further ecotoxicological investigation.

Dawson, A, Poulsen, A, Huston, W & Bengtson Nash, S 2018, 'Expression of common biomarkers in Antarctic krill (Euphausia superba) exposed to an organochlorine contaminant', Polar Biology, vol. 41, no. 3, pp. 505-513.
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© 2017, Springer-Verlag GmbH Germany. Persistent organic pollutant (POP) contamination of Polar Regions continues to present a major ecological challenge and an environmental stressor to local biota. Antarctic krill (Euphausia superba) are a keystone species of the Antarctic sea ice ecosystem. Krill have repeatedly been found to accumulate a diverse array of POPs and thereby serve as vectors of these to the remainder of the Antarctic food web. p,p′-Dichlorodiphenyldichloroethylene (p,p′-DDE) is a dominant POP compound accumulating in Antarctic krill and higher trophic level predators. Recently, p,p′-DDE uptake dynamics, associated behavioural and developmental toxicity were evaluated in this species. The present study investigated the response of enzymes with known roles in detoxification (glutathione S-transferase, GST and cytochrome P450 2B, CYP2B), neurotoxicity (acetylcholinesterase, AChE) and oxidative stress (glutathione peroxidase GPx) in Antarctic krill exposed to p,p′-DDE. CYP2B was not detectable in Antarctic krill. No strong concentration responses resulted from the exposure to p,p′-DDE. These findings do not provide evidence for an activated detoxification response to this compound via the tested biochemical pathways in Antarctic krill. This is the first time that GST, AChE and GPx have been characterised in this species following pollutant exposure. Further research with additional pollutants and compound mixtures is necessary to assess the practical role of these enzymes as biomarkers of pollutant exposure in Antarctic krill. These first exploratory findings present a valuable contribution to a critical knowledge gap in polar ecotoxicology, namely the comparative sensitivity of polar organisms relative to temperate and tropical counterparts.

Dawson, AL, Kawaguchi, S, King, CK, Townsend, KA, King, R, Huston, WM & Bengtson Nash, SM 2018, 'Turning microplastics into nanoplastics through digestive fragmentation by Antarctic krill', Nature Communications, vol. 9, no. 1.
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AbstractMicroplastics (plastics <5 mm diameter) are at the forefront of current environmental pollution research, however, little is known about the degradation of microplastics through ingestion. Here, by exposing Antarctic krill (Euphausia superba) to microplastics under acute static renewal conditions, we present evidence of physical size alteration of microplastics ingested by a planktonic crustacean. Ingested microplastics (31.5 µm) are fragmented into pieces less than 1 µm in diameter. Previous feeding studies have shown spherical microplastics either; pass unaffected through an organism and are excreted, or are sufficiently small for translocation to occur. We identify a new pathway; microplastics are fragmented into sizes small enough to cross physical barriers, or are egested as a mixture of triturated particles. These findings suggest that current laboratory-based feeding studies may be oversimplifying interactions between zooplankton and microplastics but also introduces a new role of Antarctic krill, and potentially other species, in the biogeochemical cycling and fate of plastic.

de la Hunty, M, Moret, S, Chadwick, S, Lennard, C, Spindler, X & Roux, C 2018, 'An effective Physical Developer (PD) method for use in Australian laboratories', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-6.
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© 2018, © 2018 Australian Academy of Forensic Sciences. Physical Developer (PD) is an underutilized technique for the development of latent marks on porous surfaces that have been wet, or as a subsequent technique in a development sequence. It is a multistep technique that works by selectively reducing silver ions to silver metal at nucleating sites in fingermark residue. Its use is associated with a plethora of issues, largely surrounding the inherent instability of the working solution. Recently, one of the components of the working solution, Synperonic N, has ceased production, and the recommended replacement is Tween 20. This article addresses factors during PD processing using Tween 20, other than reagent formulations that should be considered when using the technique.

De Puysseleyr, K, Kieckens, E, De Puysseleyr, L, Van den Wyngaert, H, Ahmed, B, Van Lent, S, Creasy, HH, Myers, GSA & Vanrompay, D 2018, 'Development of aChlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C', Transboundary and Emerging Diseases, vol. 65, no. 2, pp. e457-e469.
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Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.

de Vries, M, Faiz, A, Woldhuis, RR, Postma, DS, de Jong, TV, Sin, DD, Bossé, Y, Nickle, DC, Guryev, V, Timens, W, van den Berge, M & Brandsma, C-A 2018, 'Lung tissue gene-expression signature for the ageing lung in COPD', Thorax, vol. 73, no. 7, pp. 609-617.
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IntroductionCOPD is a chronic, progressive, inflammatory disease of the lungs and the third leading cause of death worldwide. The current knowledge of the pathophysiology of COPD is limited and novel insights in underlying disease mechanisms are urgently needed. Since there are clear parallels between ageing and COPD, we investigated genes underlying lung ageing in general and abnormal lung ageing in COPD.MethodsWhole genome mRNA profiling was performed on lung tissue samples (n=1197) and differential gene expression with increasing age was analysed using an adjusted linear regression model. Subsequent pathway analysis was performed using GeneNetwork and the gene-expression signature was compared with lung ageing in the Genotype-Tissue Expression (GTEx) project. In a subset of patients with COPD (n=311) and non-COPD controls (n=270), we performed an interaction analysis between age and COPD to identify genes differentially expressed with age in COPD compared with controls, followed by gene set enrichment pathway analysis.ResultsWe identified a strong gene-expression signature for lung ageing with 3509 differentially expressed genes, of which 33.5% were found nominal significant in the GTEx project. Interestingly, we foundEDA2Ras a strong candidate gene for lung ageing. The age*COPD interaction analysis revealed 69 genes significantly differentially expressed with age between COPD and controls.ConclusionsOur study indicates that processes related to lung development, cell-cell contacts, calcium signalling and immune responses are involved in lung ageing in general. Pathways related to extracellular matrix, mammalian target of rapamycin signalling, splicing of introns and exons and the ribosome comple...

Dean, S, Walsh, S, Williams, C, Zaslawski, C, Morgan, A & Levett-Jones, T 2018, 'The mystery shopper student learning experience in undergraduate health education: A case study', Nurse Education Today, vol. 70, no. 2018, pp. 69-76.
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Décary-Hétu, D, Mousseau, V & Vidal, S 2018, 'Six Years Later', Contemporary Drug Problems, vol. 45, no. 4, pp. 366-381.
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Cryptomarkets are online illicit marketplaces where drug dealers advertise the sale of illicit drugs. Anonymizing technologies such as the Tor network and virtual currencies are used to hide cryptomarket participants’ identity and to limit the ability of law enforcement agencies to make arrests. In this paper, our aim is to describe how herbal cannabis dealers and buyers in the United States have adapted to the online sale of herbal cannabis through cryptomarkets. To achieve this goal, we evaluate the size and scope of the American herbal cannabis market on cryptomarkets and compare it to other drug markets from other countries, evaluate the impact of cryptomarkets on offline sales of herbal cannabis, and evaluate the ties between the now licit herbal cannabis markets in some States and cryptomarkets. Our results suggest that only a small fraction of herbal cannabis dealers and drug users have transitioned to cryptomarkets. This can be explained by the need for technical skills to buy and sell herbal cannabis online and by the need to have access to computers that are not accessible to all. The slow rate of adoption may also be explained by the higher price of herbal cannabis relative to street prices. If cryptomarkets were to be adopted by a larger portion of the herbal cannabis market actors, our results suggest that wholesale and regional distributors who are not active on cryptomarkets would be the most affected market’s participants.

Dehn, MH, Arseneau, DJ, Buck, T, Cortie, DL, Fleming, DG, King, SR, MacFarlane, WA, McDonagh, AM, McFadden, RML, Mitchell, DRG & Kiefl, RF 2018, 'Nature of magnetism in thiol-capped gold nanoparticles investigated with Muon spin rotation', Applied Physics Letters, vol. 112, no. 5, pp. 053105-053105.
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Muon spin rotation/relaxation measurements show clear evidence for magnetism in 2.2 nm gold nanoparticles capped with butanethiol. At low temperatures (1.8 K), there is significant spin relaxation which decreases as a function of both the applied longitudinal magnetic field and increasing temperature. The results indicate that there are spatially inhomogeneous electronic moments that fluctuate with a wide distribution of correlation times. Possible explanations are discussed.

DeMaere, MZ & Darling, AE 2018, 'bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)', Genome Biology, vol. 20.
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AbstractMost microbes inhabiting the planet cannot be easily grown in the lab. Metagenomic techniques provide a means to study these organisms, and recent advances in the field have enabled the resolution of individual genomes from metagenomes, so-called Metagenome Assembled Genomes (MAGs). In addition to expanding the catalog of known microbial diversity, the systematic retrieval of MAGs stands as a tenable divide and conquer reduction of metagenome analysis to the simpler problem of single genome analysis. Many leading approaches to MAG retrieval depend upon time-series or transect data, whose effectiveness is a function of community complexity, target abundance and depth of sequencing. Without the need for time-series data, promising alternative methods are based upon the high-throughput sequencing technique called Hi-C.The Hi-C technique produces read-pairs which capture in-vivo DNA-DNA proximity interactions (contacts). The physical structure of the community modulates the signal derived from these interactions and a hierarchy of interaction rates exists (īntra-chromosomal > Inter-chromosomal > Inter-cellular).We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs from a single time-point. As a quantitative demonstration, next, we validate the method against the ground truth of a simulated human faecal microbiome. Lastly, we directly compare our method against a recently announced proprietary service ProxiMeta, which also performs MAG retrieval using Hi-C data.bin3C has been implemented as a simple open-source pipeline and makes use of the unsupervised community detection algorithm Infomap (https://github.com/cerebis/bin3C).

DeMaere, MZ & Darling, AE 2018, 'Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies', GigaScience, vol. 7, no. 2, pp. 1-12.
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Abstract Background Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. Conclusions We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respec...

Deplazes, E 2018, 'Molecular simulations of venom peptide‐membrane interactions: Progress and challenges', Peptide Science, vol. 110, no. 3, pp. e24060-e24060.
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AbstractBecause of their wide range of biological activities venom peptides are a valuable source of lead molecules for the development of pharmaceuticals, pharmacological tools and insecticides. Many venom peptides work by modulating the activity of ion channels and receptors or by irreversibly damaging cell membranes. In many cases, the mechanism of action is intrinsically linked to the ability of the peptide to bind to or partition into membranes. Thus, understanding the biological activity of these venom peptides requires characterizing their membrane binding properties. This review presents an overview of the recent developments and challenges in using biomolecular simulations to study venom peptide‐membrane interactions. The review is focused on (i) gating modifier peptides that target voltage‐gated ion channels, (ii) venom peptides that inhibit mechanosensitive ion channels, and (iii) pore‐forming venom peptides. The methods and approaches used to study venom peptide‐membrane interactions are discussed with a particular focus on the challenges specific to these systems and the type of questions that can (and cannot) be addressed using state‐of‐the‐art simulation techniques. The review concludes with an outlook on future aims and directions in the field.

Deplazes, E, Poger, D, Cornell, B & Cranfield, CG 2018, 'The effect of H3O+ on the membrane morphology and hydrogen bonding of a phospholipid bilayer', Biophysical Reviews, vol. 10, no. 5, pp. 1371-1376.
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At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3O+) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness. A first-order explanation for the effect was assigned to alterations in the steric packing of the membrane lipids. Changes in packing were described by a critical packing parameter (CPP) related to the interfacial area and volume and shape of the membrane lipids. We proposed that increasing the concentraton of H3O+ resulted in stronger hydrogen bonding between the phosphate oxygens at the water-lipid interface leading to a reduced area per lipid and slightly increased membrane thickness. At the meeting, a molecular model for these pH effects based on the result of our second study was presented. Multiple μs-long, unrestrained molecular dynamic (MD) simulations of a phosphatidylcholine lipid bilayer were carried out and showed a concentration dependent reduction in the area per lipid and an increase in bilayer thickness, in agreement with experimental data. Further, H3O+ preferentially accumulated at the water-lipid interface, suggesting the localised pH at the membrane surface is much lower than the bulk bathing solution. Another significant finding was that the hydrogen bonds formed by H3O+ ions with lipid headgroup oxygens are, on average, shorter in length and longer-lived than the ones formed in bulk water. In addition, the H3O+ ions resided for longer periods in association with the carbonyl oxygens than with either phosphate oxygen in lipids. In summary, the MD simulations support a model where the hy...

Deplazes, E, Poger, D, Cornell, B & Cranfield, CG 2018, 'The effect of hydronium ions on the structure of phospholipid membranes', Physical Chemistry Chemical Physics, vol. 20, no. 1, pp. 357-366.
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This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.

Deppeler, S, Petrou, K, Schulz, KG, Westwood, K, Pearce, I, McKinlay, J & Davidson, A 2018, 'Ocean acidification of a coastal Antarctic marine microbial community reveals a critical threshold for CO₂ tolerance in phytoplankton productivity', Biogeosciences, vol. 15, no. 1, pp. 209-231.
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Abstract. High-latitude oceans are anticipated to be some of the first regions affected by ocean acidification. Despite this, the effect of ocean acidification on natural communities of Antarctic marine microbes is still not well understood. In this study we exposed an early spring, coastal marine microbial community in Prydz Bay to CO2 levels ranging from ambient (343 µatm) to 1641 µatm in six 650 L minicosms. Productivity assays were performed to identify whether a CO2 threshold existed that led to a change in primary productivity, bacterial productivity, and the accumulation of chlorophyll a (Chl a) and particulate organic matter (POM) in the minicosms. In addition, photophysiological measurements were performed to identify possible mechanisms driving changes in the phytoplankton community. A critical threshold for tolerance to ocean acidification was identified in the phytoplankton community between 953 and 1140 µatm. CO2 levels  ≥ 1140 µatm negatively affected photosynthetic performance and Chl a-normalised primary productivity (csGPP14C), causing significant reductions in gross primary production (GPP14C), Chl a accumulation, nutrient uptake, and POM production. However, there was no effect of CO2 on C : N ratios. Over time, the phytoplankton community acclimated to high CO2 conditions, showing a down-regulation of carbon concentrating mechanisms (CCMs) and likely adjusting other intracellular processes. Bacterial abundance initially increased in CO2 treatments  ≥ 953 µatm (days 3–5), yet gross bacterial production (GBP14C) remained unchanged and cell-specific bacterial productivity (csBP14C) was reduced. Towards the end of the experiment, GBP14C and csBP14C markedly increased across all treatments regardless of CO2 availability. This coincided with increased organic matter availability (POC and PON) combined with improved efficiency of carbon uptake. Changes in phytoplankton community production could have negative effects on the Antarcti...

Deutscher, AT, Burke, CM, Darling, AE, Riegler, M, Reynolds, OL & Chapman, TA 2018, 'Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae', Microbiome, vol. 6, no. 1.
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BACKGROUND:Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). RESULTS:Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. CONCLUSIONS:Variation in the gut bac...

Devadas, R, Huete, AR, Vicendese, D, Erbas, B, Beggs, PJ, Medek, D, Haberle, SG, Newnham, RM, Johnston, FH, Jaggard, AK, Campbell, B, Burton, PK, Katelaris, CH, Newbigin, E, Thibaudon, M & Davies, JM 2018, 'Dynamic ecological observations from satellites inform aerobiology of allergenic grass pollen', Science of The Total Environment, vol. 633, pp. 441-451.
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© 2018 Allergic diseases, including respiratory conditions of allergic rhinitis (hay fever) and asthma, affect up to 500 million people worldwide. Grass pollen are one major source of aeroallergens globally. Pollen forecast methods are generally site-based and rely on empirical meteorological relationships and/or the use of labour-intensive pollen collection traps that are restricted to sparse sampling locations. The spatial and temporal dynamics of the grass pollen sources themselves, however, have received less attention. Here we utilised a consistent set of MODIS satellite measures of grass cover and seasonal greenness (EVI) over five contrasting urban environments, located in Northern (France) and Southern Hemispheres (Australia), to evaluate their utility for predicting airborne grass pollen concentrations. Strongly seasonal and pronounced pollinating periods, synchronous with satellite measures of grass cover greenness, were found at the higher latitude temperate sites in France (46–50° N. Lat.), with peak pollen activity lagging peak greenness, on average by 2–3 weeks. In contrast, the Australian sites (34–38° S. Lat.) displayed pollinating periods that were less synchronous with satellite greenness measures as peak pollen concentrations lagged peak greenness by as much as 4 to 7 weeks. The Australian sites exhibited much higher spatial and inter-annual variations compared to the French sites and at the Sydney site, broader and multiple peaks in both pollen concentrations and greenness data coincided with flowering of more diverse grasses including subtropical species. Utilising generalised additive models (GAMs) we found the satellite greenness data of grass cover areas explained 80–90% of airborne grass pollen concentrations across the three French sites (p < 0.001) and accounted for 34 to 76% of grass pollen variations over the two sites in Australia (p < 0.05). Our results demonstrate the potential of satellite sensing to augment forecast mod...

Diaz, D, Care, A & Sunna, A 2018, 'Bioengineering Strategies for Protein-Based Nanoparticles', Genes, vol. 9, no. 7, pp. 370-370.
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In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP’s intrinsic properties and to impart them with novel functionalities.

Dickel, C, Wesdorp, JJ, Langford, NK, Peiter, S, Sagastizabal, R, Bruno, A, Criger, B, Motzoi, F & DiCarlo, L 2018, 'Chip-to-chip entanglement of transmon qubits using engineered measurement fields', Physical Review B, vol. 97, no. 6.
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© 2018 American Physical Society. While the on-chip processing power in circuit QED devices is growing rapidly, an open challenge is to establish high-fidelity quantum links between qubits on different chips. Here, we show entanglement between transmon qubits on different cQED chips with 49% concurrence and 73% Bell-state fidelity. We engineer a half-parity measurement by successively reflecting a coherent microwave field off two nearly identical transmon-resonator systems. By ensuring the measured output field does not distinguish |01) from |10), unentangled superposition states are probabilistically projected onto entangled states in the odd-parity subspace. We use in situ tunability and an additional weakly coupled driving field on the second resonator to overcome imperfect matching due to fabrication variations. To demonstrate the flexibility of this approach, we also produce an even-parity entangled state of similar quality, by engineering the matching of outputs for the |00) and |11) states. The protocol is characterized over a range of measurement strengths using quantum state tomography showing good agreement with a comprehensive theoretical model.

Dietrich, A, Bürk, M, Steiger, ES, Antoniuk, L, Tran, TT, Nguyen, M, Aharonovich, I, Jelezko, F & Kubanek, A 2018, 'Observation of Fourier transform limited lines in hexagonal boron nitride', Physical Review B, vol. 98, no. 8.
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© 2018 American Physical Society. Single defect centers in layered hexagonal boron nitride are promising candidates as single-photon sources for quantum optics and nanophotonics applications. However, spectral instability hinders many applications. Here, we perform resonant excitation measurements and observe Fourier transform limited linewidths down to ≈50 MHz. We investigated the optical properties of more than 600 single-photon emitters (SPEs) in hBN. The SPEs exhibit narrow zero-phonon lines distributed over a spectral range from 580 to 800 nm and with dipolelike emission with a high polarization contrast. Finally, the emitters withstand transfer to a foreign photonic platform, namely, a silver mirror, which makes them compatible with photonic devices such as optical resonators and paves the way to quantum photonics applications.

Dinh, V, Darling, AE & Matsen IV, FA 2018, 'Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo', Systematic Biology, vol. 67, no. 3, pp. 503-517.
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© 2017 The Author(s). Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a posterior distribution on trees, have become a popular if computationally expensive means of doing phylogenetics. Modern data collection technologies are quickly adding newsequences to already substantial databases.With all current techniques for Bayesian phylogenetics, computation must start anew each time a sequence becomes available, making it costly to maintain an up-to-date estimate of a phylogenetic posterior. These considerations highlight the need for an online Bayesian phylogenetic method which can update an existing posterior with new sequences. Here, we provide theoretical results on the consistency and stability of methods for online Bayesian phylogenetic inference based on Sequential Monte Carlo (SMC) and Markov chain Monte Carlo. We first show a consistency result, demonstrating that the method samples from the correct distribution in the limit of a large number of particles. Next, we derive the first reported set of bounds on how phylogenetic likelihood surfaces change when new sequences are added. These bounds enable us to characterize the theoretical performance of sampling algorithms by bounding the effective sample size (ESS) with a given number of particles from below.We show that the ESS is guaranteed to grow linearly as the number of particles in an SMC sampler grows. Surprisingly, this result holds even though the dimensions of the phylogenetic model grow with each new added sequence.

Doble, PA & Miklos, GLG 2018, 'Distributions of manganese in diverse human cancers provide insights into tumour radioresistance', Metallomics, vol. 10, no. 9, pp. 1191-1210.
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We show that measuring manganese levels in tumours of cancer patients is predictive for their radiation treatment.

Donovan, C, Starkey, MR, Kim, RY, Rana, BMJ, Barlow, JL, Jones, B, Haw, TJ, Mono Nair, P, Budden, K, Cameron, GJM, Horvat, JC, Wark, PA, Foster, PS, McKenzie, ANJ & Hansbro, PM 2018, 'Roles for T/B lymphocytes and ILC2s in experimental chronic obstructive pulmonary disease', Journal of Leukocyte Biology, vol. 105, no. 1, pp. 143-150.
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Abstract Pulmonary inflammation in chronic obstructive pulmonary disease (COPD) is characterized by both innate and adaptive immune responses; however, their specific roles in the pathogenesis of COPD are unclear. Therefore, we investigated the roles of T and B lymphocytes and group 2 innate lymphoid cells (ILC2s) in airway inflammation and remodelling, and lung function in an experimental model of COPD using mice that specifically lack these cells (Rag1−/− and Rorafl/flIl7rCre [ILC2-deficient] mice). Wild-type (WT) C57BL/6 mice, Rag1−/−, and Rorafl/flIl7rCre mice were exposed to cigarette smoke (CS; 12 cigarettes twice a day, 5 days a week) for up to 12 weeks, and airway inflammation, airway remodelling (collagen deposition and alveolar enlargement), and lung function were assessed. WT, Rag1−/−, and ILC2-deficient mice exposed to CS had similar levels of airway inflammation and impaired lung function. CS exposure increased small airway collagen deposition in WT mice. Rag1−/− normal air- and CS-exposed mice had significantly increased collagen deposition compared to similarly exposed WT mice, which was associated with increases in IL-33, IL-13, and ILC2 numbers. CS-exposed Rorafl/flIl7rCre mice were protected from emphysema, but had increased IL-33/IL-13 expression and collagen deposition compared to WT CS-exposed mice. T/B lymphocytes and ILC2s play roles in airway collagen deposition/fibrosis, but not inflammation, in experimental COPD. T/B lymphocytes and ILC2s play roles in airway fibrosis but not inflammation in a mouse model of experimental COPD.

Douglas, A, Torpy, F, Surawski, N & Irga, P 2018, 'Mapping Urban Aerosolized Fungi: Predicting Spatial and Temporal Indoor Concentrations', Human Ecology Review, vol. 24, no. 2, pp. 81-103.
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Dowse, R, Melvold, J & McGrath, K 2018, 'Students guiding students: Integrating student peer review into a large first year science subject. A Practice Report', Student Success, vol. 9, no. 3, pp. 79-86.
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Learning how to give and receive peer review is a skill that science students need support in developing. We included student peer review in an assessment for a large first year science subject. Class time was dedicated to introducing and developing peer review skills and increasing engagement among students and between students and teachers. Students worked in pairs, small groups, and facilitated group discussions and were encouraged to learn from each other. The student peer review exercise provided students with the opportunity to reflect on and improve their work prior to submission. Survey results showed 78% of students agreed that peer review developed their ability to give constructive feedback. Training and resources provision for the teaching staff was crucial to the integration of peer review activities. Supported teaching staff were able to engage with and support the students, and the students valued this engagement and guidance.

Doyle, LE, Williams, RBH, Rice, SA, Marsili, E & Lauro, FM 2018, 'Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment', Genome Announcements, vol. 6, no. 9.
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ABSTRACT Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that Enterobacter sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia, forms a distinct clade within the Enterobacter genus.

Drake, JE, Tjoelker, MG, Vårhammar, A, Medlyn, BE, Reich, PB, Leigh, A, Pfautsch, S, Blackman, CJ, López, R, Aspinwall, MJ, Crous, KY, Duursma, RA, Kumarathunge, D, De Kauwe, MG, Jiang, M, Nicotra, AB, Tissue, DT, Choat, B, Atkin, OK & Barton, CVM 2018, 'Trees tolerate an extreme heatwave via sustained transpirational cooling and increased leaf thermal tolerance', Global Change Biology, vol. 24, no. 6, pp. 2390-2402.
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AbstractHeatwaves are likely to increase in frequency and intensity with climate change, which may impair tree function and forest C uptake. However, we have little information regarding the impact of extreme heatwaves on the physiological performance of large trees in the field. Here, we grew Eucalyptus parramattensis trees for 1 year with experimental warming (+3°C) in a field setting, until they were greater than 6 m tall. We withheld irrigation for 1 month to dry the surface soils and then implemented an extreme heatwave treatment of 4 consecutive days with air temperatures exceeding 43°C, while monitoring whole‐canopy exchange of CO2 and H2O, leaf temperatures, leaf thermal tolerance, and leaf and branch hydraulic status. The heatwave reduced midday canopy photosynthesis to near zero but transpiration persisted, maintaining canopy cooling. A standard photosynthetic model was unable to capture the observed decoupling between photosynthesis and transpiration at high temperatures, suggesting that climate models may underestimate a moderating feedback of vegetation on heatwave intensity. The heatwave also triggered a rapid increase in leaf thermal tolerance, such that leaf temperatures observed during the heatwave were maintained within the thermal limits of leaf function. All responses were equivalent for trees with a prior history of ambient and warmed (+3°C) temperatures, indicating that climate warming conferred no added tolerance of heatwaves expected in the future. This coordinated physiological response utilizing latent cooling and adjustment of thermal thresholds has implications for tree tolerance of future climate extremes as well as model predictions of future heatwave intensity at landscape and global scales.

Dua, K, Bebawy, M, Awasthi, R, Tekade, RK, Tekade, M, Gupta, G, De Jesus Andreoli Pinto, T & Hansbro, PM 2018, 'Application of Chitosan and its Derivatives in Nanocarrier Based Pulmonary Drug Delivery Systems', Pharmaceutical Nanotechnology, vol. 5, no. 4, pp. 243-249.
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The respiratory tract as a non-invasive route of drug administration is gaining increasing attention in the present time on achieving both local and the systemic therapeutic effects. Success in achieving pulmonary delivery, requires overcoming barriers including mucociliary clearance and uptake by macrophages. An effective drug delivery system delivers the therapeutically active moieties at the right time and rate to target sites. A major limitation associated with most of the currently available conventional and controlled release drug delivery devices is that not all the drug candidates are well absorbed uniformly locally or systemically.We searched and reviewed the literature focusing on chitosan and chitosan derivative based nanocarrier systems used in pulmonary drug delivery. We focused on the applications of chitosan in the development of nanoparticles for this purpose.Chitosan, a natural linear bio-polyaminosaccharide is central in the development of novel drug delivery systems (NDDS) including nanoparticles for use in the treatment of various respiratory diseases. It achieves this through its unique properties of biodegradability, biocompatibility, mucoadhesivity and its ability to enhance macromolecule permeation across membranes. It also achieves sustained and targeted effects, primary requirements for an effective pulmonary drug delivery system. This review highlights the applications and importance of chitosan with special emphasis on nanotechnology, employed in the management of respiratory diseases such as asthma, Chronic Obstructive Pulmonary Disease (COPD), lung cancer and pulmonary fibrosis.This review will be of interest to both the biological and formulation scientists as it provides a summary on the utility of chitosan in pulmonary drug delivery systems. At present, there are no patented chitosan based controlled release products available for pulmonary drug delivery and so this area has enormous potential in the field of respiratory science.

Dua, K, Hansbro, NG, Foster, PS & Hansbro, PM 2018, 'Targeting MicroRNAs: Promising Future Therapeutics in the Treatment of Allergic Airway Disease', Critical Reviews in Eukaryotic Gene Expression, vol. 28, no. 2, pp. 125-127.
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MicroRNAs (miRNAs) are short noncoding RNAs that control gene expression posttranscriptionally by directly blocking translation of their target mRNAs or by repressing protein production via mRNA destabilization. Investigations into miRNAs began approximately 12 years ago with their discovery in mammalian cells. Still, the involvement of miRNAs in the development of asthma remains unclear, and this topic needs further research to discover various molecular mechanisms responsible for the pathogenesis of asthma and new therapeutic interventions. So far, various miRNAs have been identified in allergic airway disease along with their targets. Our present mini-review highlights the latest information involving the role of miRNAs in asthma.

Dua, K, Rapalli, VK, Shukla, SD, Singhvi, G, Shastri, MD, Chellappan, DK, Satija, S, Mehta, M, Gulati, M, Pinto, TDJA, Gupta, G & Hansbro, PM 2018, 'Multi-drug resistant Mycobacterium tuberculosis & oxidative stress complexity: Emerging need for novel drug delivery approaches', Biomedicine & Pharmacotherapy, vol. 107, pp. 1218-1229.
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© 2018 Elsevier Masson SAS Tuberculosis (caused by Mycobacterium tuberculosis, Mtb) treatment involves multiple drug regimens for a prolonged period. However, the therapeutic benefit is often limited by poor patient compliance, subsequently leading to treatment failure and development of antibiotic resistance. Notably, oxidative stress is a crucial underlying factor that adversely influences the various treatment regimens in tuberculosis. Little information is available with advanced drug delivery systems that could be effectively utilized, in particular, for targeting the oxidative stress in tuberculosis. Thus, this presents an opportunity to review the utility of various available, controlled-release drug delivery systems (e.g., microspheres, liposomes, niosomes, solid lipid nanoparticles, dendrimers) that could be beneficial in tuberculosis treatments. This will help the biological and formulation scientists to pave a new path in formulating a treatment regimen for multi-drug resistant Mtb.

Duan, J, Jiang, L, Guo, X, Chen, S, Wang, G & Zhao, C 2018, 'Mxene‐Directed Dual Amphiphilicity at Liquid, Solid, and Gas Interfaces', Chemistry – An Asian Journal, vol. 13, no. 24, pp. 3850-3854.
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AbstractMXenes represent a category of two‐dimensional functional nanomaterials with remarkable structural and chemical properties, which have been manipulated into different architectures for versatile applications. These manipulation processes generally take place at the interfaces between liquid, solid, and gas; and therefore, the investigation of the interfacial property of MXenes is the key. Here we show that MXenes exhibit amphiphilic behaviours at interfaces. Different from common amphiphiles, MXenes have the dual function of both colloidal and molecular activities owing to their two abrupt structural length scales: their large lateral sheet size allows for behaving like colloidal amphiphiles for creating emulsions, while their small sheet thickness allows for serving as molecular amphiphiles for dispersing solid substances. Further, such dual colloidal‐molecular amphiphility has driven MXenes to accumulate at the interfaces of water and nitrogen gas, and the assembly into thin film electrodes for electrochemical energy storage. All these findings open up enormous opportunities for processing various MXenes‐related functional materials and devices.

Dubey, BN, Bashary, R, Mehta, M, Satija, S, Khurana, N, Sharma, N & Khatik, GL 2018, 'Identification of possible molecular targets of potential anti-Alzheimer drugs by predicting their binding affinities using molecular docking technique', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 16-21.
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Objective: The objective of this study was to study the newly selected drug molecule for Alzheimer’s disease (AD) which is under clinical trial. Methods: The structures were drawn using ChemBioDraw 2D software on the basis of the 1EVE receptor by changing the ligands. Afterward, they were converted to 3D structures using the same ChemBioDraw 3D software in which they were subjected to energy minimization using the MM2 menu and then saved as pdb extension files which can be accessed using the ADT interface. AutoDock Vina (ADT) 1.5.6 software version was used for molecular docking study. Results: The selected molecules which are under clinical trial for AD were analyzed by molecular modeling software for identification of activity on different targets. This revealed that three drugs Etozolate, PBT2, and scyllo-Inositol have shown interactions with the 1EVE receptors (acetylcholine esterase) among studied proteins. Conclusion: The study has been done by docking, each drug with its original and by cross docking them with different another receptor to determine on what receptor each drug has the greatest affinity. Among these ligands, Etozolate, PTB2, and scyllo-Inositol showed the maximum activity against the 1EVE protein (acetylcholine esterase) with the binding affinities of −8.2, −8.0, and −5.9 Kcal\ mol, respectively. This helps in identifying the best possible molecular target for the AD.

Duong, HNM, Nguyen, MAP, Kianinia, M, Abe, H, Ohshima, T, Watanabe, K, Taniguchi, T, Edgar, JH, Aharonovich, I & Toth, M 2018, 'Effects of high energy electron irradiation on quantum emitters in hexagonal boron nitride', ACS Applied Materials and Interfaces, vol. 10, no. 29, pp. 24886-24891.
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Hexagonal Boron Nitride (hBN) mono and multilayers are promising hosts forroom temperature single photon emitters (SPEs). In this work we explore highenergy (~ MeV) electron irradiation as a means to generate stable SPEs in hBN.We investigate four types of exfoliated hBN flakes - namely, high puritymultilayers, isotopically pure hBN, carbon rich hBN multilayers and monolayeredmaterial - and find that electron irradiation increases emitter concentrationsdramatically in all samples. Furthermore, the engineered emitters are locatedthroughout hBN flakes (not only at flake edges or grain boundaries), and do notrequire activation by high temperature annealing of the host material afterelectron exposure. Our results provide important insights into controlledformation of hBN SPEs and may aid in identification of their crystallographicorigin.

Duong, HTT, Chen, Y, Tawfik, SA, Wen, S, Parviz, M, Shimoni, O & Jin, D 2018, 'Systematic investigation of functional ligands for colloidal stable upconversion nanoparticles', RSC Advances, vol. 8, no. 9, pp. 4842-4849.
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Here we quantitatively investigate the competitive adsorption of polymers bearing phosphate, carboxylic acid and sulphonic acid anchoring groups onto the surface of UCNPs and study their binding strength to identify the best conjugation strategy.

Duong, NMH, Xu, Z-Q, Kianinia, M, Su, R, Liu, Z, Kim, S, Bradac, C, Li, L-J, Solntsev, A, Liu, J & Aharonovich, I 2018, 'Enhanced Emission from WSe2 Monolayers Coupled to Circular Bragg Gratings', ACS Photonics, vol. 5, no. 10, pp. 3950-3955.
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Two-dimensional transition-metal dichalcogenides (TMDC) are of great interestfor on-chip nanophotonics due to their unique optoelectronic properties. Here,we propose and realize coupling of tungsten diselenide (WSe2) monolayers tocircular Bragg grating structures to achieve enhanced emission. The interactionbetween WSe2 and the resonant mode of the structure results in Purcell-enhancedemission, while the symmetric geometrical structure improves the directionalityof the out-coupling stream of emitted photons. Furthermore, this hybridstructure produces a record high contrast of the spin valley readout (> 40%)revealed by the polarization resolved photoluminescence (PL) measurements. Ourresults are promising for on-chip integration of TMDC monolayers with opticalresonators for nanophotonic circuits.

Dyda, A, Stelzer-Braid, S, Adam, D, Chughtai, AA & MacIntyre, CR 2018, 'The association between acute flaccid myelitis (AFM) and Enterovirus D68 (EV-D68) – what is the evidence for causation?', Eurosurveillance, vol. 23, no. 3.
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Background Enterovirus D68 (EV-D68) has historically been a sporadic disease, causing occasional small outbreaks of generally mild infection. In recent years, there has been evidence of an increase in EV-D68 infections globally. Large outbreaks of EV-D68, with thousands of cases, occurred in the United States, Canada and Europe in 2014. The outbreaks were associated temporally and geographically with an increase in clusters of acute flaccid myelitis (AFM).
Aims: We aimed to evaluate a causal association between EV-D68 and AFM. 
Methods: Using data from the published and grey literature, we applied the Bradford Hill criteria, a set of nine principles applied to examine causality, to evaluate the relationship between EV-D68 and AFM. Based on available evidence, we defined the Bradford Hill Criteria as being not met, or met minimally, partially or fully. 
Results: Available evidence applied to EV-D68 and AFM showed that six of the Bradford Hill criteria were fully met and two were partially met. The criterion of biological gradient was minimally met. The incidence of EV-D68 infections is increasing world-wide. Phylogenetic epidemiology showed diversification from the original Fermon and Rhyne strains since the year 2000, with evolution of a genetically distinct outbreak strain, clade B1. Clade B1, but not older strains, is associated with AFM and is neuropathic in animal models. 
Conclusion: While more research is needed on dose–response relationship, application of the Bradford Hill criteria supported a causal relationship between EV-D68 and AFM.

Eapen, MS, Hansbro, PM, Larsson‑Callerfelt, A-K, Jolly, MK, Myers, S, Sharma, P, Jones, B, Rahman, MA, Markos, J, Chia, C, Larby, J, Haug, G, Hardikar, A, Weber, HC, Mabeza, G, Cavalheri, V, Khor, YH, McDonald, CF & Sohal, SS 2018, 'Chronic Obstructive Pulmonary Disease and Lung Cancer: Underlying Pathophysiology and New Therapeutic Modalities', Drugs, vol. 78, no. 16, pp. 1717-1740.
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© 2018, Springer Nature Switzerland AG. Chronic obstructive pulmonary disease (COPD) and lung cancer are major lung diseases affecting millions worldwide. Both diseases have links to cigarette smoking and exert a considerable societal burden. People suffering from COPD are at higher risk of developing lung cancer than those without, and are more susceptible to poor outcomes after diagnosis and treatment. Lung cancer and COPD are closely associated, possibly sharing common traits such as an underlying genetic predisposition, epithelial and endothelial cell plasticity, dysfunctional inflammatory mechanisms including the deposition of excessive extracellular matrix, angiogenesis, susceptibility to DNA damage and cellular mutagenesis. In fact, COPD could be the driving factor for lung cancer, providing a conducive environment that propagates its evolution. In the early stages of smoking, body defences provide a combative immune/oxidative response and DNA repair mechanisms are likely to subdue these changes to a certain extent; however, in patients with COPD with lung cancer the consequences could be devastating, potentially contributing to slower postoperative recovery after lung resection and increased resistance to radiotherapy and chemotherapy. Vital to the development of new-targeted therapies is an in-depth understanding of various molecular mechanisms that are associated with both pathologies. In this comprehensive review, we provide a detailed overview of possible underlying factors that link COPD and lung cancer, and current therapeutic advances from both human and preclinical animal models that can effectively mitigate this unholy relationship.

Eapen, MS, Kota, A, Vindin, H, McAlinden, KD, Xenaki, D, Oliver, BG, Deshpande, DA, Sohal, SS & Sharma, P 2018, 'Apoptosis signal-regulating kinase 1 inhibition attenuates human airway smooth muscle growth and migration in chronic obstructive pulmonary disease', Clinical Science, vol. 132, no. 14, pp. 1615-1627.
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Increased airway smooth muscle (ASM) mass is observed in chronic obstructive pulmonary disease (COPD), which is correlated with disease severity and negatively affects lung function in these patients. Thus, there is clear unmet clinical need for finding new therapies which can target airway remodeling and disease progression in COPD. Apoptosis signal-regulating kinase 1 (ASK1) is a ubiquitously expressed mitogen-activated protein kinase (MAPK) kinase kinase (MAP3K) activated by various stress stimuli, including reactive oxygen species (ROS), tumor necrosis factor (TNF)-α, and lipopolysaccharide (LPS) and is known to regulate cell proliferation. ASM cells from COPD patients are hyperproliferative to mitogens in vitro. However, the role of ASK1 in ASM growth is not established. Here, we aim to determine the effects of ASK1 inhibition on ASM growth and pro-mitogenic signaling using ASM cells from COPD patients. We found greater expression of ASK1 in ASM bundles of COPD lung when compared with non-COPD. Pre-treatment of ASM cells with highly selective ASK1 inhibitor, TC ASK 10 resulted in a dose-dependent reduction in mitogen (FBS, PDGF, and EGF; 72 h)-induced ASM growth as measured by CyQUANT assay. Further, molecular targetting of ASK1 using siRNA in ASM cells prevented mitogen-induced cell growth. In addition, to anti-mitogenic potential, ASK1 inhibitor also prevented TGFβ1-induced migration of ASM cells in vitro. Immunoblotting revealed that anti-mitogenic effects are mediated by C-Jun N-terminal kinase (JNK) and p38MAP kinase-signaling pathways as evident by reduced phosphorylation of downstream effectors JNK1/2 and p38MAP kinases, respectively, with no effect on extracellular signal-regulated kinase (ERK) 1/2 (ERK1/2). Collectively, these findings establish the anti-mitogenic effect of ASK1 inhibition and identify a novel pathway that can be targetted to reduce or prevent excessive ASM mass in COPD.

Edwards, RJ, Tuipulotu, DE, Amos, TG, O'Meally, D, Richardson, MF, Russell, TL, Vallinoto, M, Carneiro, M, Ferrand, N, Wilkins, MR, Sequeira, F, Rollins, LA, Holmes, EC, Shine, R & White, PA 2018, 'Draft genome assembly of the invasive cane toad, Rhinella marina', GigaScience, vol. 7, no. 9.
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Abstract Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly. Conclusions The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.

Egilmezer, E, Walker, GJ, Bakthavathsalam, P, Peterson, JR, Gooding, JJ, Rawlinson, W & Stelzer‐Braid, S 2018, 'Systematic review of the impact of point‐of‐care testing for influenza on the outcomes of patients with acute respiratory tract infection', Reviews in Medical Virology, vol. 28, no. 5, pp. e1995-e1995.
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SummaryAcute respiratory tract infections are a major cause of morbidity and mortality and represent a significant burden on the health care system. Laboratory testing is required to definitively distinguish infecting influenza virus from other pathogens, resulting in prolonged emergency department (ED) visits and unnecessary antibiotic use. Recently available rapid point‐of‐care tests (POCT) may allow for appropriate use of antiviral and antibiotic treatments and decrease patient lengths of stay.We undertook a systematic review to assess the effect of POCT for influenza on three outcomes: (1) antiviral prescription, (2) antibiotic prescription, and (3) patient length of stay in the ED.The databases Medline and Embase were searched using MeSH terms and keywords for influenza, POCT, antivirals, antibiotics, and length of stay.Amongst 245 studies screened, 30 were included. The majority of papers reporting on antiviral prescription found that a positive POCT result significantly increased use of antivirals for influenza compared with negative POCT results and standard supportive care. A positive POCT result also led to decreased antibiotic use. The results of studies assessing the effect of POCT on ED length of stay were not definitive.The studies assessed in this systematic review support the use of POCT for diagnosis of influenza in patients suffering an acute respiratory infection. Diagnosis using POCT may lead to more appropriate prescription of treatments for infectious agents. Further studies are needed to assess the effect of POCT on the length of stay in ED.

Elbadawi, C, Queralt, RT, Xu, Z-Q, Bishop, J, Ahmed, T, Kuriakose, S, Walia, S, Toth, M, Aharonovich, I & Lobo, CJ 2018, 'Encapsulation-Free Stabilization of Few-Layer Black Phosphorus', ACS Applied Materials & Interfaces, vol. 10, no. 29, pp. 24327-24331.
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© 2018 American Chemical Society. Under ambient conditions and in H2O and O2 environments, reactive oxygen species (ROS) cause immediate degradation of the mobility of few-layer black phosphorus (FLBP). Here, we show that FLBP degradation can be prevented by maintaining the temperature in the range ∼125-300 °C during ROS exposure. FLBP devices maintained at elevated temperature show no deterioration of electrical conductance, in contrast to the immediate degradation of pristine FLBP held at room temperature. Our results constitute the first demonstration of stable FLBP in the presence of ROS without requiring encapsulation or a protective coating. The stabilization method will enable applications based on the surface properties of intrinsic FLBP.

El-Sayed, H, Sankar, S, Daraghmi, Y-A, Tiwari, P, Rattagan, E, Mohanty, M, Puthal, D & Prasad, M 2018, 'Accurate Traffic Flow Prediction in Heterogeneous Vehicular Networks in an Intelligent Transport System Using a Supervised Non-Parametric Classifier', Sensors, vol. 18, no. 6, pp. 1696-1696.
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Heterogeneous vehicular networks (HETVNETs) evolve from vehicular ad hoc networks (VANETs), which allow vehicles to always be connected so as to obtain safety services within intelligent transportation systems (ITSs). The services and data provided by HETVNETs should be neither interrupted nor delayed. Therefore, Quality of Service (QoS) improvement of HETVNETs is one of the topics attracting the attention of researchers and the manufacturing community. Several methodologies and frameworks have been devised by researchers to address QoS-prediction service issues. In this paper, to improve QoS, we evaluate various traffic characteristics of HETVNETs and propose a new supervised learning model to capture knowledge on all possible traffic patterns. This model is a refinement of support vector machine (SVM) kernels with a radial basis function (RBF). The proposed model produces better results than SVMs, and outperforms other prediction methods used in a traffic context, as it has lower computational complexity and higher prediction accuracy.

El-Sayed, H, Sankar, S, Prasad, M, Puthal, D, Gupta, A, Mohanty, M & Lin, C-T 2018, 'Edge of Things: The Big Picture on the Integration of Edge, IoT and the Cloud in a Distributed Computing Environment', IEEE Access, vol. 6, pp. 1706-1717.
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© 2013 IEEE. A centralized infrastructure system carries out existing data analytics and decision-making processes from our current highly virtualized platform of wireless networks and the Internet of Things (IoT) applications. There is a high possibility that these existing methods will encounter more challenges and issues in relation to network dynamics, resulting in a high overhead in the network response time, leading to latency and traffic. In order to avoid these problems in the network and achieve an optimum level of resource utilization, a new paradigm called edge computing (EC) is proposed to pave the way for the evolution of new age applications and services. With the integration of EC, the processing capabilities are pushed to the edge of network devices such as smart phones, sensor nodes, wearables, and on-board units, where data analytics and knowledge generation are performed which removes the necessity for a centralized system. Many IoT applications, such as smart cities, the smart grid, smart traffic lights, and smart vehicles, are rapidly upgrading their applications with EC, significantly improving response time as well as conserving network resources. Irrespective of the fact that EC shifts the workload from a centralized cloud to the edge, the analogy between EC and the cloud pertaining to factors such as resource management and computation optimization are still open to research studies. Hence, this paper aims to validate the efficiency and resourcefulness of EC. We extensively survey the edge systems and present a comparative study of cloud computing systems. After analyzing the different network properties in the system, the results show that EC systems perform better than cloud computing systems. Finally, the research challenges in implementing an EC system and future research directions are discussed.

Enosi Tuipulotu, D, Netzler, NE, Lun, JH, Mackenzie, JM & White, PA 2018, 'TLR7 Agonists Display Potent Antiviral Effects against Norovirus Infection via Innate Stimulation', Antimicrobial Agents and Chemotherapy, vol. 62, no. 5.
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ABSTRACT Norovirus infections are a significant health and economic burden globally, accounting for hundreds of millions of cases of acute gastroenteritis every year. In the absence of an approved norovirus vaccine, there is an urgent need to develop antivirals to treat chronic infections and provide prophylactic therapy to limit viral spread during epidemics and pandemics. Toll-like receptor (TLR) agonists have been explored widely for their antiviral potential, and several are progressing through clinical trials for the treatment of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) and as adjuvants for norovirus viruslike particle (VLP) vaccines. However, norovirus therapies in development are largely direct-acting antivirals (DAAs) with fewer compounds that target the host. Our aim was to assess the antiviral potential of TLR7 agonist immunomodulators on norovirus infection using the murine norovirus (MNV) and human Norwalk replicon models. TLR7 agonists R-848, Gardiquimod, GS-9620, R-837, and loxoribine were screened using a plaque reduction assay, and each displayed inhibition of MNV replication (50% effective concentrations [EC 50 s], 23.5 nM, 134.4 nM, 0.59 μM, 1.5 μM, and 79.4 μM, respectively). RNA sequencing of TLR7-stimulated cells revealed a predominant upregulation of innate immune response genes and interferon (IFN)-stimulated genes (ISGs) that are known to drive an antiviral state. Furthermore, the combination of R-848 and the nucleoside analogue (NA) 2′C-methylcytidine elicited a synergistic antiviral effect against MNV, demonstrating that combinational therapy of host modulators and DAAs might be used to reduce drug cytotoxicity. In summary, we have identified that TLR7 agonists display potent inhibition of norovirus replication and are a therapeutic option to combat norovirus infections.

Faiz, A, Heijink, IH, Vermeulen, CJ, Guryev, V, van den Berge, M, Nawijn, MC & Pouwels, SD 2018, 'Cigarette smoke exposure decreases CFLAR expression in the bronchial epithelium, augmenting susceptibility for lung epithelial cell death and DAMP release', Scientific Reports, vol. 8, no. 1, pp. 12426-12426.
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AbstractCigarette smoking is a major risk factor for the inflammatory disease, chronic obstructive pulmonary disease (COPD). The mechanism by which cigarette smoke (CS) induces chronic lung inflammation is still largely unknown. We hypothesize that immunogenic airway epithelial cell death is involved in the initiation of the inflammatory response. We previously identified CFLAR, the gene encoding the cell death regulator protein c-FLIP, to be associated with CS-induced release of damage-associated molecular patterns (DAMPs). Here, we investigated the effect of CS on expression levels of CFLAR in bronchial biopsies from smokers and non-smokers and CFLAR transcript isoform-expression in a dataset of air-liquid interface-differentiated bronchial epithelial cells. Furthermore, CFLAR was down-regulated by siRNA in lung epithelial A549 cells, followed by investigation of the effects on apoptosis, necrosis and DAMP release. CS exposure significantly decreased CFLAR expression in bronchial epithelial cells. Moreover, we observed a shift in relative abundance of the isoforms c-FLIPS and c-FLIPL transcripts in bronchial biopsies of current smokers compared to non-smokers, consistent with a shift towards necroptosis. In vitro, down-regulation of CFLAR increased apoptosis at baseline as well as CS extract-induced necrosis and DAMP release. In conclusion, CS exposure decreases CFLAR expression, which might increase susceptibility to immunogenic cell death.

Faiz, A, Weckmann, M, Tasena, H, Vermeulen, CJ, Van den Berge, M, ten Hacken, NHT, Halayko, AJ, Ward, JPT, Lee, TH, Tjin, G, Black, JL, Haghi, M, Xu, C-J, King, GG, Farah, CS, Oliver, BG, Heijink, IH & Burgess, JK 2018, 'Profiling of healthy and asthmatic airway smooth muscle cells following interleukin-1β treatment: a novel role for CCL20 in chronic mucus hypersecretion', European Respiratory Journal, vol. 52, no. 2, pp. 1800310-1800310.
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Chronic mucus hypersecretion (CMH) contributes to the morbidity and mortality of asthma, and remains uncontrolled by current therapies in the subset of patients with severe, steroid-resistant disease. Altered cross-talk between airway epithelium and airway smooth muscle cells (ASMCs), driven by pro-inflammatory cytokines such as interleukin (IL)-1β, provides a potential mechanism that influences CMH. This study investigated mechanisms underlying CMH by comparing IL-1β-induced gene expression profiles between asthma and control-derived ASMCs and the subsequent paracrine influence on airway epithelial mucus productionin vitro.IL-1β-treated ASMCs from asthmatic patients and healthy donors were profiled using microarray analysis and ELISA. Air–liquid interface (ALI)-cultured CALU-3 and primary airway epithelial cells were treated with identified candidates and mucus production assessed.The IL-1β-inducedCCL20expression and protein release was increased in ASMCs from moderate compared with mild asthmatic patients and healthy controls.IL-1β induced lowerMIR146Aexpression in asthma-derived ASMCs compared with controls. DecreasedMIR146Aexpression was validatedin vivoin bronchial biopsies from 16 asthmatic patientsversus39 healthy donors. miR-146a-5p overexpression abrogated CCL20 release in ASMCs. CCL20 treatment of ALI-cultured CALU-3 and primary airway epithelial cells induced mucus production, while CCL20 levels in sputum were associated with increased levels of CMH in asthmatic patients.Elevated CCL20 production by ASMCs, possibly resulting from dysregulated expression of the anti-inflammatory miR-146a-5p, may contribute to enhanced mucus production in asthma.

Faiz, MB, Amal, R, Marquis, CP, Harry, EJ, Sotiriou, GA, Rice, SA & Gunawan, C 2018, 'Nanosilver and the microbiological activity of the particulate solids versus the leached soluble silver', Nanotoxicology, vol. 12, no. 3, pp. 263-273.
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© 2018 Informa UK Limited, trading as Taylor & Francis Group. Nanosilver (Ag NPs) is currently one of the most commercialized antimicrobial nanoparticles with as yet, still unresolved cytotoxicity origins. To date, research efforts have mostly described the antimicrobial contribution from the leaching of soluble silver, while the undissolved solid Ag particulates are often considered as being microbiologically inert, serving only as source of the cytotoxic Ag ions. Here, we show the rapid stimulation of lethal cellular oxidative stress in bacteria by the presence of the undissolved Ag particulates. The cytotoxicity characteristics are distinct from those arising from the leached soluble Ag, the latter being locked in organic complexes. The work also highlights the unique oxidative stress-independent bacterial toxicity of silver salt. Taken together, the findings advocate that future enquiries on the antimicrobial potency and also importantly, the environmental and clinical impact of Ag NPs use, should pay attention to the potential bacterial toxicological responses to the undissolved Ag particulates, rather than just to the leaching of soluble silver. The findings also put into question the common use of silver salt as model material for evaluating bacterial toxicity of Ag NPs.

Faizi, M, Zavřel, T, Loureiro, C, Červený, J & Steuer, R 2018, 'A model of optimal protein allocation during phototrophic growth', Biosystems, vol. 166, pp. 26-36.
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© 2018 Elsevier B.V. Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function typically reduces the proteome available for other cellular functions. Here, we develop a semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parameterized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that coarse-grained growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.

FALLETTA, J & WOODCOCK, S 2018, 'A SIMULATION STUDY OF TEXAS HOLD ’EM POKER: WHAT TAYLOR SWIFT UNDERSTANDS AND JAMES BOND DOESN’T', The ANZIAM Journal, vol. 60, no. 1, pp. 55-64.
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Recent years have seen a large increase in the popularity of Texas hold ’em poker. It is now the most commonly played variant of the game, both in casinos and through online platforms. In this paper, we present a simulation study for games of Texas hold ’em with between two and 23 players. From these simulations, we estimate the probabilities of each player having been dealt the winning hand. These probabilities are calculated conditional on both partial information (that is, the player only having knowledge of his/her cards) and also on fuller information (that is, the true probabilities of each player winning given knowledge of the cards dealt to each player). Where possible, our estimates are compared to exact analytic results and are shown to have converged to three significant figures.With these results, we assess the poker strategies described in two recent pieces of popular culture. In comparing the ideas expressed in Taylor Swift’s song, New Romantics, and the betting patterns employed by James Bond in the 2006 film, Casino Royale, we conclude that Ms Swift demonstrates a greater understanding of the true probabilities of winning a game of Texas hold ’em poker.

Fan, X, McLaughlin, C, Ravasini, J, Robinson, C & George, AM 2018, 'Zeolite protects mice from iron‐induced damage in a mouse model trial', FEBS Open Bio, vol. 8, no. 11, pp. 1773-1781.
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For centuries, zeolites have been used for their utility in binding metals, and they feature in a multitude of agricultural and industrial applications in which the honeycombed zeolite structures form ideal ion exchangers, catalysts and binding agents. Zeolites are currently in a transition period, moving towards implementation in human ailments and diseases. Here, we postulated that zeolites may be able to counter the effects of excess iron and conducted a mouse model trial to gauge the utility of this notion. We used the transgenic mouse strain MexTAg299 for a thirty‐week pilot trial in which iron polymaltose and/or the zeolite clinoptilolite was injected into the peritoneum twice weekly. Mice were sacrificed at the end of the trial period and examined by postmortem and histology for significant physiological differences between mouse subgroups. In this study, we demonstrated that a common zeolite, clinoptilolite, is able to maintain the general health and well‐being of mice and prevent iron‐induced deleterious effects following iron overload. When zeolites are given with iron biweekly as intraperitoneal injections, mice showed far less macroscopic visual organ discoloration, along with near normal histology, under iron overload conditions when compared to mice injected with iron only. The purpose of the present pilot study was to examine potential alternatives to current iron chelation treatments, and the results indicate an advantage to using zeolites in conditions of iron excess. Zeolites may have translational potential for use in cases of human iron overload.

Farjana, SH, Huda, N & Mahmud, MAP 2018, 'Life-Cycle environmental impact assessment of mineral industries', IOP Conference Series: Materials Science and Engineering, vol. 351, pp. 012016-012016.
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Farjana, SH, Huda, N & Parvez Mahmud, MA 2018, 'Environmental impact assessment of european non-ferro mining industries through life-cycle assessment', IOP Conference Series: Earth and Environmental Science, vol. 154, pp. 012019-012019.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2018, 'Comparative life-cycle assessment of uranium extraction processes', Journal of Cleaner Production, vol. 202, pp. 666-683.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2018, 'Towards sustainable TiO2 production: An investigation of environmental impacts of ilmenite and rutile processing routes in Australia', Journal of Cleaner Production, vol. 196, pp. 1016-1025.
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Farjana, SH, Huda, N, Mahmud, MAP & Saidur, R 2018, 'Solar industrial process heating systems in operation – Current SHIP plants and future prospects in Australia', Renewable and Sustainable Energy Reviews, vol. 91, pp. 409-419.
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Farjana, SH, Huda, N, Mahmud, MAP & Saidur, R 2018, 'Solar process heat in industrial systems – A global review', Renewable and Sustainable Energy Reviews, vol. 82, pp. 2270-2286.
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Farooq, A, Ashraf, MA, Rasheed, A, Khan, JU & Irshad, F 2018, 'Development of a novel method for natural dyeing of cotton fabrics using ultrasonic radiations and acacia bark', Journal of Natural Fibers, vol. 15, no. 5, pp. 680-686.
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Farooq, U, Ahmed, Z, Naeem, K, Bertram, M, Brito, B, Stenfeldt, C, Pauszek, SJ, LaRocco, M, Rodriguez, L & Arzt, J 2018, 'Characterization of naturally occurring, new and persistent subclinical foot‐and‐mouth disease virus infection in vaccinated Asian buffalo in Islamabad Capital Territory, Pakistan', Transboundary and Emerging Diseases, vol. 65, no. 6, pp. 1836-1850.
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© 2018 Blackwell Verlag GmbH The convalescent subclinical carrier state of foot-and-mouth disease virus (FMDV) infection has been thoroughly investigated; contrastingly, the subclinical form of new infections of vaccinated and naïve hosts is recognized, but poorly understood. To investigate the natural dynamics of subclinical FMDV infections, a prospective, 12-month, longitudinal study was conducted in vaccinated Asian buffalo (Bubalus bubalis) under natural conditions in Pakistan, where FMDV is hyperendemic. Oropharyngeal fluid (OPF) samples were obtained quarterly from 300 buffalo on 30 farms which reported no clinical FMD during the 12-month study period. At the start of the study, 77.7% of buffalo had FMDV anti-NSP antibodies, and all farms had at least one seropositive buffalo. Based upon the presence of viral RNA and viral VP1 sequences obtained, distinct subcategories of subclinical infections were documented, including new, persistent, and serial infections with different FMDV strains. Viral RNA was detected in at least one OPF sample from 180 (60%) of the 300 buffalo. Over the course of the study, FMDV was detected in OPF of 80 buffalo that had been FMDV-free in previous OPF samples, indicating the occurrence of new subclinical infections. Eight buffalo were confirmed to be persistently infected, and serial infection with different FMDVs was confirmed in 13 animals. The most prevalent serotype detected was Asia-1, followed by A, and O. Phylogenetic analysis indicated multiple distinct clusters of serotypes Asia-1 and A. This study indicates a high prevalence of subclinical FMDV infection in vaccinated buffalo in Pakistan and emphasizes the importance of clinically undetected infection in FMD dynamics in endemic regions.

Farrell, H, Ajani, P, Murray, S, Baker, P, Webster, G, Brett, S & Zammit, A 2018, 'Diarrhetic Shellfish Toxin Monitoring in Commercial Wild Harvest Bivalve Shellfish in New South Wales, Australia', Toxins, vol. 10, no. 11, pp. 446-446.
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An end-product market survey on biotoxins in commercial wild harvest shellfish (Plebidonax deltoides, Katelysia spp., Anadara granosa, Notocallista kingii) during three harvest seasons (2015–2017) from the coast of New South Wales, Australia found 99.38% of samples were within regulatory limits. Diarrhetic shellfish toxins (DSTs) were present in 34.27% of 321 samples but only in pipis (P. deltoides), with two samples above the regulatory limit. Comparison of these market survey data to samples (phytoplankton in water and biotoxins in shellfish tissue) collected during the same period at wild harvest beaches demonstrated that, while elevated concentrations of Dinophysis were detected, a lag in detecting bloom events on two occasions meant that wild harvest shellfish with DSTs above the regulatory limit entered the marketplace. Concurrently, data (phytoplankton and biotoxin) from Sydney rock oyster (Saccostrea glomerata) harvest areas in estuaries adjacent to wild harvest beaches impacted by DSTs frequently showed elevated Dinophysis concentrations, but DSTs were not detected in oyster samples. These results highlighted a need for distinct management strategies for different shellfish species, particularly during Dinophysis bloom events. DSTs above the regulatory limit in pipis sampled from the marketplace suggested there is merit in looking at options to strengthen the current wild harvest biotoxin management strategies.

Farrell, H, Baker, P, Webster, G, Jansson, E, Szabo, E & Zammit, A 2018, 'An assessment of potential heavy metal contaminants in bivalve shellfish from aquaculture zones along the coast of New South Wales, Australia', Food Protection Trends, vol. 38, no. 1, pp. 18-25.
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Evaluation of shellfish aquaculture for potential contaminants is essential for consumer confidence and safety. Every three years, between 1999 and 2014, bivalve shellfish from aquaculture zones in up to 31 estuaries across 2,000 km of Australia's east coast were tested for cadmium, copper, lead, mercury, selenium and zinc. Inorganic arsenic was included in the analyses in 2002, and total arsenic was used as a screen for the inorganic form in subsequent years. Concentrations of inorganic arsenic, cadmium, lead and mercury were low and did not exceed maximum limits mandated in the Australia New Zealand Food Standards Code. As maximum limits have not been assigned to copper, selenium and zinc, accepted international dietary guidelines were used as a benchmark. Dietary exposure assessments for these elements demonstrated that shellfish from the aquaculture areas investigated do not present a food safety risk. Continued surveillance is essential, given increasing pressure on Australia's coastal resources.

Faunce, TA, Prest, J, Su, D, Hearne, SJ & Iacopi, F 2018, 'On-grid batteries for large-scale energy storage: Challenges and opportunities for policy and technology', MRS Energy & Sustainability, vol. 5, no. 1.
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ABSTRACT

Feit, B, Gordon, CE, Webb, JK, Jessop, TS, Laffan, SW, Dempster, T & Letnic, M 2018, 'Invasive cane toads might initiate cascades of direct and indirect effects in a terrestrial ecosystem', Biological Invasions, vol. 20, no. 7, pp. 1833-1847.
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© Springer International Publishing AG, part of Springer Nature 2017. Understanding the impacts that invasive vertebrates have on terrestrial ecosystems extends primarily to invaders’ impacts on species with which they interact directly through mechanisms such as predation, competition and habitat modification. In addition to direct effects, invaders can also initiate ecological cascades via indirect population level effects on species with which they do not directly interact. However, evidence that invasive vertebrates initiate ecological cascades in terrestrial ecosystems remains scarce. Here, we ask whether the invasion of the cane toad, a vertebrate invader that is toxic to many of Australia’s vertebrate predators, has induced ecological cascades in a semi-arid rangeland. We compared activity of a large predatory lizard, the sand-goanna, and abundances of smaller lizards preyed upon by goannas in areas of high toad activity near toads’ dry season refuges and areas of low toad activity distant from toads’ dry season refuges. Consistent with the hypothesis that toad invasion has led to declines of native predators susceptible to poisoning, goanna activity was lower in areas of high toad activity. Consistent with the hypothesis that toad-induced goanna decline lead to increases in abundance the prey of goannas, smaller lizards were more abundant in areas of high toad activity. Structural equation modelling showed a positive correlation between goanna activity and distance from dry season refuge habitats used by toads. The abundances of small lizards was correlated negatively with goanna activity and distance from dry season refuges of toads. Our findings provide support for the notion that invasions by terrestrial vertebrates can trigger ecological cascades.

Feng, Y, Rudd, R, Baker, C, Mashalaba, Q, Mavuso, M & Schlögl, E 2018, 'Quantifying the Model Risk Inherent in the Calibration and Recalibration of Option Pricing Models', Risks, vol. 9, no. 1, pp. 13-13.
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We focus on two particular aspects of model risk: the inability of a chosenmodel to fit observed market prices at a given point in time (calibrationerror) and the model risk due to recalibration of model parameters (incontradiction to the model assumptions). In this context, we follow theapproach of Glasserman and Xu (2014) and use relative entropy as a pre-metricin order to quantify these two sources of model risk in a common framework, andconsider the trade-offs between them when choosing a model and the frequencywith which to recalibrate to the market. We illustrate this approach applied tothe models of Black and Scholes (1973) and Heston (1993), using option data forApple (AAPL) and Google (GOOG). We find that recalibrating a model morefrequently simply shifts model risk from one type to another, without anysubstantial reduction of aggregate model risk. Furthermore, moving to a morecomplicated stochastic model is seen to be counterproductive if one requires ahigh degree of robustness, for example as quantified by a 99 percent quantileof aggregate model risk.

Fernandez-Rojo, MA, Deplazes, E, Pineda, SS, Brust, A, Marth, T, Wilhelm, P, Martel, N, Ramm, GA, Mancera, RL, Alewood, PF, Woods, GM, Belov, K, Miles, JJ, King, GF & Ikonomopoulou, MP 2018, 'Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells', Cell Death Discovery, vol. 4, no. 1.
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AbstractThe Tasmanian devil faces extinction due to devil facial tumour disease (DFTD), a highly transmittable clonal form of cancer without available treatment. In this study, we report the cell-autonomous antiproliferative and cytotoxic activities exhibited by the spider peptide gomesin (AgGom) and gomesin-like homologue (HiGom) in DFTD cells. Mechanistically, both peptides caused a significant reduction at G0/G1 phase, in correlation with an augmented expression of the cell cycle inhibitory proteins p53, p27, p21, necrosis, exacerbated generation of reactive oxygen species and diminished mitochondrial membrane potential, all hallmarks of cellular stress. The screening of a novel panel of AgGom-analogues revealed that, unlike changes in the hydrophobicity and electrostatic surface, the cytotoxic potential of the gomesin analogues in DFTD cells lies on specific arginine substitutions in the eight and nine positions and alanine replacement in three, five and 12 positions. In conclusion, the evidence supports gomesin as a potential antiproliferative compound against DFTD disease.

Firasat, S, Kaul, H, Ashfaq, UA & Idrees, S 2018, 'In silico analysis of five missense mutations in CYP1B1 gene in Pakistani families affected with primary congenital glaucoma', International Ophthalmology, vol. 38, no. 2, pp. 807-814.
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Fourment, M & Darling, AE 2018, 'Local and relaxed clocks: the best of both worlds', PeerJ, vol. 6, pp. e5140-e5140.
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Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from https://www.github.com/4ment/flc.

Fourment, M, Claywell, BC, Dinh, V, McCoy, C, Matsen IV, FA & Darling, AE 2018, 'Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals', Systematic Biology, vol. 67, no. 3, pp. 490-502.
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© 2017 The Author(s). Modern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phylogenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein newdata can be continuously incorporated to update the estimate of the posterior probability distribution. In this article,we describe and evaluate several different online phylogenetic sequential Monte Carlo (OPSMC) algorithms. We show that proposing new phylogenies with a density similar to the Bayesian prior suffers from poor performance, and we develop 'guided' proposals that better match the proposal density to the posterior. Furthermore, we show that the simplest guided proposals can exhibit pathological behavior in some situations, leading to poor results, and that the situation can be resolvedby heating theproposal density. The results demonstrate that relative to the widely used MCMC-based algorithm implemented in MrBayes, the total time required to compute a series of phylogenetic posteriors as sequences arrive can be significantly reduced by the use of OPSMC, without incurring a significant loss in accuracy.

Fowler, AM, Chick, RC & Stewart, J 2018, 'Patterns and drivers of movement for a coastal benthopelagic fish, Pseudocaranx georgianus, on Australia’s southeast coast', Scientific Reports, vol. 8, no. 1.
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AbstractKnowledge of connectivity and population structure is integral to the sustainable management of fished populations, yet such information is unavailable for many species over scales relevant to their exploitation. We examined broad-scale patterns and drivers of adult movement for a putatively mobile carangid (Pseudocaranx georgianus) on Australia’s southeast coast using an angler tag-recapture dataset. More than 6300 individuals were tagged and released across 1007 km of coastline, with anglers recapturing 157 (2.48%) individuals during a 14-year period. Median distance moved was 5 km and a substantial proportion of individuals (19%) were recaptured at their release location. Recapture latitude was also strongly predicted by release latitude (r2 = 0.87). However, a broad range of movements were observed (0–508 km), with 6% of individuals moving further than 100 km. Most individuals recaptured in areas now designated as Marine Protected Areas (MPAs) were originally released in the same area (79.2%). Larger body size, longer periods at liberty, and releases during Spring all positively influenced distance moved. Results support restricted movement over an intermediate scale, punctuated by occasional large movements. Our findings suggest adult movement of P. georgianus in southeastern Australia primarily occurs over smaller distances than the current spatial scale of management.

Fowler, AM, Jørgensen, A, Svendsen, JC, Macreadie, PI, Jones, DOB, Boon, AR, Booth, DJ, Brabant, R, Callahan, E, Claisse, JT, Dahlgren, TG, Degraer, S, Dokken, QR, Gill, AB, Johns, DG, Leewis, RJ, Lindeboom, HJ, Linden, O, May, R, Murk, AJ, Ottersen, G, Schroeder, DM, Shastri, SM, Teilmann, J, Todd, V, Van Hoey, G, Vanaverbeke, J & Coolen, JWP 2018, 'Environmental benefits of leaving offshore infrastructure in the ocean', Frontiers in Ecology and the Environment, vol. 16, no. 10, pp. 571-578.
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The removal of thousands of structures associated with oil and gas development from the world's oceans is well underway, yet the environmental impacts of this decommissioning practice remain unknown. Similar impacts will be associated with the eventual removal of offshore wind turbines. We conducted a global survey of environmental experts to guide best decommissioning practices in the North Sea, a region with a substantial removal burden. In contrast to current regulations, 94.7% of experts (36 out of 38) agreed that a more flexible case‐by‐case approach to decommissioning could benefit the North Sea environment. Partial removal options were considered to deliver better environmental outcomes than complete removal for platforms, but both approaches were equally supported for wind turbines. Key considerations identified for decommissioning were biodiversity enhancement, provision of reef habitat, and protection from bottom trawling, all of which are negatively affected by complete removal. We provide recommendations to guide the revision of offshore decommissioning policy, including a temporary suspension of obligatory removal.

Fowler, AM, Parkinson, K & Booth, DJ 2018, 'New poleward observations of 30 tropical reef fishes in temperate southeastern Australia', Marine Biodiversity, vol. 48, no. 4, pp. 2249-2254.
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© 2017, Senckenberg Gesellschaft für Naturforschung and Springer-Verlag GmbH Germany. A major outcome of climate change is the poleward shift of species ranges. We use a long-term (16-year) monitoring program to report new poleward observations of the juvenile stages of 30 tropical reef fishes expatriating to temperate southeastern Australia, a global hotspot for ocean warming. Expatriated juveniles (vagrants) from 10 families and 20 genera were observed for the first time on rocky reefs in southern New South Wales, between 57 and 801 km poleward of their previously recorded locations. Vagrants were functionally diverse, ranging from small planktivores (e.g. Dascyllus trimaculatus) through to a large piscivore/invertivore (Epinephelus cyanopodus). Tropical herbivores comprised 20% of vagrant species, with four species (Acanthurus dussumieri, A. lineatus, A. nigrofuscus, A. olivaceus) recognised as grazers of epilithic algae and one species (Naso unicornis) known to feed selectively on macroalgae. Pelagic larval duration (PLD) ranged greatly among vagrant species, with shorter PLDs suggesting sub-tropical breeding populations for some species. As water temperatures continue to increase in southeastern Australia under climate change, the greater supply and survival of tropical vagrants may alter the functioning of temperate reefs in this region.

Fransen, J, Bush, S, Woodcock, S, Novak, A, Deprez, D, Baxter-Jones, ADG, Vaeyens, R & Lenoir, M 2018, 'Improving the Prediction of Maturity From Anthropometric Variables Using a Maturity Ratio', Pediatric Exercise Science, vol. 30, no. 2, pp. 296-307.
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Purpose: This study aimed to improve the prediction accuracy of age at peak height velocity (APHV) from anthropometric assessment using nonlinear models and a maturity ratio rather than a maturity offset. Methods: The dataset used to develop the original prediction equations was used to test a new prediction model, utilizing the maturity ratio and a polynomial prediction equation. This model was then applied to a sample of male youth academy soccer players (n = 1330) to validate the new model in youth athletes. Results: A new equation was developed to estimate APHV more accurately than the original model (new model: Akaike information criterion: −6062.1, R2 = 90.82%; original model: Akaike information criterion = 3048.7, R2 = 88.88%) within a general population of boys, particularly with relatively high/low APHVs. This study has also highlighted the successful application of the new model to estimate APHV using anthropometric variables in youth athletes, thereby supporting the use of this model in sports talent identification and development. Conclusion: This study argues that this newly developed equation should become standard practice for the estimation of maturity from anthropometric variables in boys from both a general and an athletic population.

French, J, Arscott, E, Morgan, R & Meakin, G 2018, 'Reply to letter to the editor: Response to “A study of the perception of verbal expressions of the strength of evidence”', Science & Justice, vol. 58, no. 4, pp. 299-299.
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Fricker, M, Goggins, BJ, Mateer, S, Jones, B, Kim, RY, Gellatly, SL, Jarnicki, AG, Powell, N, Oliver, BG, Radford-Smith, G, Talley, NJ, Walker, MM, Keely, S & Hansbro, PM 2018, 'Chronic cigarette smoke exposure induces systemic hypoxia that drives intestinal dysfunction', JCI Insight, vol. 3, no. 3.
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Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract (GIT). Cigarette smoke (CS) exposure and chronic obstructive pulmonary disease (COPD) are risk factors for CD, although the mechanisms involved are poorly understood. We employed a mouse model of CS-induced experimental COPD and clinical studies to examine these mechanisms. Concurrent with the development of pulmonary pathology and impaired gas exchange, CS-exposed mice developed CD-associated pathology in the colon and ileum, including gut mucosal tissue hypoxia, HIF-2 stabilization, inflammation, increased microvasculature, epithelial cell turnover, and decreased intestinal barrier function. Subsequent smoking cessation reduced GIT pathology, particularly in the ileum. Dimethyloxaloylglycine, a pan-prolyl hydroxylase inhibitor, ameliorated CS-induced GIT pathology independently of pulmonary pathology. Prior smoke exposure exacerbated intestinal pathology in 2,4,6-trinitrobenzenesulfonic acid-induced (TNBS-induced) colitis. Circulating vascular endothelial growth factor, a marker of systemic hypoxia, correlated with CS exposure and CD in mice and humans. Increased mucosal vascularisation was evident in ileum biopsies from CD patients who smoke compared with nonsmokers, supporting our preclinical data. We provide strong evidence that chronic CS exposure and, for the first time to our knowledge, associated impaired gas exchange cause systemic and intestinal ischemia, driving angiogenesis and GIT epithelial barrier dysfunction, resulting in increased risk and severity of CD.

Fronzi, M, Assadi, MHN & Ford, MJ 2018, 'Ab Initio Investigation of Water Adsorption and Hydrogen Evolution on Co₉S₈ and Co₃S₄ Low-Index Surfaces', ACS Omega, vol. 3, no. 9, pp. 12215-12228.
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Copyright © 2018 American Chemical Society. We used density functional theory approach, with the inclusion of a semiempirical dispersion potential to take into account van der Waals interactions, to investigate the water adsorption and dissociation on cobalt sulfide Co9S8 and Co3S4(100) surfaces. We first determined the nanocrystal shape and selected representative surfaces to analyze. We then calculated water adsorption and dissociation energies, as well as hydrogen and oxygen adsorption energies, and we found that sulfur vacancies on Co9S8(100) surface enhance the catalytic activity toward water dissociation by raising the energy level of unhybridized Co 3d states closer to the Fermi level. Sulfur vacancies, however, do not have a significant impact on the energetics of Co3S4(100) surface.

Fronzi, M, Tawfik, SA, Stampfl, C & Ford, MJ 2018, 'Magnetic properties of stoichiometric and defective Co₉S₈', Physical Chemistry Chemical Physics, vol. 20, no. 4, pp. 2356-2362.
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Our theoretical investigation confirms the antiferromagnetic nature of pentlandite Co₉S₈ and predicts a change in the local magnetic properties upon sulfur vacancy formation.

Fujimoto, R, Uezono, K, Ishikura, S, Osabe, K, Peacock, WJ & Dennis, ES 2018, 'Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems', Breeding Science, vol. 68, no. 2, pp. 145-158.
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Fujise, L, Nitschke, MR, Frommlet, JC, Serôdio, J, Woodcock, S, Ralph, PJ & Suggett, DJ 2018, 'Cell Cycle Dynamics of Cultured Coral Endosymbiotic Microalgae (Symbiodinium) Across Different Types (Species) Under Alternate Light and Temperature Conditions', Journal of Eukaryotic Microbiology, vol. 65, no. 4, pp. 505-517.
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AbstractDinoflagellates of the genus Symbiodinium live in symbiosis with many invertebrates, including reef‐building corals. Hosts maintain this symbiosis through continuous regulation of Symbiodinium cell density via expulsion and degradation (postmitotic) and/or constraining cell growth and division through manipulation of the symbiont cell cycle (premitotic). Importance of premitotic regulation is unknown since little data exists on cell cycles for the immense genetic diversity of Symbiodinium. We therefore examined cell cycle progression for several distinct SymbiodiniumITS2‐types (B1, C1, D1a). All types exhibited typical microalgal cell cycle progression, G1 phase through to S phase during the light period, and S phase to G2/M phase during the dark period. However, the proportion of cells in these phases differed between strains and reflected differences in growth rates. Undivided larger cells with 3n DNA content were observed especially in type D1a, which exhibited a distinct cell cycle pattern. We further compared cell cycle patterns under different growth light intensities and thermal regimes. Whilst light intensity did not affect cell cycle patterns, heat stress inhibited cell cycle progression and arrested all strains in G1 phase. We discuss the importance of understanding Symbiodinium functional diversity and how our findings apply to clarify stability of host‐Symbiodinium symbioses.

Funari, R, Bhalla, N, Chu, K-Y, Söderström, B & Shen, AQ 2018, 'Nanoplasmonics for Real-Time and Label-Free Monitoring of Microbial Biofilm Formation', ACS Sensors, vol. 3, no. 8, pp. 1499-1509.
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Microbial biofilms possess intrinsic resistance against conventional antibiotics and cleaning procedures; thus, a better understanding of their complex biological structures is crucial in both medical and industrial applications. Existing laboratory methodologies have focused on macroscopic and mostly indirect characterization of mechanical and microbiological properties of biofilms adhered on a given substrate. However, the kinetics underlying the biofilm formation is not well understood, while such information is critical to understanding how drugs and chemicals influence the biofilm formation. Herein, we report the use of localized surface plasmon resonance (LSPR) for real-time, label-free monitoring of E. coli biofilm assembly on a nanoplasmonic substrate consisting of gold mushroom-like structures. Our LSPR sensor is able to capture the signatures of biofilm formation in real-time by measuring the wavelength shift in the LSPR resonance peak with high temporal resolution. We employ this sensor feature to elucidate how biofilm formation is affected by different drugs, including conventional antibiotics (kanamycin and ampicillin) as well as rifapentine, a molecule preventing cell adhesion yet barely affecting bacterial viability and vitality. Due to its flexibility and simplicity, our LSPR based platform can be used on a wide variety of clinically relevant bacteria, thus representing a valuable tool in biofilm characterization and drug screening.

Fung, E, Yang, X, Newton, PJ, Ferguson, C, Gastelurrutia, P, Lupón, J, Bayés-Genís, A, Jha, S & Macdonald, PS 2018, 'Letter by Fung et al Regarding Article, “Frailty and Clinical Outcomes in Heart Failure: A Systematic Review and Meta-analysis”', Journal of the American Medical Directors Association, vol. 19, no. 12, pp. 1143-1146.
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Gai, S, Yang, G, Yang, P, He, F, Lin, J, Jin, D & Xing, B 2018, 'Recent advances in functional nanomaterials for light–triggered cancer therapy', Nano Today, vol. 19, pp. 146-187.
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© 2018 Elsevier Ltd Photo–triggered therapeutic modalities for cancer have attracted enormous attention in recent years due to the easily focused and tuned properties of irradiation light that enable the localized treatment with non–invasive, direct and accurate characteristics. In addition, by using new developed functional nanomaterials, different therapeutic modalities can be integrated into a single platform, and co–therapies with dramatically enhanced anti–cancer ability by synergetic therapeutic effects are obtained. In the view of the fast development of anti–cancer strategy, we present an in–depth review of major breakthroughs in recent advanced functional nanomaterials for photo–triggered therapy. This review first summarizes the organic and inorganic photosensitizers for photodynamic therapy (PDT), four kinds of photothermal materials for photothermal therapy (PTT), as well as photo–switchable molecules or photolabile chemical groups bonded materials for chemotherapy. For each part, the therapeutic materials, mechanisms, superiorities and typical representatives are examined extensively. Then, we systematically discuss the optimized multifunctional nanomaterials consist of the above materials for PTT/PDT co–therapy, PTT/chemo co–therapy, PDT/chemo co–therapy and radiotherapy–composed co–therapy etc. And the synergetic therapeutic mechanism, anti–cancer efficiency, safety and design of therapeutic materials are highlighted. Finally, we give an outlook of the future directions of the rapidly growing functional nanomaterials for photo–triggered therapy, and propose several associated challenges and potential solutions.

Gale, PA & Caltagirone, C 2018, 'Fluorescent and colorimetric sensors for anionic species', Coordination Chemistry Reviews, vol. 354, pp. 2-27.
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Gale, PA, Howe, ENW, Wu, X & Spooner, MJ 2018, 'Anion receptor chemistry: Highlights from 2016', Coordination Chemistry Reviews, vol. 375, pp. 333-372.
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Gali, M & Arnold, M 2018, 'Recurrent approach to effective material properties with application to anisotropic binarized random fields', Phys. Rev. B, vol. 99, no. 5, p. 054210.
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Building on the foundation work of Brown, Milton and Torquato, we present atractable approach to analyse the effective permittivity of anisotropictwo-phase structures. This methodology accounts for successive dipolarinteractions, providing a recurrent series expansion of the effectivepermittivity to arbitrary order. Within this framework, we also demonstrate aprogressive method to determine tight bounds that converge towards the exactsolution. We illustrate the utility of these methods by using ensembleaveraging to determine the micro-structural parameters of anisotropic level-cutGaussian fields. We find that the depolarization factor of these structures isequivalent to that of an isolated ellipse with the same stretchingratio, anddiscuss the contribution of the fourth order term to the exact anisotropy.

Gan, R, Zhang, Y, Shi, H, Yang, Y, Eamus, D, Cheng, L, Chiew, FHS & Yu, Q 2018, 'Use of satellite leaf area index estimating evapotranspiration and gross assimilation for Australian ecosystems', Ecohydrology, vol. 11, no. 5, pp. e1974-e1974.
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AbstractAccurate quantification of terrestrial evapotranspiration and ecosystem productivity is of significant merit to better understand and predict the response of ecosystem energy, water, and carbon budgets under climate change. Existing diagnostic models have different focus on either water or carbon flux estimates with various model complexity and uncertainties induced by distinct representation of the coupling between water and carbon processes. Here, we propose a diagnostic model to estimate evapotranspiration and gross primary production that is based on biophysical mechanism yet simple for practical use. This is done by coupling the carbon and water fluxes via canopy conductance used in the Penman–Monteith–Leuning equation (named as PML_V2 model). The PML_V2 model takes Moderate Resolution Imaging Spectrometer leaf area index and meteorological variables as inputs. The model was tested against evapotranspiration and gross primary production observations at 9 eddy‐covariance sites in Australia, which are spread across wide climate conditions and ecosystems. Results indicate that the simulated evapotranspiration and gross primary production by the PML_V2 model are in good agreement with the measurements at 8‐day timescale, indicated by the cross site Nash–Sutcliffe efficiency being 0.70 and 0.66, R2 being 0.80 and 0.75, and root mean square error being 0.96 mm d−1 and 1.14 μmol m−2 s−1 for evapotranspiration and gross primary production, respectively. As the PML_V2 model only requires readily available climate and Moderate Resolution Imaging Spectrometer vegetation dynamics data and has few parameters, it can potentially be applied to estimate evapotranspiration and carbon assimilation simultaneously at long‐term and large spatial scales.

Gao, J, Wu, S, Tan, F, Tian, H, Liu, J & Lu, GQM 2018, 'Nanoengineering of amino - functionalized mesoporous silica nanospheres as nanoreactors', Progress in Natural Science: Materials International, vol. 28, no. 2, pp. 242-245.
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Garrastazu Pereira, G, Rawling, T, Pozzoli, M, Pazderka, C, Chen, Y, Dunstan, CR, Murray, M & Sonvico, F 2018, 'Nanoemulsion-Enabled Oral Delivery of Novel Anticancer ω-3 Fatty Acid Derivatives', Nanomaterials, vol. 8, no. 10, pp. 825-825.
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Lipid-based drugs are emerging as an interesting class of novel anticancer drugs with the potential to target specific cancer cell metabolic pathways linked to their proliferation and invasiveness. In particular, ω-3 polyunsaturated fatty acids (PUFA) derivatives such as epoxides and their bioisosteres have demonstrated the potential to suppress growth and promote apoptosis in triple-negative human breast cancer cells MDA-MB-231. In this study, 16-(4′-chloro-3′-trifluorophenyl)carbamoylamino]hexadecanoic acid (ClFPh-CHA), an anticancer lipid derived from ω-3,17,18-epoxyeicosanoic acid, was formulated as a stable nanoemulsion with size around 150 nm and narrow droplet size distribution (PDI < 0.200) through phase-inversion emulsification process followed by high pressure homogenization in view of an oral administration. The ClFPh-CHA-loaded nanoemulsions were able to significantly decrease the relative tumor volume in mice bearing an intramammary tumor xenograft at all doses tested (2.5, 10 and 40 mg/kg) after 32 days of daily oral administration. Furthermore, absolute tumor weight was decreased to 50% of untreated control at 10 and 40 mg/kg, while intraperitoneal administration could achieve a significant reduction only at the highest dose of 40 mg/kg. Results suggest that oral administration of ClFPh-CHA formulated as a nanoemulsion has a sufficient bioavailability to provide an anticancer effect in mice and that the activity is at least equal if not superior to that obtained by a conventional parenteral administration of equivalent doses of the same drug.

Gellert, K & Schlogl, E 2018, 'Parameter Learning and Change Detection Using a Particle Filter With Accelerated Adaptation', Risks, vol. 9, no. 12, pp. 228-228.
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This paper presents the construction of a particle filter, which incorporates elements inspired by genetic algorithms, in order to achieve accelerated adaptation of the estimated posterior distribution to changes in model parameters. Specifically, the filter is designed for the situation where the subsequent data in online sequential filtering does not match the model posterior filtered based on data up to a current point in time. The examples considered encompass parameter regime shifts and stochastic volatility. The filter adapts to regime shifts extremely rapidly and delivers a clear heuristic for distinguishing between regime shifts and stochastic volatility, even though the model dynamics assumed by the filter exhibit neither of those features.

Giardina, M, Cheong, S, Marjo, CE, Clode, PL, Guagliardo, P, Pickford, R, Pernice, M, Seymour, JR & Raina, J-B 2018, 'Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study', Frontiers in Microbiology, vol. 9, no. NOV.
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Copyright © 2018 Giardina, Cheong, Marjo, Clode, Guagliardo, Pickford, Pernice, Seymour and Raina. Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.

Giffard, PM, Andersson, P, Wilson, J, Buckley, C, Lilliebridge, R, Harris, TM, Kleinecke, M, O’Grady, K-AF, Huston, WM, Lambert, SB, Whiley, DM & Holt, DC 2018, 'CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments', PLOS ONE, vol. 13, no. 4, pp. e0195454-e0195454.
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© 2018 Giffard et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phyloge-netically coherent “classical ocular lineage”. However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.

Gill, GK, Singh, A, Lal, UR, Kaur, H, Mehta, M, Satija, S & Mahajan, S 2018, 'Effect of fermentation on chemical changes in Vitis vinifera fruits used in alcoholic ayurvedic formulation', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 29-34.
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Background: Arishtas are weakly alcoholic Ayurvedic formulations prepared by fermenting the decoction of medicinal plants in an airtight sealed vessels. The presence of Vitis vinifera is considered essential to initiate the fermentation process. The fruits of V. vinifera were reported to have different polar components such as phenolics, phenolic acids, flavonoids, and flavonoid glycosides. Literature has mentioned the impact of fermentation in altering the chemical skeleton of molecules. Materials and Methods: Considering this fact, the present study was designed to understand the possible impact of fermentation on the chemical profile of V. vinifera by reversed-phase high-performance liquid chromatography (RP-HPLC) studies. Both fermented and non-fermented extract of V. vinifera was prepared by the traditional method and analyzed for chemical changes by RP-HPLC-ultraviolet method. Results and Conclusions: It was observed that the chromatogram of non-fermented extract of V. vinifera showed comparatively very few peaks as compared to the chromatogram of its fermented extract. This is probably due to the fact that the large molecular weight polyphenolics particularly flavonoid glycosides and tannins are hydrolyzed during ferat mention and degraded into small molecules of phenolics or phenolic acids. This change will modify significantly the biological activity of the fermented extracts and the final Ayurvedic formulation, particularly fermented biomedicine like Arishtas.

Giltrap, AM, Haeckl, FPJ, Kurita, KL, Linington, RG & Payne, RJ 2018, 'Synthetic Studies Toward the Skyllamycins: Total Synthesis and Generation of Simplified Analogues', The Journal of Organic Chemistry, vol. 83, no. 13, pp. 7250-7270.
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Gissibl, A, Care, A, Parker, LM, Iqbal, S, Hobba, G, Nevalainen, H & Sunna, A 2018, 'Microwave pretreatment of paramylon enhances the enzymatic production of soluble β-1,3-glucans with immunostimulatory activity', Carbohydrate Polymers, vol. 196, pp. 339-347.
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A hydrothermal microwave pretreatment was established to facilitate the enzymatic production of soluble bioactive β-1,3-glucans from the recalcitrant substrate paramylon. The efficacy of this pretreatment was monitored with a newly developed direct Congo Red dye-based assay over a range of temperatures. Microwave pretreatment at 170 °C for 2 min resulted in a significantly enhanced enzymatic hydrolysis of paramylon. The action of endo-β-1,3- and exo- β-1,3-glucanases on the microwave-pretreated paramylon produced soluble β-1,3-glucans with degrees of polymerisation (DP) ranging from 2-59 and 2-7, respectively. In comparison, acid-mediated hydrolysis of untreated paramylon resulted in β-1,3-glucans with a DP range of 2-38. The hydrolysates were assayed on their immunostimulatory effect on murine macrophages by measuring the production of the inflammation-linked marker tumour necrosis factor alpha (TNFα) using immunofluorescence. All of the tested hydrolysis products were shown to induce TNFα production, with the most significant immunostimulatory effect observed with the hydrolysate from the exo-β-1,3-glucanase treatment.

Glastras, SJ, Chen, H, Pollock, CA & Saad, S 2018, 'Maternal obesity increases the risk of metabolic disease and impacts renal health in offspring', Bioscience Reports, vol. 38, no. 2.
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Obesity, together with insulin resistance, promotes multiple metabolic abnormalities and is strongly associated with an increased risk of chronic disease including type 2 diabetes (T2D), hypertension, cardiovascular disease, non-alcoholic fatty liver disease (NAFLD) and chronic kidney disease (CKD). The incidence of obesity continues to rise in astronomical proportions throughout the world and affects all the different stages of the lifespan. Importantly, the proportion of women of reproductive age who are overweight or obese is increasing at an alarming rate and has potential ramifications for offspring health and disease risk. Evidence suggests a strong link between the intrauterine environment and disease programming. The current review will describe the importance of the intrauterine environment in the development of metabolic disease, including kidney disease. It will detail the known mechanisms of fetal programming, including the role of epigenetic modulation. The evidence for the role of maternal obesity in the developmental programming of CKD is derived mostly from our rodent models which will be described. The clinical implication of such findings will also be discussed.

Gleason, SM, Stephens, AEA, Tozer, WC, Blackman, CJ, Butler, DW, Chang, Y, Cook, AM, Cooke, J, Laws, CA, Rosell, JA, Stuart, SA & Westoby, M 2018, 'Shoot growth of woody trees and shrubs is predicted by maximum plant height and associated traits', Functional Ecology, vol. 32, no. 2, pp. 247-259.
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AbstractThe rate of elongation and thickening of individual branches (shoots) varies across plant species. This variation is important for the outcome of competition and other plant–plant interactions. Here, we compared rates of shoot growth across 44 species from tropical, warm temperate and cool temperate forests of eastern Australia.Shoot growth rate was found to correlate with a suite of traits including the potential height of the species, xylem‐specific conductivity, leaf size, leaf area per xylem cross‐section (LA/XA), twig diameter (at 40 cm length), wood density and modulus of elasticity.Within this suite of traits, maximum plant height was the clearest correlate of growth rates, explaining 50%–67% of the variation in growth overall (p < .0001), and 23%–32% of the variation (p < .05) in growth when holding the influence of the other traits constant. Structural equation models suggest that traits associated with “hydraulics,” “biomechanics” and the “leaf economics spectrum” represent three clearly separated axes of variation, with the hydraulic axis exhibiting the strongest alignment with height and largest independent contribution to growth (in the case of branch thickening). However, most of the capacity of these axes to predict growth was also associated with maximum height, presumably reflecting coordinated selection on multiple traits that together influence life histories.Growth rates were not strongly correlated with leaf nitrogen or leaf mass per unit leaf area.Correlations between growth and maximum height arose both across latitude (47%, p < .0001) and from within‐site diff...

Godecke, E, Rai, T, Cadilhac, DA, Armstrong, E, Middleton, S, Ciccone, N, Whitworth, A, Rose, ML, Holland, A, Ellery, F, Hankey, GJ & Bernhardt, J 2018, 'Statistical analysis plan (SAP) for the Very Early Rehabilitation in Speech (VERSE) after stroke trial: an international 3-arm clinical trial to determine the effectiveness of early, intensive, prescribed, direct aphasia therapy', International Journal of Stroke, vol. 13, no. 8, pp. 863-880.
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Background Limited evidence exists to support very early intensive aphasia rehabilitation after stroke. VERSE is a PROBE trial designed to determine whether two types of intensive aphasia therapy, beginning within 14 days of acute stroke, provide greater therapeutic and cost-effectiveness than usual care. Objective To publish the detailed statistical analysis plan for the VERSE trial prior to unblinding. This statistical analysis plan was based on the published and registered VERSE trial protocol and was developed by the blinded steering committee and management team, led by the trial statistician. This plan was developed using outcome measures and trial data collection forms. Results The VERSE statistical analysis plan is consistent with reporting standards for clinical trials and provides for clear and open reporting. Conclusions Publication of a statistical analysis plan serves to reduce potential trial reporting bias and outlines transparent pre-specified analyses. Australian New Zealand Clinical Trials Registry (ANZCTR) Registration number: ACTRN12613000776707; Universal Trial Number (UTN) is U1111-1145-4130.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2018, 'A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen', Frontiers in Genetics, vol. 9, no. AUG.
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© 2018 Goodswen, Kennedy and Ellis. Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates...

Goodwin, C, Higgins, D, Tobe, SS, Austin, J, Wotherspoon, A, Gahan, ME & McNevin, D 2018, 'Singleplex quantitative real-time PCR for the assessment of human mitochondrial DNA quantity and quality', Forensic Science, Medicine and Pathology, vol. 14, no. 1, pp. 70-75.
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. Mitochondrial DNA (mtDNA) can provide a means for forensic identity testing when genotyping of nuclear DNA (nuDNA) targets is not possible due to degradation or lack of template. For degraded samples, an indication of the quantity and quality of mtDNA is essential to allow selection of appropriately sized targets for hypervariable region (HVR) analysis, which may conserve sample and resources. Three human-specific mtDNA targets of increasing length (86, 190 and 452 base pairs) were amplified by singleplex quantitative real-time PCR (qPCR), capable of providing an index of mtDNA degradation from fragment length information. Quantification was achieved by preparation of a standard curve for each target, using a purified mtDNA standard containing all three targets of interest, which produced a linear, accurate and precise result from 1×108 to 10 copies. These novel assays demonstrated excellent sensitivity, specificity and reproducibility in line with the minimum information for qPCR experiments (MIQE) guidelines. Further, a separate inhibition control reaction was included to guide sample clean-up and ensure the validity of degradation assays. This protocol assists the selection and analysis of appropriately sized targets to maximize the chance of obtaining an informative result in downstream assays like sequencing.

Gorlach, MA, Dobrykh, DA, Slobozhanyuk, AP, Belov, PA & Lapine, M 2018, 'Nonlinear symmetry breaking in photometamaterials', Physical Review B, vol. 97, no. 11.
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© 2018 American Physical Society. We design and analyze theoretically photometamaterials with each meta-atom containing both photodiode and light-emitting diode. Illumination of the photodiode by the light-emitting diode gives rise to an additional optical feedback within each unit cell, which strongly affects resonant properties and nonlinear response of the meta-atom. In particular, we demonstrate that inversion symmetry breaking occurs upon a certain threshold magnitude of the incident wave intensity resulting in an abrupt emergence of second-harmonic generation, which was not originally available, as well as in the reduced third-harmonic signal.

Grüning, B, Dale, R, Sjödin, A, Chapman, BA, Rowe, J, Tomkins-Tinch, CH, Valieris, R & Köster, J 2018, 'Bioconda: sustainable and comprehensive software distribution for the life sciences', Nature Methods, vol. 15, no. 7, pp. 475-476.
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Gu, H, Kononov, A, Memar, J & Zinder, Y 2018, 'Efficient Lagrangian heuristics for the two-stage flow shop with job dependent buffer requirements', Journal of Discrete Algorithms, vol. 52-53, pp. 143-155.
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© 2018 Elsevier B.V. The paper is concerned with minimisation of the total weighted completion time for the two-stage flow shop with a buffer. In contrast to the vast literature on this topic, the buffer requirement varies from job to job and a job occupies the buffer continuously from the start of its first operation till the completion of its second operation rather than only between operations. Such problems arise in supply chains requiring unloading and loading of minerals and in some multimedia systems. The problem is NP-hard in the strong sense, and we prove that if the order of jobs is fixed for one of the stages, then even for the criteria of the maximum completion time or the total completion time the problem remains NP-hard in the strong sense. Straightforward integer programming approach is impossible even for modest problem sizes. The paper presents a Lagrangian relaxation based decomposition approach that allows to use for each problem, obtained by this decomposition, a very fast algorithm. Several Lagrangian heuristics are evaluated by means of computational experiments.

Guan, M, Zhou, Z, Mei, L, Zheng, H, Ren, W, Wang, L, Du, Y, Jin, D & Zhou, J 2018, 'Direct cation exchange of surface ligand capped upconversion nanocrystals to produce strong luminescence', Chemical Communications, vol. 54, no. 69, pp. 9587-9590.
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We develop a facile and rapid cation exchange method for upconversion nanocrystals (UCNCs) without removing surface ligands.

Gunawan, D, Dang, K-D, Quiroz, M, Kohn, R & Tran, M-N 2018, 'Subsampling Sequential Monte Carlo for Static Bayesian Models', Statistics and Computing, vol. 30, no. 6, pp. 1741-1758.
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We show how to speed up Sequential Monte Carlo (SMC) for Bayesian inferencein large data problems by data subsampling. SMC sequentially updates a cloud ofparticles through a sequence of distributions, beginning with a distributionthat is easy to sample from such as the prior and ending with the posteriordistribution. Each update of the particle cloud consists of three steps:reweighting, resampling, and moving. In the move step, each particle is movedusing a Markov kernel; this is typically the most computationally expensivepart, particularly when the dataset is large. It is crucial to have anefficient move step to ensure particle diversity. Our article makes twoimportant contributions. First, in order to speed up the SMC computation, weuse an approximately unbiased and efficient annealed likelihood estimator basedon data subsampling. The subsampling approach is more memory efficient than thecorresponding full data SMC, which is an advantage for parallel computation.Second, we use a Metropolis within Gibbs kernel with two conditional updates. AHamiltonian Monte Carlo update makes distant moves for the model parameters,and a block pseudo-marginal proposal is used for the particles corresponding tothe auxiliary variables for the data subsampling. We demonstrate both theusefulness and limitations of the methodology for estimating four generalizedlinear models and a generalized additive model with large datasets.

Gunduz, O, Yetmez, M, Ekren, N, Kilic, O, Ben Nissan, B & Oktar, FN 2018, 'Microstructural and Mechanical Properties of Nano-Yttria-Oxide Doped Hydroxyapatite Composites', Materials Science Forum, vol. 923, pp. 89-92.
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Nowadays hydroxyapatite (HA) bioceramics are very important because increasing traffic accidents and ageing of the population. They can be produced from synthetic or natural sources with different production methods. The biggest negative issue of HA is being very brittle and unstable under pressure. Various materials are added for restoring these weaknesses, but there is not so much studies adding nano-ingredients for restoring the mechanical properties of HA. In this study, 5-10% nano-yittria-oxide is added to bovine derived HA (BHA) and to commercial synthetic (CSHA) as a control group. Physical and mechanical properties are examined. Results show that adding of nano-ingredients are really helping to mechanical properties of HA.

Guo, X, Li, K, Bao, W, Zhao, Y, Xu, J, Liu, H & Wang, G 2018, 'Highly Reversible Lithium Polysulfide Semiliquid Battery with Nitrogen‐Rich Carbon Fiber Electrodes', Energy Technology, vol. 6, no. 2, pp. 251-256.
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AbstractFreestanding nitrogen‐doped carbon fiber (NCF) webs saturated with lithium polysulfide solution were prepared as semiliquid cathodes for lithium–sulfur batteries. The NCF webs not only facilitated the transportation of electrons and ions but also immobilized the polysulfide at the cathode side because of strong affinity between the polysulfide and the N‐doped carbon. As a result, these semiliquid cells demonstrated superior electrochemical performance at various current loads. A high reversible capacity of 900 mAh g−1 was achieved after 200 cycles at a current rate of 1 C.

Guo, X, Zhang, J, Song, J, Wu, W, Liu, H & Wang, G 2018, 'MXene encapsulated titanium oxide nanospheres for ultra-stable and fast sodium storage', Energy Storage Materials, vol. 14, pp. 306-313.
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© 2018 Sodium-ion batteries with high power density present tremendous potential for large-scale energy storage applications. However, it remains a big challenge to develop suitable anode materials for ultrafast and highly reversible sodium ion storage. Herein, for the first time, we report a novel strategy to fabricate highly conductive MXene Ti3C2Tx encapsulated titanium oxide spheres (TiO2@Ti3C2Tx) as an excellent anode material for sodium-ion batteries. The MXene layers significantly improve the electronic conductivity of the whole electrode and protect the structural integrity of the TiO2 spheres from electrochemical pulverization, which hence contributes to the formation of a stable solid-electrolyte interface. Meanwhile, the pseudocapacitance of the as-fabricated TiO2@Ti3C2Tx composites enables high-rate capability and long cycle life in sodium-ion batteries. As a result, the hybrid electrode delivers a high reversible capacity of 116 mAh g-1 at 960 mA g-1 up to 5000 cycles. By coupling with a NaCrO2 cathode, a prototype Na-ion full cell achieved a capacity of 103.4 mAh g-1 at 960 mA g-1 and an excellent cycling performance with 73.5% capacity retention after 1000 cycles.

Guo, Y, Seo, DH, Hong, J, Su, D, Wang, H, Zheng, J, Li, X, Murphy, AB & Ostrikov, KK 2018, 'Controlling the adsorption behavior of hydrogen at the interface of polycrystalline CVD graphene', International Journal of Hydrogen Energy, vol. 43, no. 41, pp. 18735-18744.
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© 2018 Hydrogen Energy Publications LLC Polycrystalline graphene films were synthesized from renewable biomaterials in ambient air using a facile and rapid thermal chemical vapour deposition technique. Characterization of the graphene reveals a large surface area, the presence of nanoscale domains and open edges, atomic-level stacking, and high electrical conductivity, which are favorable features for electrochemical hydrogen evolution reactions (HERs). The numerous boundaries and open edges accelerate the gas diffusion process and enlarge the effective reactive surface area for gas evolution, which is responsible for a significant improvement of HER performance and stability compared to a commercial graphene film. The hydrogen adhesion behavior in investigated for both bare Ni foil/foam and graphene grown on Ni foil/foam samples. The hydrogen gas bubbles adhere to the polycrystalline graphene for a long period of time before detaching, in contrast to their behavior on the pristine Ni foil surface. Post treatment of the graphene film using plasma treatment increases the desorption rate of hydrogen bubbles from the surface. The results indicate a wide range of possibilities for use of graphene-based catalysts in electrocatalytic gas evolution reactions.

Gupta, G, Chellappan, DK, de Jesus Andreoli Pinto, T, Hansbro, PM, Bebawy, M & Dua, K 2018, 'Tumor suppressor role of miR-503', Panminerva Medica, vol. 60, no. 1, pp. 17-24.
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© 2017 EDIZIONI MINERVA MEDICA. MicroRNAs (miRNAs) are non-coding RNAs of around 20-25 nucleotides in length with highly conserved characteristics. They moderate posttranscriptional silencing by precisely combining with 3' untranslated regions (UTRs) of target mRNAs at a complementary site. miR-503, an associate of the 'canonical' miRNA-16 family, is expressed in numerous types of tumors such as breast cancer, prostate cancer, lung cancer, colorectal cancer, hepatocellular carcinoma, glioblastoma and several others. There is convincing evidence to show that miR-503 functions as a tumor suppressor gene through its effects on target genes that regulate cell proliferation, migration, and invasion in tumor cells. In this current assessment, we discuss the biology and tumor suppressor role of miR-503 in different cancers and elaborate on its mechanism of action.

Gupta, V, Trivedi, N, Simoni, S & Reddy, CRK 2018, 'Marine macroalgal nursery: A model for sustainable production of seedlings for large scale farming', Algal Research, vol. 31, pp. 463-468.
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Gushchin, A, Kordzakhia, N & Novikov, A 2018, 'Translation invariant statistical experiments with independent increments', Statistical Inference for Stochastic Processes, vol. 21, no. 2, pp. 363-383.
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© 2018, Springer Science+Business Media B.V., part of Springer Nature. We provide a full description of the class of translation invariant experiments with independent increments. Necessary and sufficient conditions for the weak convergence and the comparison of experiments within this class are given. Finally, we prove exponential boundedness of Pitman estimators in these models.

Gutiérrez Moreno, JJ, Fronzi, M, Lovera, P, O’Riordan, A & Nolan, M 2018, 'Stability of Adsorbed Water on TiO₂–TiN Interfaces. A First-Principles and Ab Initio Thermodynamics Investigation', The Journal of Physical Chemistry C, vol. 122, no. 27, pp. 15395-15408.
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© 2018 American Chemical Society. Titanium nitride (TiN) surfaces can oxidize, and the growth of a TiOx layer on the surface along with the likely presence of water in the surrounding environment can modify the properties of this widely used coating material. The present density functional theory study, including Hubbard + U correction (DFT+U), investigates the stability of adsorbed water at TiO2-TiN interfaces with different defects that serve as a model for an oxide layer grown on a TiN surface. Surface free energy calculations show the stability of a perfect TiN-TiO2 interface at regular O pressures, while oxygen vacancy-rich TiO1.88-TiN is more favorable at reducing conditions. An isolated water is preferentially adsorbed dissociatively at perfect and oxygen-defective interfaces, while molecular adsorption is more stable at higher coverages. The adsorption energy is stronger at the oxygen-defective interfaces which arise from the high concentration of reduced Ti3+ and strong interfacial atomic relaxations. Ab initio atomistic thermodynamics show that water will be present at high coverage on TiO2-TiN interfaces at ambient conditions, and the pristine interface is only stable at very low pressure of O and H2O. The results of these DFT+U simulations are important for the fundamental understanding of wettability of interfacial systems involving metal oxides.

Haddadi, N, Lin, Y, Travis, G, Simpson, AM, Nassif, NT & McGowan, EM 2018, 'PTEN/PTENP1: ‘Regulating the regulator of RTK-dependent PI3K/Akt signalling’, new targets for cancer therapy', Molecular Cancer, vol. 17, no. 1.
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© 2018 The Author(s). Regulation of the PI-3 kinase (PI3K)/Akt signalling pathway is essential for maintaining the integrity of fundamental cellular processes, cell growth, survival, death and metabolism, and dysregulation of this pathway is implicated in the development and progression of cancers. Receptor tyrosine kinases (RTKs) are major upstream regulators of PI3K/Akt signalling. The phosphatase and tensin homologue (PTEN), a well characterised tumour suppressor, is a prime antagonist of PI3K and therefore a negative regulator of this pathway. Loss or inactivation of PTEN, which occurs in many tumour types, leads to overactivation of RTK/PI3K/Akt signalling driving tumourigenesis. Cellular PTEN levels are tightly regulated by a number of transcriptional, post-transcriptional and post-translational regulatory mechanisms. Of particular interest, transcription of the PTEN pseudogene, PTENP1, produces sense and antisense transcripts that exhibit post-transcriptional and transcriptional modulation of PTEN expression respectively. These additional levels of regulatory complexity governing PTEN expression add to the overall intricacies of the regulation of RTK/PI-3K/Akt signalling. This review will discuss the regulation of oncogenic PI3K signalling by PTEN (the regulator) with a focus on the modulatory effects of the sense and antisense transcripts of PTENP1 on PTEN expression, and will further explore the potential for new therapeutic opportunities in cancer treatment.

Hall, P, Johnstone, IM, Ormerod, JT, Wand, MP & Yu, JCF 2018, 'Fast and Accurate Binary Response Mixed Model Analysis via Expectation Propagation', Journal of the American Statistical Association, vol. 115, no. 532, pp. 1902-1916.
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Expectation propagation is a general prescription for approximation ofintegrals in statistical inference problems. Its literature is mainly concernedwith Bayesian inference scenarios. However, expectation propagation can also beused to approximate integrals arising in frequentist statistical inference. Wefocus on likelihood-based inference for binary response mixed models and showthat fast and accurate quadrature-free inference can be realized for the probitlink case with multivariate random effects and higher levels of nesting. Theapproach is supported by asymptotic theory in which expectation propagation isseen to provide consistent estimation of the exact likelihood surface.Numerical studies reveal the availability of fast, highly accurate and scalablemethodology for binary mixed model analysis.

Hamidian, M & Hall, RM 2018, 'Genetic structure of four plasmids found in Acinetobacter baumannii isolate D36 belonging to lineage 2 of global clone 1', PLOS ONE, vol. 13, no. 9, pp. e0204357-e0204357.
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Four plasmids ranging in size from 4.7 to 44.7 kb found in the extensively antibiotic resistant Acinetobacter baumannii isolate D36 that belongs to lineage 2 of global clone 1 were examined. D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. The smallest plasmid pD36-1 (4.7 kb) carries no resistance genes but includes mobA and mobC mobilisation genes related to those found in pRAY* (pD36-2, 6,078 bp) that also carries the aadB gentamicin, kanamycin and tobramycin resistance gene cassette. These two plasmids do not encode a Rep protein. Plasmid pRAY* was found to be mobilised at high frequency by the large conjugative plasmid pA297-3 but a pRAY* derivative lacking the mobA and mobC genes was not. The two larger plasmids, pD36-3 and pD36-4, encode Rep_3 family proteins (Pfam1051). The cryptic plasmid pD36-3 (6.2 kb) has RepAci1 and pD36-4 (44.7 kb) encodes two novel Rep_3 family proteins suggesting a co-integrate. Plasmid pD36-4 includes the sul2 sulfonamide resistance gene, the aphA1a kanamycin/neomycin resistance gene in Tn4352::ISAba1 and a mer module in a hybrid Tn501/Tn1696 transposon conferring resistance to mercuric ions. New examples of dif modules flanked by pdif sites (XerC-XerD binding sites) that are part of many A. baumannii plasmids were also identified in pD36-3 and pD36-4 which carry three and two dif modules, respectively. Homologs of three dif modules, the sup sulphate permease module in pD36-3, and of the abkAB toxin-antitoxin module and the orf module in pD36-4, were found in different contexts in diverse Acinetobacter plasmids, consistent with module mobility. A novel insertion sequence named ISAba32 found next to the pdif site in the abkAB dif module is related to members of the ISAjo2 group which also are associated with the pdif sites of dif modules. Plasmids found in D36 were also found in some other members of GC1 lineage 2.

Hamidian, M & Hall, RM 2018, 'The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 – Structure, origin and evolution', Drug Resistance Updates, vol. 41, pp. 26-39.
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In multiply resistant Acinetobacter baumannii, complex transposons located in the chromosomal comM gene carry antibiotic and heavy metal resistance determinants. For one type, known collectively as AbaR, the ancestral form, AbaR0, entered a member of global clone 1 (GC1) in the mid 1970s and continued to evolve in situ forming many variants. In AbaR0, antibiotic and mercuric ion resistance genes are located between copies of a cadmium-zinc resistance transposon, Tn6018, and this composite transposon is in a class III transposon, Tn6019, carrying arsenate/arsenite resistance genes and five tni transposition genes. The antibiotic resistance genes in the AbaR0 and derived AbaR3 configurations are aphA1b, blaTEM, catA1, sul1, tetA(A), and cassette-associated aacC1 and aadA1 genes. These genes are in a specific arrangement of fragments from well-known transposons, e.g. Tn1, Tn1721, Tn1696 and Tn2670, that arose in an IncM1 plasmid. All known GC1 lineage 1 isolates carry AbaR0 or AbaR3, which arose around 1990, or a variant derived from one of them. Variants arose via deletions caused by one of three internal IS26s, by recombination between duplicate copies of sul1 or Tn6018, or by gene cassette addition or replacement. A few GC2 isolates also carry an AbaR island with different cassette-associated genes, aacA4 and oxa20.

Hare, DJ, Cardoso, BR, Szymlek-Gay, EA & Biggs, B-A 2018, 'Neurological effects of iron supplementation in infancy: finding the balance between health and harm in iron-replete infants', The Lancet Child & Adolescent Health, vol. 2, no. 2, pp. 144-156.
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© 2018 Elsevier Ltd Iron mediates many biochemical processes in neural networks that proliferate during brain development. Insufficient iron causes irreversible neurodevelopmental deficits, and most high-income countries recommend that infants older than 4–6 months receive additional iron via food fortification or supplementation to prevent iron-deficiency anaemia. Now that the prevalence of iron-deficiency anaemia in children has decreased to less than 10% in most developed countries, concerns that the recommended intakes far exceed those required to prevent iron-deficiency anaemia have been raised, and emerging evidence suggests that iron overexposure could be linked to adverse outcomes later in life. In this Viewpoint, we discuss the importance of iron for neurodevelopment, investigate the biochemical markers used to assess iron stores, summarise the disparity in public health policies among high-income countries, and discuss the potential association between iron overexposure and adverse neurological outcomes later in life. We present a case for new studies to establish the optimal amount of iron that both prevents deficiency and reduces the potential risk of long-term negative health outcomes.

Hart, G, Bradfield, LA & Balleine, BW 2018, 'Prefrontal Corticostriatal Disconnection Blocks the Acquisition of Goal-Directed Action', The Journal of Neuroscience, vol. 38, no. 5, pp. 1311-1322.
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The acquisition of goal-directed action requires encoding of the association between an action and its specific consequences or outcome. At a neural level, this encoding has been hypothesized to involve a prefrontal corticostriatal circuit involving the projection from the prelimbic cortex (PL) to the posterior dorsomedial striatum (pDMS); however, no direct evidence for this claim has been reported. In a series of experiments, we performed functional disconnection of this pathway using targeted lesions of the anterior corpus callosum to disrupt contralateral corticostriatal projections with asymmetrical lesions of the PL and/or pDMS to block plasticity in this circuit in rats. We first demonstrated that unilaterally blocking the PL input to the pDMS prevented the phosphorylation of extracellular signal-related kinase/mitogen activated protein kinase (pERK/pMAPK) induced by instrumental training. Next, we used a full bilateral disconnection of the PL from the pDMS and assessed goal-directed action using an outcome-devaluation test. Importantly, we found evidence that rats maintaining an ipsilateral and/or contralateral connection between the PL and the pDMS were able to acquire goal-directed actions. In contrast, bilateral PL–pDMS disconnection abolished the acquisition of goal-directed actions. Finally, we used a temporary pharmacological disconnection to disrupt PL inputs to the pDMS by infusing the NMDA antagonistdl-2-amino-5-phosphonopentanoic acid into the pDMS during instrumental training and found that this manipulation also disrupted goal-directed learning. These results establish that, in rats, the acquisition of new goal-directed actions depends on a prefrontal–corticostriatal circuit involving a connection between the PL and the pDMS.SIGNIFICANCE STATEMENTIt has been hypothesized that the prelimbic cortex (PL) and posterior dorsomedial striatum (pDMS) in rodents interact in a ...

Hart, G, Bradfield, LA, Fok, SY, Chieng, B & Balleine, BW 2018, 'The Bilateral Prefronto-striatal Pathway Is Necessary for Learning New Goal-Directed Actions', Current Biology, vol. 28, no. 14, pp. 2218-2229.e7.
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The acquisition of new goal-directed actions requires the encoding of action-outcome associations. At a neural level, this encoding has been hypothesized to involve a prefronto-striatal circuit extending between the prelimbic cortex (PL) and the posterior dorsomedial striatum (pDMS); however, no research identifying this pathway with any precision has been reported. We started by mapping the prelimbic input to the dorsal and ventral striatum using a combination of retrograde and anterograde tracing with CLARITY and established that PL-pDMS projections share some overlap with projections to the nucleus accumbens core (NAc) in rats. We then tested whether each of these pathways were functionally required for goal-directed learning; we used a pathway-specific dual-virus chemogenetic approach to selectively silence pDMS-projecting or NAc-projecting PL neurons during instrumental training and tested rats for goal-directed action. We found that silencing PL-pDMS projections abolished goal-directed learning, whereas silencing PL-NAc projections left goal-directed learning intact. Finally, we used a three-virus approach to silence bilateral and contralateral pDMS-projecting PL neurons and again blocked goal-directed learning. These results establish that the acquisition of new goal-directed actions depends on the bilateral PL-pDMS pathway driven by intratelencephalic cortical neurons.

Hartigan, J, MacNamara, S & Leslie, LM 2018, 'Comparing precipitation and temperature trends between inland and coastal locations', ANZIAM Journal, vol. 60, pp. C109-C126.
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Motivated by the Millennium Drought and the current drought over much of southern and eastern Australia, this detailed statistical study compares trends in annual wet season precipitation and temperature between a coastal site (Newcastle) and an inland site (Scone). Bootstrap permutation tests reveal Scone precipitation has decreased significantly over the past 40 years (p-value=0.070) whereas Newcastle has recorded little to no change (p-value=0.800). Mean maximum and minimum temperatures for Newcastle have increased over the past 40 years (p-values of 0.002 and 0.015, respectively) while the mean maximum temperature for Scone has increased (p-value = 0.058) and the mean minimum temperature has remained stable. This suggests mean temperatures during the wet season for both locations are increasing. Considering these trends along with those for precipitation, water resources in the Hunter region will be increasingly strained as a result of increased evaporation with either similar or less precipitation falling in the region. Wavelet analysis reveals that both sites have similar power spectra for precipitation and mean maximum temperature with a statistically significant signal in the two to seven year period, typically indicative of the El-Nino Southern Oscillation climate driver. The El-Nino Southern Oscillation also drives the Newcastle mean minimum temperature, whereas the Scone power spectra has no indication of a definitive driver for mean minimum temperature. References R. A., R. L. Kitching, F. Chiew, L. Hughes, P. C. D. Newton, S. S. Schuster, A. Tait, and P. Whetton. Climate change 2014: Impacts, adaptation, and vulnerability. Part B: Regional aspects. Contribution of Working Group II to the Fifth Assessment of the Intergovernmental Panel on Climate Change. Technical report, Intergovernmental Panel on Climate Change, 2014. URL https://www.ipcc.ch/report/ar5/wg2/. Bureau of Meteorology. Climate Gl...

Hartjes, FJ, Vonk, JM, Faiz, A, Hiemstra, PS, Lapperre, TS, Kerstjens, HAM, Postma, DS & van den Berge, M 2018, 'Predictive value of eosinophils and neutrophils on clinical effects of ICS in COPD', Respirology, vol. 23, no. 11, pp. 1023-1031.
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ABSTRACTBackground and objectiveInflammation is present to a variable degree and composition in patients with COPD. This study investigates associations between both eosinophils and neutrophils in blood, sputum, airway wall biopsies and bronchoalveolar lavage (BAL) and their potential use as biomarkers for clinical response to inhaled corticosteroids (ICS).MethodsIn total, 114 steroid‐naïve COPD patients of the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease (GLUCOLD) study using ICS or placebo during 30‐month follow‐up were included. Cell counts in blood, sputum, biopsies and BAL were evaluated at baseline. In addition, at baseline, 6 and 30 months, forced expiratory flow in 1 s (FEV1), residual volume/total lung capacity (hyperinflation) and Clinical COPD Questionnaire were evaluated.ResultsCross‐sectional analyses at baseline showed that higher blood eosinophils were significantly associated with higher eosinophil counts in sputum, biopsies and BAL. However, blood neutrophils did not significantly correlate with neutrophil counts in the other compartments. Baseline eosinophils and neutrophils, in whichever compartment measured, did not predict longitudinal FEV1 changes. Higher baseline biopsy eosinophils were associated with an increase in symptoms during 6‐ and 30‐month ICS treatment. In addition, higher biopsy neutrophils were associated with a more marked reduction in hyperinflation during 6‐month ICS treatment compared with placebo.ConclusionOur findings indicate that blood eosinophils reflect eosinophils in other compartments, in contrast to neutrophils, in ICS‐naïve COPD patients. Both baseline eosinophils and neutrophils do ...

Hassan, KA, Liu, Q, Elbourne, LDH, Ahmad, I, Sharples, D, Naidu, V, Chan, CL, Li, L, Harborne, SPD, Pokhrel, A, Postis, VLG, Goldman, A, Henderson, PJF & Paulsen, IT 2018, 'Pacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens', Research in Microbiology, vol. 169, no. 7-8, pp. 450-454.
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Haw, TJ, Starkey, MR, Pavlidis, S, Fricker, M, Arthurs, AL, Mono Nair, P, Liu, G, Hanish, I, Kim, RY, Foster, PS, Horvat, JC, Adcock, IM & Hansbro, PM 2018, 'Toll-like receptor 2 and 4 have Opposing Roles in the Pathogenesis of Cigarette Smoke-induced Chronic Obstructive Pulmonary Disease', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 314, no. 2, pp. ajplung.00154.2-ajplung.00154.2.
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© 2018 American Physiological Society. All rights reserved. Chronic obstructive pulmonary disease (COPD) is the third leading cause of morbidity and death and imposes major socioeconomic burdens globally. It is a progressive and disabling condition that severely impairs breathing and lung function. There is a lack of effective treatments for COPD, which is a direct consequence of the poor understanding of the underlying mechanisms involved in driving the pathogenesis of the disease. Toll-like receptor (TLR)2 and TLR4 are implicated in chronic respiratory diseases, including COPD, asthma and pulmonary fibrosis. However, their roles in the pathogenesis of COPD are controversial and conflicting evidence exists. In the current study, we investigated the role of TLR2 and TLR4 using a model of cigarette smoke (CS)-induced experimental COPD that recapitulates the hallmark features of human disease. TLR2, TLR4, and associated coreceptor mRNA expression was increased in the airways in both experimental and human COPD. Compared with wild-type (WT) mice, CS-induced pulmonary inflammation was unaltered in TLR2-deficient (Tlr2-/-) and TLR4-deficient (Tlr4-/-) mice. CS-induced airway fibrosis, characterized by increased collagen deposition around small airways, was not altered in Tlr2-/- mice but was attenuated in Tlr4-/- mice compared with CS-exposed WT controls. However, Tlr2-/- mice had increased CS-induced emphy-sema-like alveolar enlargement, apoptosis, and impaired lung function, while these features were reduced in Tlr4-/- mice compared with CS-exposed WT controls. Taken together, these data highlight the complex roles of TLRs in the pathogenesis of COPD and suggest that activation of TLR2 and/or inhibition of TLR4 may be novel therapeutic strategies for the treatment of COPD.

Hawkins, PME, Giltrap, AM, Nagalingam, G, Britton, WJ & Payne, RJ 2018, 'Total Synthesis of Ecumicin', Organic Letters, vol. 20, no. 4, pp. 1019-1022.
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Haydon, TD, Seymour, JR & Suggett, DJ 2018, 'Soft corals are significant DMSP producers in tropical and temperate reefs', Marine Biology, vol. 165, no. 7.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Corals synthesise large quantities of the sulphur metabolite dimethylsulphoniopropionate (DMSP), which contributes to key roles in coral reef ecology including the capacity of corals to withstand various stressors. While closely related to scleractinian corals and often occupying similar ecological niche space, it is currently poorly defined to what extent soft corals produce DMSP. We, therefore, examined DMSP content within four key species of soft coral in February and July–August of 2017, including two temperate species from Sydney Harbour (Erythropodium hicksoni, Capnella gaboensis) and two tropical species from the Great Barrier Reef (Sinularia sp., Sarcophyton sp.). We compared DMSP content of these soft coral species to that of commonly occurring temperate (Plesiastrea versipora) and tropical (Acropora aspera) scleractinian coral species. DMSP content was normalised to coral protein content, with soft coral DMSP content highly variable across species and locations [56–539 nmol (mg protein)−1], and lower than for the tropical [1242–4710 nmol (mg protein)−1], but not temperate [465–1984 nmol (mg protein)−1] scleractinian species. Further comparison with previously published values demonstrated that soft coral DMSP content falls within the “low–mid range” of scleractinian corals. Notably, DMSP content was also higher in summer samples than winter samples for the scleractinian corals, but did not differ between seasons for soft corals. Such contrasting dynamics of DMSP production by soft corals compared to scleractinian corals indicates that the regulation of DMSP content differs between these two important benthic cnidarian groups, potentially as a consequence of dissimilar ecophysiological roles for this compound.

He, H, Howard, CB, Chen, Y, Wen, S, Lin, G, Zhou, J, Thurecht, KJ & Jin, D 2018, 'Bispecific Antibody-Functionalized Upconversion Nanoprobe', Analytical Chemistry, vol. 90, no. 5, pp. 3024-3029.
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© 2018 American Chemical Society. Upconversion nanoparticles (UCNPs) are new optical probes for biological applications. For specific biomolecular recognition to be realized for diagnosis and imaging, the key lies in developing a stable and easy-to-use bioconjugation method for antibody modification. Current methods are not yet satisfactory regarding conjugation time, stability, and binding efficiency. Here, we report a facile and high-yield approach based on a bispecific antibody (BsAb) free of chemical reaction steps. One end of the BsAb is designed to recognize methoxy polyethylene glycol-coated UCNPs, and the other end of the BsAb is designed to recognize the cancer antigen biomarker. Through simple vortexing, BsAb-UCNP nanoprobes form within 30 min and show higher (up to 54%) association to the target than that of the traditional UCNP nanoprobes in the ELISA-like assay. We further demonstrate its successful binding to the cancer cells with high efficiency and specificity for background-free fluorescence imaging under near-infrared excitation. This method suggests a general approach broadly suitable for functionalizing a range of nanoparticles to specifically target biomolecules.

He, H, Liu, B, Wen, S, Liao, J, Lin, G, Zhou, J & Jin, D 2018, 'Quantitative Lateral Flow Strip Sensor Using Highly Doped Upconversion Nanoparticles', Analytical Chemistry, vol. 90, no. 21, pp. 12356-12360.
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© 2018 American Chemical Society. Paper-based lateral flow assays, though being low-cost and widely used for rapid in vitro diagnostics, are indicative and do not provide sufficient sensitivity for the detection and quantification of low abundant biomarkers for early stage cancer diagnosis. Here, we design a compact device to create a focused illumination spot with high irradiance, which activates a range of highly doped 50 nm upconversion nanoparticles (UCNPs) to produce orders of magnitude brighter emissions. The device employs a very low-cost laser diode, simplified excitation, and collection optics and permits a mobile phone camera to record the results. Using highly erbium ion (Er 3+ )-doped and thulium ion (Tm 3+ )-doped UCNPs as two independent reporters on two-color lateral flow strips, new records of limit of detection (LOD), 89 and 400 pg/mL, have been achieved for the ultrasensitive detection of prostate specific antigen (PSA) and ephrin type-A receptor 2 (EphA2) biomarkers, respectively, without crosstalk. The technique and device presented in this work suggests a broad scope of low-cost, rapid, and quantitative lateral flow assays in early detection of bioanalytes.

Heffernan, AL & Hare, DJ 2018, 'Tracing Environmental Exposure from Neurodevelopment to Neurodegeneration', Trends in Neurosciences, vol. 41, no. 8, pp. 496-501.
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Interplay between genetic and environmental factors during critical time windows can have effects that span from neurodevelopment to neurodegeneration. We present the concept of the 'neuroexposome', emphasizing the brain's distinctive response to environmental exposure, and how current 'omics' sciences can inform on both disease pathogenesis and future public health policies.

Høj, L, Levy, N, Baillie, BK, Clode, PL, Strohmaier, RC, Siboni, N, Webster, NS, Uthicke, S & Bourne, DG 2018, 'Crown-of-Thorns Sea Star Acanthaster cf. solaris Has Tissue-Characteristic Microbiomes with Potential Roles in Health and Reproduction', Applied and Environmental Microbiology, vol. 84, no. 13.
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ABSTRACT Outbreaks of coral-eating crown-of-thorns sea stars (CoTS; Acanthaster species complex) cause substantial coral loss; hence, there is considerable interest in developing prevention and control strategies. We characterized the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, in which the microbiomes were highly variable among individuals. Male gonads were dominated (>97% of reads) by a single Mollicutes -related operational taxonomic unit (OTU). Detailed phylogenetic and microscopy analysis demonstrated the presence of a novel Spiroplasma -related bacterium in the spermatogenic layer. Body wall samples had high relative abundance (43 to 64% of reads) of spirochetes, likely corresponding to subcuticular symbionts reported from many echinoderms. Tube feet were characterized by Hyphomonadaceae (24 to 55% of reads). Pyloric cecal microbiomes had high alpha diversity, comprising many taxa commonly found in gastrointestinal systems. The order Oceanospirillales (genera Endozoicomonas and Kistimonas ) was detected in all tissues. A microbiome shift occurred in diseased individuals although differences between tissue ...

Ho-Le, TP, Pham, HM, Center, JR, Eisman, JA, Nguyen, HT & Nguyen, TV 2018, 'Prediction of changes in bone mineral density in the elderly: contribution of “osteogenomic profile”', Archives of Osteoporosis, vol. 13, no. 1.
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© 2018, International Osteoporosis Foundation and National Osteoporosis Foundation. Summary: The contribution of genetic variants to longitudinal bone loss has not been well documented. We constructed an “osteogenomic profile” based on 62 BMD-associated genetic variants and showed that the profile was significantly associated with bone loss, independently from baseline BMD and age. The osteogenomic profile can help predict bone loss in an individual. Introduction: The rate of longitudinal bone loss (ΔBMD) is a risk factor for fracture. The variation in ΔBMD is partly determined by genetic factors. This study sought to define the association between an osteogenomic profile and ΔBMD. Methods: The osteogenomic profile was created from 62 BMD-associated SNPs from genome-wide association studies (GWAS) that were genotyped in 1384 elderly men and women aged 60+ years. Weighted genetic risk scores (GRS) were constructed for each individual by summing the products of the number of risk alleles and the sex-specific regression coefficients [associated with BMD from GWAS]. ΔBMD, expressed as annual percent change-in-BMD, was determined by linear regression analysis for each individual who had had at least two femoral neck BMD measurements. Results: The mean ΔBMD was − 0.65% (SD 1.64%) for women and − 0.57% (SD 1.40%) for men, and this difference was not statistically significant (P = 0.32). In women, each unit increase in GRS was associated with 0.21% (SE 0.10) higher ΔBMD at the femoral neck (P = 0.036), and this association was independent of baseline BMD and age. In logistic regression analysis, each unit increase of GRS was associated with 41% odds (95%CI: 1.07–1.87) of rapid bone loss (ΔBMD ≤ − 1.2%/year; mean of rapid loss group = − 2.2%/year). There was no statistically significant association between ΔBMD and GRS in men. Conclusions: We conclude that the osteogenomic profile constructed from BMD-associated genetic variants is modestly associated with long-...

Ho-Pham, LT, Ho-Le, TP, Mai, LD, Do, TM, Doan, MC & Nguyen, TV 2018, 'Sex-difference in bone architecture and bone fragility in Vietnamese', Scientific Reports, vol. 8, no. 1.
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AbstractThis study sought to define the sex-difference in trabecular and cortical bone parameters in Vietnamese individuals. The study involved 1404 women and 864 men aged between 20 and 86 years who were recruited from Ho Chi Minh City, Vietnam. Trabecular and cortical volumetric BMD were measured at the proximal tibia and proximal radius at 4%, 38%, and 66% points, using a peripheral quantitative computed tomography XCT2000 (Stratec, Germany). Polar strength strain index was estimated from cortical bone parameters. Changes in bone parameters were assessed by the multiple linear regression model. Among individuals aged 20–39 years, women had significantly lower peak trabecular BMD at both the radius (40%) and tibia (16%) than men, but the age-related reduction in trabecular BMD were similar between two sexes. For cortical BMD, peak values in women and men were comparable, but the age-related diminution was greater in women than men. At any age, polar strength strain index in women was lower than men, and the difference was mainly attributable to cortical bone area and total bone mass. We conclude that in the elderly, sex-related difference in trabecular BMD is originated during growth, but sex-related difference in cortical BMD is determined by differential age-related bone loss.

Hoseini, SJ, Bahrami, M, Maddahfar, M, Hashemi Fath, R & Roushani, M 2018, 'Polymerization of graphene oxide nanosheet by using of aminoclay: Electrocatalytic activity of its platinum nanohybrids', Applied Organometallic Chemistry, vol. 32, no. 1, pp. e3894-e3894.
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This study describes the polymerization of graphene oxide (GO) nanosheet to reduced‐GO‐aminoclay (RGC) by covalent functionalization of chemically reactive epoxy groups on the basal planes of GO with amine groups of magnesium phyllosilicate clay (known as aminoclay). The resulting RGC sheets were characterized and applied to support platinum nanostructures at toluene/water interface. Pt nanoparticles (NPs) with diameters about several nanometers were adhered to RGC sheets by chemical reduction of [PtCl2(cod)] (cod = cis,cis‐1,5‐cyclooctadiene) complex. Catalytic activity of Pt NPs thin films were investigated in the methanol oxidation reaction. Cyclic voltammetry results exhibit that the Pt/reduced‐GO (RGO) and Pt/RGC thin films showed improved catalytic activity in methanol oxidation reaction in comparison to other Pt NPs thin films, demonstrating that the prepared Pt/RGO and Pt/RGC thin films are promising catalysts for direct methanol fuel cell.

Hoseini, SJ, Bahrami, M, Sadri, N, Aramesh, N, Fard, ZS, Iran, HR, Agahi, BH, Maddahfar, M, Dehghani, M, Arabi, AZB, Heidari, N, Fard, SFH & Moradi, Z 2018, 'Multi-metal nanomaterials obtained from oil/water interface as effective catalysts in reduction of 4-nitrophenol', Journal of Colloid and Interface Science, vol. 513, pp. 602-616.
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Hsieh, M-H, Huang, P-T, Liou, H-H, Liang, P-H, Chen, P-M, Holt, SA, Yu, IF, James, M, Shiau, Y-S, Lee, M-T, Lin, T-L & Lou, K-L 2018, 'The Penetration Depth for Hanatoxin Partitioning into the Membrane Hydrocarbon Core Measured with Neutron Reflectivity', Langmuir, vol. 34, no. 30, pp. 9036-9046.
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Hanatoxin (HaTx) from spider venom works as an inhibitor of Kv2.1 channels, most likely by interacting with the voltage sensor (VS). However, the way in which this water-soluble peptide modifies the gating remains poorly understood as the VS is deeply embedded within the bilayer, although it would change its position depending on the membrane potential. To determine whether HaTx can indeed bind to the VS, the depth at which HaTx penetrates into the POPC membranes was measured with neutron reflectivity. Our results successfully demonstrate that HaTx penetrates into the membrane hydrocarbon core (∼9 Å from the membrane surface), not lying on the membrane-water interface as reported for another voltage sensor toxin (VSTx). This difference in penetration depth suggests that the two toxins fix the voltage sensors at different positions with respect to the membrane normal, thereby explaining their different inhibitory effects on the channels. In particular, results from MD simulations constrained by our penetration data clearly demonstrate an appropriate orientation for HaTx to interact with the membranes, which is in line with the biochemical information derived from stopped-flow analysis through delineation of the toxin-VS binding interface.

Hu, P, Chen, H, McGowan, EM, Ren, N, Xu, M & Lin, Y 2018, 'Assessment of FGFR1 Over-Expression and Over-Activity in Lung Cancer Cells: A Toolkit for Anti-FGFR1 Drug Screening', Human Gene Therapy Methods, vol. 29, no. 1, pp. 30-43.
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© Copyright 2018, Mary Ann Liebert, Inc. Lung cancer, caused mainly by smoking, is one of the most prevalent diseases in China, resulting in high mortality rates. The increasing incidence of chronic disease due to lung cancer places a huge burden on the welfare and cost to the Chinese society. Amplification of the fibroblast growth factor receptor 1 (FGFR1) is associated with high incidence and mortality in lung cancer patients. FGFR1 signaling is implicated in oncogenic traits such as proliferation, cell survival, angiogenesis, and migration. Targeting FGFR1 and its ligand basic FGF (bFGF) is a key step forward in developing new therapies for this crippling disease. Lung adenocarcinoma is the most common subtype of non-small-cell lung cancer. In this study, A549, a lung adenocarcinoma cell line widely used in vitro as a model for drug metabolism and as a transfection host, was used to study FGFR1. A stable lentiviral FGFR1 over-expression system in lung cancer cells is described for the study of anti-lung cancer drug candidates targeting FGFR1. Ligand binding to FGFR1 activates the PI3K/Akt/mTOR signaling pathway and increases adhesion, invasion, and migration in this model. Using a unique FGF monoclonal antibody developed in the laboratory, the overactive PI3K pathway was effectively blocked, abrogating the negative metastatic signaling pathways in lung cancer cells. Importantly, this model provides an effective and simple screening kit for anti-FGF1 drug compounds for lung cancer treatment and a tool for understanding the molecular mechanisms of the FGFR1 signaling pathway in lung cancer. Furthermore, this toolkit based on a FGFR1 lentiviral construct model is transferrable to study FGFR1 signaling in any type of cancer cell.

Huang, S, Li, X, Li, G & Jin, D 2018, 'Effect of Bacillus thuringiensis CAB109 on the growth, development, and generation mortality of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidea)', Egyptian Journal of Biological Pest Control, vol. 28, no. 1.
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Hughes, DJ, Campbell, DA, Doblin, MA, Kromkamp, JC, Lawrenz, E, Moore, CM, Oxborough, K, Prášil, O, Ralph, PJ, Alvarez, MF & Suggett, DJ 2018, 'Roadmaps and Detours: Active Chlorophyll-a Assessments of Primary Productivity Across Marine and Freshwater Systems', Environmental Science & Technology, vol. 52, no. 21, pp. 12039-12054.
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Copyright © 2018 American Chemical Society. Assessing phytoplankton productivity over space and time remains a core goal for oceanographers and limnologists. Fast Repetition Rate fluorometry (FRRf) provides a potential means to realize this goal with unprecedented resolution and scale yet has not become the 'go-to' method despite high expectations. A major obstacle is difficulty converting electron transfer rates to equivalent rates of C-fixation most relevant for studies of biogeochemical C-fluxes. Such difficulty stems from methodological inconsistencies and our limited understanding of how the electron requirement for C-fixation (φ e,C ) is influenced by the environment and by differences in the composition and physiology of phytoplankton assemblages. We outline a 'roadmap' for limiting methodological bias and to develop a more mechanistic understanding of the ecophysiology underlying φ e,C . We 1) re-evaluate core physiological processes governing how microalgae invest photosynthetic electron transport-derived energy and reductant into stored carbon versus alternative sinks. Then, we 2) outline steps to facilitate broader uptake and exploitation of FRRf, which could transform our knowledge of aquatic primary productivity. We argue it is time to 3) revise our historic methodological focus on carbon as the currency of choice, to 4) better appreciate that electron transport fundamentally drives ecosystem biogeochemistry, modulates cell-to-cell interactions, and ultimately modifies community biomass and structure.

Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen‐Vogels, V & Suggett, DJ 2018, 'Impact of nitrogen availability upon the electron requirement for carbon fixation in Australian coastal phytoplankton communities', Limnology and Oceanography, vol. 63, no. 5, pp. 1891-1910.
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AbstractNitrogen (N) availability affects phytoplankton photosynthetic performance and regulates marine primary production (MPP) across the global coast and oceans. Bio‐optical tools including Fast Repetition Rate fluorometry (FRRf) are particularly well suited to examine MPP variability in coastal regions subjected to dynamic spatio‐temporal fluctuations in nutrient availability. FRRf determines photosynthesis as an electron transport rate through Photosystem II (ETRPSII), requiring knowledge of an additional parameter, the electron requirement for carbon fixation (KC), to retrieve rates of CO2‐fixation. KC strongly depends upon environmental conditions regulating photosynthesis, yet the importance of N‐availability to this parameter has not been examined. Here, we use nutrient bioassays to isolate how N (relative to other macronutrients P, Si) regulates KC of phytoplankton communities from the Australian coast during summer, when N‐availability is often highly variable. KC consistently responded to N‐amendment, exhibiting up to a threefold reduction and hence an apparent increase in the efficiency with which electrons were used to drive C‐fixation. However, the process driving this consistent reduction was dependent upon initial conditions. When diatoms dominated assemblages and N was undetectable (e.g., post bloom), KC decreased predominantly via a physiological adjustment of the existing community to N‐amendment. Conversely, for mixed assemblages, N‐addition achieved a similar reduction in KC through a change in community structure toward diatom domination. We generate new understanding and pa...

Huque, MH, Anderson, C, Walton, R, Woolford, S & Ryan, L 2018, 'Smooth individual level covariates adjustment in disease mapping', Biometrical Journal, vol. 60, no. 3, pp. 597-615.
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AbstractSpatial models for disease mapping should ideally account for covariates measured both at individual and area levels. The newly available “indiCAR” model fits the popular conditional autoregresssive (CAR) model by accommodating both individual and group level covariates while adjusting for spatial correlation in the disease rates. This algorithm has been shown to be effective but assumes log‐linear associations between individual level covariates and outcome. In many studies, the relationship between individual level covariates and the outcome may be non‐log‐linear, and methods to track such nonlinearity between individual level covariate and outcome in spatial regression modeling are not well developed. In this paper, we propose a new algorithm, smooth‐indiCAR, to fit an extension to the popular conditional autoregresssive model that can accommodate both linear and nonlinear individual level covariate effects while adjusting for group level covariates and spatial correlation in the disease rates. In this formulation, the effect of a continuous individual level covariate is accommodated via penalized splines. We describe a two‐step estimation procedure to obtain reliable estimates of individual and group level covariate effects where both individual and group level covariate effects are estimated separately. This distributed computing framework enhances its application in the Big Data domain with a large number of individual/group level covariates. We evaluate the performance of smooth‐indiCAR through simulation. Our results indicate that the smooth‐indiCAR method provides reliable estimates of all regression and random effect parameters. We illustrate our proposed methodology with an analysis of data on neutropenia admissions in New South Wales (NSW), Australia.

Huynh, TT, Lem, LLC, Kuramata, A, Phillips, MR & Ton-That, C 2018, 'Kinetics of charge carrier recombination in β−Ga2O3 crystals', Physical Review Materials, vol. 2, no. 10.
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© 2018 American Physical Society. Cathodoluminescence (CL) spectra were measured to determine the characteristics of luminescence bands and carrier dynamics in β-Ga2O3 bulk single crystals. The CL emission was found to be dominated by a broad UV emission peaked at 3.40 eV, which exhibits strong quenching with increasing temperature; however, its spectral shape and energy position remain virtually unchanged. We observed a superlinear increase of CL intensity with excitation density; this kinetics of carrier recombination can be explained in terms of carrier trapping and charge transfer at Fe impurity centers. The temperature-dependent properties of this UV band are consistent with weakly bound electrons in self-trapped excitons with an activation energy of 48±10meV. In addition to the self-trapped exciton emission, a blue luminescence (BL) band is shown to be related to a donor-like defect, which increases significantly in concentration after hydrogen plasma annealing. The point defect responsible for the BL, likely an oxygen vacancy, is strongly coupled to the lattice exhibiting a Huang-Rhys factor of ∼7.3.

Indigo, N, Smith, J, Webb, JK & Phillips, B 2018, 'Not such silly sausages: Evidence suggests northern quolls exhibit aversion to toads after training with toad sausages', Austral Ecology, vol. 43, no. 5, pp. 592-601.
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AbstractThe invasion of toxic cane toads (Rhinella marina) is a major threat to northern quolls (Dasyurus hallucatus) which are poisoned when they attack this novel prey item. Quolls are now endangered as a consequence of the toad invasion. Conditioned taste aversion can be used to train individual quolls to avoid toads, but we currently lack a training technique that can be used at a landscape scale to buffer entire populations from toad impact. Broad‐scale deployment requires a bait that can be used for training, but there is no guarantee that such a bait will ultimately elicit aversion to toads. Here, we test a manufactured bait – a ‘toad sausage’ – in a small captive trial, for its ability to elicit aversion to toads in northern quolls. To do this, we exposed one group of quolls to a toad sausage and another to a control sausage and compared the quolls' predatory responses when presented with a dead adult toad. Captive quolls that consumed a single toad sausage showed a reduced interest in cane toads, interacting with them for less than half the time of their untrained counterparts and showing reduced Attack behaviour. We also quantified bait uptake in the field, by both quolls and non‐target species. These field trials showed that wild quolls were the most frequent species attracted to the baits, and that approx. 61% of quolls consumed toad‐aversion baits when first encountered. Between 40% and 68% of these animals developed aversion to further bait consumption. Our results suggest that toad‐aversion sausages may be used to train wild quolls to avoid cane toads. This opens the possibility for broad‐scale quoll training with toad aversion sausages: a technique that may allow wildlife managers to prevent quoll extinctions at a landscape scale.

Irga, PJ, Barker, K & Torpy, FR 2018, 'Conservation mycology in Australia and the potential role of citizen science', Conservation Biology, vol. 32, no. 5, pp. 1031-1037.
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AbstractFungi are undoubtedly important for ecosystem functioning; however, they have been omitted or given scant attention in most biodiversity policy documents, management plans, and formal conservation schedules throughout the world. This oversight may be due to a general lack of awareness in the scientific community and compounded by a scarcity of mycology‐associated curricula at the tertiary level and a lack of mycologists in research institutions. Although molecular techniques advance the systematic cataloging of fungi and facilitate insights into fungal communities, the scarcity of professional mycologists in the environmental sciences hampers conservation efforts. Conversely, citizen science initiatives are making significant contributions to the mycology discipline by increasing awareness and extending the scope of fungal surveys. Future research by professional and amateur mycologists into the distribution of fungi and their function in ecosystems will help identify wider and more effective conservation goals.

Irga, PJ, Pettit, TJ & Torpy, FR 2018, 'The phytoremediation of indoor air pollution: a review on the technology development from the potted plant through to functional green wall biofilters', Reviews in Environmental Science and Bio/Technology, vol. 17, no. 2, pp. 395-415.
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© 2018, Springer Science+Business Media B.V., part of Springer Nature. Poor indoor air quality is a health problem of escalating magnitude, as communities become increasingly urbanised and people’s behaviours change, lending to lives spent almost exclusively in indoor environments. The accumulation of, and continued exposure to, indoor air pollution has been shown to result in detrimental health outcomes. Particulate matter penetrating into the building, volatile organic compounds (VOCs) outgassing from synthetic materials and carbon dioxide from human respiration are the main contributors to these indoor air quality concerns. Whilst a range of physiochemical methods have been developed to remove contaminants from indoor air, all methods have high maintenance costs. Despite many years of study and substantial market demand, a well evidenced procedure for indoor air bioremediation for all applications is yet to be developed. This review presents the main aspects of using horticultural biotechnological tools for improving indoor air quality, and explores the history of the technology, from the humble potted plant through to active botanical biofiltration. Regarding the procedure of air purification by potted plants, many researchers and decades of work have confirmed that the plants remove CO2 through photosynthesis, degrade VOCs through the metabolic action of rhizospheric microbes, and can sequester particulate matter through a range of physical mechanisms. These benefits notwithstanding, there are practical barriers reducing the value of potted plants as standalone air cleaning devices. Recent technological advancements have led to the development of active botanical biofilters, or functional green walls, which are becoming increasingly efficient and have the potential for the functional mitigation of indoor air pollutant concentrations.

Isaacs, SR, Kim, KW, Cheng, JX, Bull, RA, Stelzer-Braid, S, Luciani, F, Rawlinson, WD & Craig, ME 2018, 'Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples', Scientific Reports, vol. 8, no. 1, pp. 11889-11889.
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AbstractMore than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks.

Ishikawa, AA, Bordin, DM, de Campos, EG, Blanes, L, Doble, P & De Martinis, BS 2018, 'A Gas Chromatography–Mass Spectrometry Method for Toxicological Analysis of MDA, MDEA and MDMA in Vitreous Humor Samples from Victims of Car Accidents', Journal of Analytical Toxicology, vol. 42, no. 9, pp. 661-666.
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© The Author(s) 2018. Published by Oxford University Press. All rights reserved. Vitreous humor (VH) shows excellent potential as a matrix of choice for postmortem analytical toxicology due to the ease of sampling and low metabolic activity. This study demonstrates a simple and rapid analytical method to identify and quantify 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine and 3,4-methylenedioxy-ethylamphetamine in VH. Samples were collected with a simple eye puncture procedure, followed by liquid-liquid extraction and derivatization with heptafluorobutyric anhydride and analysis via gas chromatography-mass spectrometry. The accuracy of the method ranged 97-103%, intra-assay precision was between 4.54 and 9.14% relative standard deviation (RSD) and interassay precision ranged from 6.92 to 10.59% RSD. Limits of detection and quantification ranged from 1.0 to 2.5 ng/mL and 10 ng/mL, respectively. The validated method was successfully applied to detect methylenedioxyamphetamine derivatives in VH samples collected from victims of fatal car crashes.

Islam, MM, Jelocnik, M, Huston, WM, Timms, P & Polkinghorne, A 2018, 'Characterization of the In Vitro Chlamydia pecorum Response to Gamma Interferon', Infection and Immunity, vol. 86, no. 4.
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ABSTRACT Chlamydia pecorum is an important intracellular bacterium that causes a range of diseases in animals, including a native Australian marsupial, the koala. In humans and animals, a gamma interferon (IFN-γ)-mediated immune response is important for the control of intracellular bacteria. The present study tested the hypotheses that C. pecorum can escape IFN-γ-mediated depletion of host cell tryptophan pools. In doing so, we demonstrated that, unlike Chlamydia trachomatis , C. pecorum is completely resistant to IFN-γ in human epithelial cells. While the growth of C. pecorum was inhibited in tryptophan-deficient medium, it could be restored by the addition of kynurenine, anthranilic acid, and indole, metabolites that could be exploited by the gene products of the C. pecorum tryptophan biosynthesis operon. We also found that expression of trp genes was detectable only when C. pecorum was grown in tryptophan-free medium, with gene repression occurring in response to the addition of kynurenine, anthranilic acid, and indole. When grown in bovine kidney epithelial cells, bovine IFN-γ also failed to restrict the growth of C. pecorum ...

Jaffar, J, Yang, S-H, Kim, SY, Kim, H-W, Faiz, A, Chrzanowski, W & Burgess, JK 2018, 'Greater cellular stiffness in fibroblasts from patients with idiopathic pulmonary fibrosis', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 315, no. 1, pp. L59-L65.
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Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease involving degenerative breathing capacity. Fibrotic disease is driven by dysregulation in mechanical forces at the organ, tissue, and cellular level. While it is known that, in certain pathologies, diseased cells are stiffer than healthy cells, it is not known if fibroblasts derived from patients with IPF are stiffer than their normal counterparts. Using IPF patient-derived cell cultures, we measured the stiffness of individual lung fibroblasts via high-resolution force maps using atomic force microscopy. Fibroblasts from patients with IPF were stiffer and had an augmented cytoskeletal response to transforming growth factor-β1 compared with fibroblasts from donors without IPF. The results from this novel study indicate that the increased stiffness of lung fibroblasts of IPF patients may contribute to the increased rigidity of fibrotic lung tissue.

Jayaratne, HE, Wijeratne, D, Fernando, S, Kamaladasa, A, Gomes, L, Wijewickrama, A, Ogg, GS & Malavige, GN 2018, 'Regulatory T‐cells in acute dengue viral infection', Immunology, vol. 154, no. 1, pp. 89-97.
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SummaryAlthough regulatory T‐cells (Tregs) have been shown to be expanded in acute dengue, their role in pathogenesis and their relationship to clinical disease severity and extent of viraemia have not been fully evaluated. The frequency of Tregs was assessed in 56 adult patients with acute dengue by determining the proportion of forkhead box protein 3 (FoxP3) expressing CD4+ CD25+T‐cells (FoxP3+ cells). Dengue virus (DENV) viral loads were measured by quantitative real‐time polymerase chain reaction (PCR) and DENV‐specific T‐cell responses were measured by ex‐vivo interferon (IFN)‐γ enzyme‐linked immunospot (ELISPOT) assays to overlapping peptide pools of DENV‐NS3, NS1 and NS5. CD45RA and CCR4 were used to phenotype different subsets of T‐cells and their suppressive potential was assessed by their expression of cytotoxic T lymphocyte‐antigen 4 (CTLA‐4) and Fas. While the frequency of FoxP3+ cells in patients was significantly higher (P < 0·0001) when compared to healthy individuals, they did not show any relationship with clinical disease severity or the degree of viraemia. The frequency of FoxP3+ cells did not correlate with either ex‐vivo IFN‐γ DENV‐NS3‐, NS5‐ or NS1‐specific T‐cell responses. FoxP3+ cells of patients with acute dengue were predominantly CD45RA+ FoxP3low, followed by CD45RA‐FoxP3low, with only a small proportion of FoxP3+ cells being of the highly suppressive effector Treg subtype. Expression of CCR4 was also low in the majority of T‐cells, with only CCR4 only being expressed at high levels in the effector Tr...

Jenkins, C, Jelocnik, M, Micallef, ML, Galea, F, Taylor–Brown, A, Bogema, DR, Liu, M, O’Rourke, B, Chicken, C, Carrick, J & Polkinghorne, A 2018, 'An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots', Emerging Microbes & Infections, vol. 7, no. 1, pp. 1-13.
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© 2018 The Author(s). Chlamydia psittaci is an avian pathogen capable of spill-over infections to humans. A parrot C. psittaci strain was recently detected in an equine reproductive loss case associated with a subsequent cluster of human C. psittaci infections. In this study, we screened for C. psittaci in cases of equine reproductive loss reported in regional New South Wales, Australia during the 2016 foaling season. C. psittaci specific-PCR screening of foetal and placental tissue samples from cases of equine abortion (n = 161) and foals with compromised health status (n = 38) revealed C. psittaci positivity of 21.1% and 23.7%, respectively. There was a statistically significant geographical clustering of cases ~170 km inland from the mid-coast of NSW (P < 0.001). Genomic analysis and molecular typing of C. psittaci positive samples from this study and the previous Australian equine index case revealed that the equine strains from different studs in regional NSW were clonal, while the phylogenetic analysis revealed that the C. psittaci strains from both Australian equine disease clusters belong to the parrot-associated 6BC clade, again indicative of spill-over of C. psittaci infections from native Australian parrots. The results of this work suggest that C. psittaci may be a more significant agent of equine reproductive loss than thought. A range of studies are now required to evaluate (a) the exact role that C. psittaci plays in equine reproductive loss; (b) the range of potential avian reservoirs and factors influencing infection spill-over; and (c) the risk that these equine infections pose to human health.

Jessop, TS, Webb, J, Dempster, T, Feit, B & Letnic, M 2018, 'Interactions between corticosterone phenotype, environmental stressor pervasiveness and irruptive movement-related survival', Journal of Experimental Biology, vol. 221, no. 24.
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Animals use irruptive movement to avoid exposure to stochastic and pervasive environmental stressors that impact fitness. Beneficial irruptive movements transfer individuals from high-stress areas (conferring low fitness) to alternate localities that may improve survival or reproduction. However, being stochastic, environmental stressors can limit an animal's preparatory capacity to enhance irruptive movement performance. Thus individuals must rely on standing, or rapidly induced, physiological and behavioural responses. Rapid elevation of glucocorticoid hormones in response to environmental stressors are widely implicated in adjusting physiological and behaviour processes that could influence irruptive movement capacity. However, there remains little direct evidence to demonstrate that corticosterone regulated movement performance, nor the interaction with the pervasiveness of environmental stress, confers adaptive movement outcomes. Here we compared how movement-related survival of cane toads (Rhinella marina) varied with three different experimental corticosterone phenotypes across four increments of increasing environmental stressor pervasiveness (i.e. distance from water in a semi-arid landscape). Our results indicated that toads with phenotypically increased corticosterone levels attained higher movement-related survival compared to individuals with control or lowered corticosterone phenotypes. However, the effects of corticosterone phenotypes on movement-related survival to some extent co-varied with stressor pervasiveness. Thus our study demonstrates how the interplay among an individual's corticosterone phenotype and movement capacity alongside the arising costs of movement and the pervasiveness of the environmental stressor can affect survival outcomes.

Jha, SR, McDonagh, J, Prichard, R, Newton, PJ, Hickman, LD, Fung, E, Macdonald, PS & Ferguson, C 2018, '#Frailty: A snapshot Twitter report on frailty knowledge translation', Australasian Journal on Ageing, vol. 37, no. 4, pp. 309-312.
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ObjectivesThe objectives of this short report are to: (i) explore #Frailty Twitter activity over a six‐month period; and (ii) provide a snapshot Twitter content analysis of #Frailty usage.MethodsA mixed‐method study was conducted to explore Twitter data related to frailty. The primary search term was #Frailty. Objective 1: data were collected using Symplur analytics, including variables for total number of tweets, unique tweeters (users) and total number of impressions. Objective 2: a retrospectively conducted snapshot content analysis of 1500 #Frailty tweets was performed using TweetReach™.ResultsOver a six‐month period (1 January 2017–31 June 2017), there was a total of 6545 #Frailty tweets, generating 14.8 million impressions across 3986 participants. Of the 1500 tweets (814 retweets; 202 replies; 484 original tweets), 56% were relevant to clinical frailty. The main contributors (‘who’) were as follows: the public (29%), researchers (25%), doctors (21%), organisations (18%) and other allied health professionals (7%). Tweet main message intention (‘what’) was public health/advocacy (41%), social communication (28%), research‐based evidence/professional education (24%), professional opinion/case studies (15%) and general news/events (7%).ConclusionsTwitter is increasingly being used to communicate about frailty. It is important that thought leaders contribute to the conversation. There is potential to leverage Twitter to promote and disseminate frailty‐related knowledge and research.

Jin, D & Cao, J 2018, '“Perspective” – A new approach to serve our Light community', Light: Science & Applications, vol. 7, no. 1.
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Jin, D, Xi, P, Wang, B, Zhang, L, Enderlein, J & van Oijen, AM 2018, 'Nanoparticles for super-resolution microscopy and single-molecule tracking', Nature Methods, vol. 15, no. 6, pp. 415-423.
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© 2018 The Author(s). We review the use of luminescent nanoparticles in super-resolution imaging and single-molecule tracking, and showcase novel approaches to super-resolution imaging that leverage the brightness, stability, and unique optical-switching properties of these nanoparticles. We also discuss the challenges associated with their use in biological systems, including intracellular delivery and molecular targeting. In doing so, we hope to provide practical guidance for biologists and continue to bridge the fields of super-resolution imaging and nanoparticle engineering to support their mutual advancement.

Johansen, MD, de Silva, K, Plain, KM, Begg, DJ, Whittington, RJ & Purdie, AC 2018, 'Sheep and cattle exposed to Mycobacterium avium subspecies paratuberculosis exhibit altered total serum cholesterol profiles during the early stages of infection', Veterinary Immunology and Immunopathology, vol. 202, pp. 164-171.
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Pathogenic mycobacteria such as Mycobacterium tuberculosis are capable of utilising cholesterol as a primary carbon-based energy source in vitro but there has been little research examining the significance of cholesterol in vivo. Johne's disease is a chronic enteric disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). This study sought to evaluate the levels of total serum cholesterol in the host following exposure to MAP. Blood samples were collected from both sheep and cattle prior to experimental challenge with MAP and at monthly intervals post-challenge. Total serum cholesterol levels in sheep challenged with MAP were significantly elevated at 9 weeks post-inoculation (wpi) in comparison to controls. When stratified based on disease outcome, there was no significant difference in serum cholesterol at the timepoints examined between MAP exposed sheep that were susceptible and those that were resistant to Johne's disease. There was a similar elevation in serum cholesterol at 9 wpi in cattle with histopathological gut lesions associated with disease or those with an early high IFN-γ response. Total serum cholesterol in exposed cattle was significantly lower when compared to controls at 13 wpi. Taken together, these results demonstrate changes in serum cholesterol following MAP exposure and disease progression which could reflect novel aspects of the pathogenesis and immune response associated with MAP infection in both sheep and cattle.

Johansen, MD, Hortle, E, Kasparian, JA, Romero, A, Novoa, B, Figueras, A, Britton, WJ, de Silva, K, Purdie, AC & Oehlers, SH 2018, 'Analysis of mycobacterial infection-induced changes to host lipid metabolism in a zebrafish infection model reveals a conserved role for LDLR in infection susceptibility', Fish & Shellfish Immunology, vol. 83, pp. 238-242.
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Changes to lipid metabolism are well-characterised consequences of human tuberculosis infection but their functional relevance are not clearly elucidated in these or other host-mycobacterial systems. The zebrafish-Mycobacterium marinum infection model is used extensively to model many aspects of human-M. tuberculosis pathogenesis but has not been widely used to study the role of infection-induced lipid metabolism. We find mammalian mycobacterial infection-induced alterations in host Low Density Lipoprotein metabolism are conserved in the zebrafish model of mycobacterial pathogenesis. Depletion of LDLR, a key lipid metabolism node, decreased M. marinum burden, and corrected infection-induced altered lipid metabolism resulting in decreased LDL and reduced the rate of macrophage transformation into foam cells. Our results demonstrate a conserved role for infection-induced alterations to host lipid metabolism, and specifically the LDL-LDLR axis, across host-mycobacterial species pairings.

Johansen, MD, Kasparian, JA, Hortle, E, Britton, WJ, Purdie, AC & Oehlers, SH 2018, 'Mycobacterium marinum infection drives foam cell differentiation in zebrafish infection models', Developmental & Comparative Immunology, vol. 88, pp. 169-172.
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Host lipid metabolism is an important target for subversion by pathogenic mycobacteria such as Mycobacterium tuberculosis. The appearance of foam cells within the granuloma are well-characterised effects of chronic tuberculosis. The zebrafish-Mycobacterium marinum infection model recapitulates many aspects of human-M. tuberculosis infection and is used as a model to investigate the structural components of the mycobacterial granuloma. Here, we demonstrate that the zebrafish-M. marinum granuloma contains foam cells and that the transdifferentiation of macrophages into foam cells is driven by the mycobacterial ESX1 pathogenicity locus. This report demonstrates conservation of an important aspect of mycobacterial infection across species.

Johnson, GC, Pezner, AK, Sura, SA & Fong, P 2018, 'Nutrients and herbivory, but not sediments, have opposite and independent effects on the tropical macroalga, Padina boryana', Journal of Experimental Marine Biology and Ecology, vol. 507, pp. 17-22.
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Johnson, L, Tan, S, Jenkins, E, Wood, B & Marks, DC 2018, 'Characterization of biologic response modifiers in the supernatant of conventional, refrigerated, and cryopreserved platelets', Transfusion, vol. 58, no. 4, pp. 927-937.
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BACKGROUNDAlternatives to room temperature storage of platelets (PLTs) are of interest to support blood banking logistics. The aim of this study was to compare the presence of biologic response modifiers (BRMs) in PLT concentrates stored under conventional room temperature conditions with refrigerated or cryopreserved PLTs.STUDY DESIGN AND METHODSA three‐arm pool‐and‐split study was carried out using buffy coat–derived PLTs stored in 30% plasma/70% SSP+. The three matched treatment arms were as follows: room temperature (20‐24°C), cold (2‐6°C), and cryopreserved (–80°C with DMSO). Liquid‐stored PLTs were tested over a 21‐day period, while cryopreserved PLTs were tested immediately after thawing and reconstitution in 30% plasma/70% SSP+ and after storage at room temperature.RESULTSCoagulation factor activity was comparable between room temperature and cold PLTs, with the exception of protein S, while cryopreserved PLTs had reduced Factor (F)V and FVIII activity. Cold‐stored PLTs retained α‐granule proteins better than room temperature or cryopreserved PLTs. Cryopreservation resulted in 10‐fold higher microparticle generation than cold‐stored PLTs, but both groups contained significantly more microparticles than those stored at room temperature. The supernatant from both cold and cryopreserved PLTs initiated faster clot formation and thrombin generation than room temperature PLTs.CONCLUSIONCold storage and cryopreservation alter the composition of the soluble fraction of stored PLTs. These differences in coagulation proteins, cytokines, and microparticles likely influence both the hemostatic capacity of the components and the auxiliary functions.

Johnson, TG, Schelch, K, Cheng, YY, Williams, M, Sarun, KH, Kirschner, MB, Kao, S, Linton, A, Klebe, S, McCaughan, BC, Lin, RCY, Pirker, C, Berger, W, Lasham, A, van Zandwijk, N & Reid, G 2018, 'Dysregulated Expression of the MicroRNA miR-137 and Its Target YBX1 Contribute to the Invasive Characteristics of Malignant Pleural Mesothelioma', Journal of Thoracic Oncology, vol. 13, no. 2, pp. 258-272.
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© 2017 International Association for the Study of Lung Cancer Introduction: Malignant pleural mesothelioma (MPM) is an aggressive malignancy linked to asbestos exposure. On a genomic level, MPM is characterized by frequent chromosomal deletions of tumor suppressors, including microRNAs. MiR-137 plays a tumor suppressor role in other cancers, so the aim of this study was to characterize it and its target Y-box binding protein 1 (YBX1) in MPM. Methods: Expression, methylation, and copy number status of miR-137 and its host gene MIR137HG were assessed by polymerase chain reaction. Luciferase reporter assays confirmed a direct interaction between miR-137 and Y-box binding protein 1 gene (YBX1). Cells were transfected with a miR-137 inhibitor, miR-137 mimic, and/or YBX1 small interfering RNA, and growth, colony formation, migration and invasion assays were conducted. Results: MiR-137 expression varied among MPM cell lines and tissue specimens, which was associated with copy number variation and promoter hypermethylation. High miR-137 expression was linked to poor patient survival. The miR-137 inhibitor did not affect target levels or growth, but interestingly, it increased miR-137 levels by means of mimic transfection suppressed growth, migration, and invasion, which was linked to direct YBX1 downregulation. YBX1 was overexpressed in MPM cell lines and inversely correlated with miR-137. RNA interference–mediated YBX1 knockdown significantly reduced cell growth, migration, and invasion. Conclusions: MiR-137 can exhibit a tumor-suppressive function in MPM by targeting YBX1. YBX1 knockdown significantly reduces tumor growth, migration, and invasion of MPM cells. Therefore, YBX1 represents a potential target for novel MPM treatment strategies.

Jolly, CJ, Kelly, E, Gillespie, GR, Phillips, B & Webb, JK 2018, 'Out of the frying pan: Reintroduction of toad‐smart northern quolls to southern Kakadu National Park', Austral Ecology, vol. 43, no. 2, pp. 139-149.
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AbstractInvasive species are a leading cause of native biodiversity loss. In Australia, the toxic, invasive cane toad Rhinella marina has caused massive and widespread declines of northern quolls Dasyurus hallucatus. Quolls are fatally poisoned if they mistakenly prey on adult toads. To prevent the extinction of this native dasyurid from the Top End, an insurance population was set up in 2003 on two toad‐free islands in Arnhem Land. In 2015, quolls were collected from one of these islands (Astell) for reintroduction. We used conditioned taste aversion to render 22 of these toad‐naïve quolls toad averse. Seven quolls received no taste aversion training. The source island was also predator‐free, so all quolls received very basic predator‐aversion training. In an attempt to re‐establish the mainland population, we reintroduced these 29 northern quolls into Kakadu National Park in northern Australia where cane toads have been established for 13 years. The difference in survival between toad‐averse and toad‐naive quolls was immediately apparent. Toad‐naive quolls were almost all killed by toads within 3 days. Toad‐averse quolls, on the other hand, not only survived longer but also were recorded mating. Our predator training, however, was far less effective. Dingo predation accounted for a significant proportion of toad‐smart quoll mortality. In Kakadu, dingoes have been responsible for high levels of quoll predation in the past and reintroduced animals are often vulnerable to predation‐mediated population extinction. Dingoes may also be more effective predators in fire degraded landscapes. Together, these factors could explain the extreme predation mortality that we witnessed. In addition, predator aversion may have been lost from the predator‐free island populations. These possibilities are not mutually exclusive but need to be investigated because they have clear bearing...

Jolly, CJ, Webb, JK & Phillips, BL 2018, 'The perils of paradise: an endangered species conserved on an island loses antipredator behaviours within 13 generations', Biology Letters, vol. 14, no. 6, pp. 20180222-20180222.
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When imperilled by a threatening process, the choice is often made to conserve threatened species on offshore islands that typically lack the full suite of mainland predators. While keeping the species extant, this releases the conserved population from predator-driven natural selection. Antipredator traits are no longer maintained by natural selection and may be lost. It is implicitly assumed that such trait loss will happen slowly, but there are few empirical tests. In Australia, northern quolls ( Dasyurus hallucatus ) were moved onto a predator-free offshore island in 2003 to protect the species from the arrival of invasive cane toads on the mainland. We compared the antipredator behaviours of wild-caught quolls from the predator-rich mainland with those from this predator-free island. We compared the responses of both wild-caught animals and their captive-born offspring, to olfactory cues of two of their major predators (feral cats and dingoes). Wild-caught, mainland quolls recognized and avoided predator scents, as did their captive-born offspring. Island quolls, isolated from these predators for only 13 generations, showed no recognition or aversion to these predators. This study suggests that predator aversion behaviours can be lost very rapidly, and that this may make a population unsuitable for reintroduction to a predator-rich mainland.

Jowett, LA, Howe, ENW, Wu, X, Busschaert, N & Gale, PA 2018, 'New Insights into the Anion Transport Selectivity and Mechanism of Tren‐based Tris‐(thio)ureas', Chemistry – A European Journal, vol. 24, no. 41, pp. 10475-10487.
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AbstractThe anion transport properties of a series of previously reported tren‐based anionophores have been revisited using new assays designed to measure anion uniport. This study provides new insights into the transport mechanism and selectivity of this important class of transporters. Specifically, we report the chloride and nitrate transport selectivity of these systems and quantify sulfate transport to determine EC50 values for sulfate transport for the first time. Two new assays were developed to study bicarbonate transport allowing accurate quantification of chloride/bicarbonate exchange.

Kabakova, IV, Azuri, I, Chen, Z, Nayak, PK, Snaith, HJ, Kronik, L, Paterson, C, Bakulin, AA & Egger, DA 2018, 'The Effect of Ionic Composition on Acoustic Phonon Speeds in Hybrid Perovskites from Brillouin Spectroscopy and Density Functional Theory', Journal of Materials Chemistry C, vol. 6, no. 15, pp. 3861-3868.
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Hybrid organic-inorganic perovskites (HOIPs) have recently emerged as highlypromising solution-processable materials for photovoltaic (PV) and otheroptoelectronic devices. HOIPs represent a broad family of materials withproperties highly tuneable by the ions that make up the perovskite structure aswell as their multiple combinations. Interestingly, recent high-efficiency PVdevices using HOIPs with substantially improved long-term stability have usedcombinations of different ionic compositions. The structural dynamics of thesesystems are unique for semiconducting materials and are currently argued to becentral to HOIPs stability and charge-transport properties. Here, we studiedthe impact of ionic composition on phonon speeds of HOIPs from Brillouinspectroscopy experiments and density functional theory calculations forFAPbBr$_3$, MAPbBr$_3$, MAPbCl$_3$, and the mixed halideMAPbBr$_{1.25}$Cl$_{1.75}$. Our results show that the acoustic phonon speedscan be strongly modified by ionic composition, which we explain by analysingthe lead-halide sublattice in detail. The vibrational properties of HOIPs aretherefore tuneable by using targeted ionic compositions in the perovskitestructure. This tuning can be rationalized with non-trivial effects, forexample, considering the influence of the shape and dipole moment of organiccations. This has an important implication to further improvements in thestability and charge-transport properties of these systems.

Kanniah, KD, Tan, KP, Cracknell, AP, Huete, AR, Idris, NH, Lau, AMS, Abd Rahman, MZ, Rasib, AW & Ahmad, A 2018, 'Assessment of biophysical properties of Royal Belum tropical forest, Malaysia', Singapore Journal of Tropical Geography, vol. 39, no. 1, pp. 90-106.
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The Royal Belum forest reserve is one of the oldest tropical rainforests in the world and it is one of the largest virgin forest reserves in Malaysia. However, not many studies have been conducted to understand the ecology of this forest. In this study we estimated the aboveground biomass (AGB) of the forest using diameter at breast height (DBH) and height of trees (h), tree species and hemispherical photographs of tree canopy. We estimated AGB using five allometric equations. Our results demonstrated that the AGB given by the one tree species specific allometric equation does not show any significant differences from the values given by the non‐tree species specific allometric equations at tree and plot levels. The AGB of Intsia bijuga species, Koompassia malaccensis species and Shorea genera were comparatively higher, owing to their greater wood density, DBH and h. This has added importance because some of these species are categorized as threatened species. Our results demonstrated that mean AGB values in this forest (293.16 t ha‐1) are the highest compared to some studies of other areas in Malaysia, tropical Africa and tropical Bazilian Amazonia, implying that the Royal Belum forest reserve, is an important carbon reservoir.

Karami, A, Karbalaei, S, Ebrahimi, M, Ismail, A, Jahromi, MF, Simpson, SL, Eghtesadi Araghi, P, Lim, RP & Liang, JB 2018, 'Changes in nutritional values induced by butachlor in juvenile diploid and triploid Clarias gariepinus', International Journal of Environmental Science and Technology, vol. 15, no. 10, pp. 2117-2128.
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© 2017, Islamic Azad University (IAU). There is a paucity of information about the effects of environmental stressors on nutritional values in fish. This study investigated the effects of the organochlorine pesticide, butachlor, on key indicators of nutritional value in both diploid and triploid African catfish (Clarias gariepinus). Amino acids (AA), fatty acids (FA), and the proximate composition (protein, lipid, moisture, and ash content) in the white muscle of full-sibling juvenile fish were measured following a 21-day exposure to graded butachlor concentrations [mean measured: 26.3, 48.4, and 66.1 µg/L]. No significant differences in AAs, FAs, protein, lipid, moisture, or ash content were observed between unexposed diploid and triploid fish. In diploids, exposure to butachlor significantly altered the concentrations of some of the AAs and FAs, and protein content, when compared to the control group. In triploid fish, however, butachlor treatments had no effect on the AA or proximate composition, but significantly changed the concentration of two individual FAs in the muscle. Butachlor treatments showed fewer changes in the nutritional values of triploid fish. This research is the first to study the nutritional values in any polyploid animals following the exposure to a contaminant.

Kaur, A, Shimoni, O & Wallach, M 2018, 'Novel screening test for celiac disease using peptide functionalised gold nanoparticles', World Journal of Gastroenterology, vol. 24, no. 47, pp. 5379-5390.
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© The Author(s) 2018. Published by Baishideng Publishing Group Inc. All rights reserved. AIM To develop a screening test for celiac disease based on the coating of gold nanoparticles with a peptide sequence derived from gliadin, the protein that triggers celiac disease. METHODS 20 nm gold nanoparticles were first coated with NeutrAvidin. A long chain Polyethylene glycol (PEG) linker containing Maleimide at the Ω-end and Biotin group at the α-end was used to ensure peptide coating to the gold nanoparticles. The maleimide group with the thiol (-SH) side chain reacted with the cysteine amino acid in the peptide sequence and the biotinylated and PEGylated peptide was added to the NeutrAvidin coated gold nanoparticles. The peptide coated gold nanoparticles were then converted into a serological assay. We used the peptide functionalised gold nanoparticle-based assay on thirty patient serum samples in a blinded assessment and compared our results with the previously run serological and pathological tests on these patients. RESULTS A stable colloidal suspension of peptide coated gold nanoparticles was obtained without any aggregation. An absorbance peak shift as well as color change was caused by the aggregation of gold nanoparticles following the addition of anti-gliadin antibody to peptide coated nanoparticles at levels associated with celiac disease. The developed assay has been shown to detect anti-gliadin antibody not only in quantitatively spiked samples but also in a small-scale study on real non-hemolytic celiac disease patient’s samples. CONCLUSION The study demonstrates the potential of gold nanoparticle-peptide based approach to be adapted for developing a screening assay for celiac disease diagnosis. The assay could be a part of an exclusion based diagnostic strategy and prove particularly useful for testing high celiac disease risk populations.

KC, R, Shukla, SD, Gautam, SS, Hansbro, PM & O’Toole, RF 2018, 'The role of environmental exposure to non‐cigarette smoke in lung disease', Clinical and Translational Medicine, vol. 7, no. 1, pp. 39-12.
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AbstractChronic exposure to household indoor smoke and outdoor air pollution is a major contributor to global morbidity and mortality. The majority of these deaths occur in low and middle‐income countries. Children, women, the elderly and people with underlying chronic conditions are most affected. In addition to reduced lung function, children exposed to biomass smoke have an increased risk of developing lower respiratory tract infections and asthma‐related symptoms. In adults, chronic exposure to biomass smoke, ambient air pollution, and opportunistic exposure to fumes and dust are associated with an increased risk of developing chronic bronchitis, chronic obstructive pulmonary disease (COPD), lung cancer and respiratory infections, including tuberculosis. Here, we review the evidence of prevalence of COPD in people exposed to non‐cigarette smoke. We highlight mechanisms that are likely involved in biomass‐smoke exposure‐related COPD and other lung diseases. Finally, we summarize the potential preventive and therapeutic strategies for management of COPD induced by non‐cigarette smoke exposure.

Kelly, E, Phillips, BL & Webb, JK 2018, 'Taste overshadows less salient cues to elicit food aversion in endangered marsupial', Applied Animal Behaviour Science, vol. 209, pp. 83-87.
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© 2018 Elsevier B.V. Conditioned taste aversion is an emerging conservation tool that can be used to limit inter-species conflict, for example decreasing predation on endangered species, or limiting the consumption of invasive toxic prey. Typically, managers wish to elicit an aversion that will be associated with visual or odour cues so that the target species maintains an “arm's length” relationship, and does not have to attack or taste the prey. Combining multiple cues in conditioned taste aversion can cause cue overshadowing, so reducing the effectiveness of the training. Here, we examine the northern quoll (Dasyurus hallucatus), a carnivorous marsupial threatened because they attack the toxic invasive cane toad (Rhinella marina). Conditioned taste aversion has been suggested as a way to reduce quoll's predation on toads, but for training to be effective it must elicit an aversion to stimuli before the quolls attack the toad. Using baits containing distinct novel meat, odour and visual cues, we test whether quolls will generalise their aversion to visual or odour cues. We found that quolls associate their aversion with the compound stimulus of meat taste and meat odour, and that this overshadows the less salient artificial odour and visual cues. Quolls ate 87% of taste cue substituted baits, compared to 38% and 42% of the odour and visual cue substituted baits respectively, which represented a significant interaction between bait type and substituted cue (χ2(4) = 14.70, p = 0.005). We show that although quolls do not generalise their aversions to novel artificial stimuli, they can distinguish subtle visual and odour cues in meat that still elicit an aversion without them needing to attack and taste prey.

Kendig, MD, Fu, MX, Rehn, S, Martire, SI, Boakes, RA & Rooney, KB 2018, 'Metabolic and cognitive improvement from switching to saccharin or water following chronic consumption by female rats of 10% sucrose solution', Physiology & Behavior, vol. 188, pp. 162-172.
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High consumption of sugar-sweetened beverages (SSBs) is a risk factor for weight gain and metabolic disease. Whether this risk is reduced by switching to 'diet' beverages containing low-calorie sweeteners (LCS) is controversial. Two experiments modeled whether a switch from SSB to LCS beverages produced positive outcomes on behavioral and metabolic measures. Both experiments consisted of a Stage 1, in which adult female rats received unrestricted access to 10% sucrose solution in addition to chow and water for 4 (Experiment 1) or 8 weeks (Experiment 2). In Stage 2 rats were switched to either saccharin (Suc-Sacch) or water (Suc-Water) or remained on 10% sucrose (Suc-Suc) for a further 4 (Experiment 1) or 7 weeks (Experiment 2). Experiment 2 contained a fourth group that was maintained on water throughout (Water-Water). In both experiments energy intake and weight gain in Stage 2 was reduced for Suc-Sacch and Suc-Water groups relative to the Suc-Suc groups and at cull the Suc-Suc groups showed poorer insulin sensitivity and greater g/kg fat than Suc-Water and Suc-Sacch groups. In Experiment 2 short-term place recognition memory was impaired at the end of Stage 1 but recovered to a similar extent in the Suc-Water and Suc-Sacch groups; when the latter groups were compared with the Water-Water group, recovery was found to be essentially complete. A higher saccharin concentration in Experiment 2 than in Experiment 1 increased absolute amounts of saccharin ingested but intake solution volumes remained low. These results show that switching from sucrose to either water or saccharin produces equivalent improvements on both metabolic and cognitive measures.

Khuu, A, Chadwick, S, Moret, S, Spindler, X, Gunn, P & Roux, C 2018, 'Impact of one-step luminescent cyanoacrylate treatment on subsequent DNA analysis', Forensic Science International, vol. 286, pp. 1-7.
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© 2018 Elsevier B.V. Fingermarks can be exploited for both their ridge detail and touch DNA. One-step luminescent cyanoacrylate (CA) fuming techniques used for fingermark enhancement, such as PolyCyano UV (Foster + Freeman Ltd) and Lumicyano™ (Crime Science Technology), claim to be compatible with DNA analysis as they reduce the need for post‐staining to increase contrast of the developed fingermark. The aim of this study was to determine the impact that these one-step luminescent cyanoacrylates have on DNA analysis and how they compare to conventional CA techniques. Four donors each deposited five sets of natural fingermarks, to which a known amount of washed saliva cells was dispensed onto half of each set of fingermarks. Each set was treated with either a conventional CA technique or a one‐step luminescent CA technique prior to collection and processing of DNA, with one set left as a non-fumed control. It was found that DNA was still recoverable and detectable following each of the treatments. Lumicyano™ had a similar impact on DNA profiles as conventional CA fuming and with post‐stain, however, the degradation effect of PolyCyano UV on DNA was greater than the conventional treatments. For quantities of DNA such as that from touch DNA, the use of PolyCyano UV to enhance fingermarks may impact subsequent DNA analysis by causing allele drop out at larger fragment sizes.

Kianinia, M, Bradac, C, Nguyen, M, Zhu, T, Toth, M, Oliver, R & Aharonovich, I 2018, 'Resonant excitation of quantum emitters in gallium nitride', Optica, vol. 5, no. 8, pp. 932-932.
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Kim, ASI & Wand, MP 2018, 'On expectation propagation for generalised, linear and mixed models', Australian & New Zealand Journal of Statistics, vol. 60, no. 1, pp. 75-102.
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SummaryExpectation propagation is a general approach to deterministic approximate Bayesian inference for graphical models, although its literature is confined mostly to machine learning applications. We investigate the utility of expectation propagation in generalised, linear, and mixed model settings. We show that, even though the algebra and computations are complicated, the notion of message passing on factor graphs affords streamlining of the required calculations and we list the algorithmic steps explicitly. Numerical studies indicate expectation propagation is marginally more accurate than a competing method for the models considered, but at the expense of bigger algebraic and computational overheads.

Kim, JS, Staicu, A-M, Maity, A, Carroll, RJ & Ruppert, D 2018, 'Additive Function-on-Function Regression', Journal of Computational and Graphical Statistics, vol. 27, no. 1, pp. 234-244.
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© 2018 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America. We study additive function-on-function regression where the mean response at a particular time point depends on the time point itself, as well as the entire covariate trajectory. We develop a computationally efficient estimation methodology based on a novel combination of spline bases with an eigenbasis to represent the trivariate kernel function. We discuss prediction of a new response trajectory, propose an inference procedure that accounts for total variability in the predicted response curves, and construct pointwise prediction intervals. The estimation/inferential procedure accommodates realistic scenarios, such as correlated error structure as well as sparse and/or irregular designs. We investigate our methodology in finite sample size through simulations and two real data applications. Supplementary material for this article is available online.

Kim, M, Brodersen, KE, Szabó, M, Larkum, AWD, Raven, JA, Ralph, PJ & Pernice, M 2018, 'Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri', Photosynthesis Research, vol. 136, no. 2, pp. 147-160.
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© 2017, Springer Science+Business Media B.V. Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C3 and C4, or other CO2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.

Kim, RY, Ng, AM, Persaud, AK, Furmanek, SP, Kothari, YN, Price, JD, Wiemken, TL, Saad, MA, Guardiola, JJ & Cavallazzi, RS 2018, 'Antibiotic Timing and Outcomes in Sepsis', The American Journal of the Medical Sciences, vol. 355, no. 6, pp. 524-529.
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Kim, S, Fröch, JE, Christian, J, Straw, M, Bishop, J, Totonjian, D, Watanabe, K, Taniguchi, T, Toth, M & Aharonovich, I 2018, 'Photonic Crystal Cavities from Hexagonal Boron Nitride', Nature Communications, vol. 9, no. 1, pp. 2623-2623.
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Development of scalable quantum photonic technologies requires on-chipintegration of components such as photonic crystal cavities and waveguides withnonclassical light sources. Recently, hexagonal boron nitride (hBN) has emergedas a promising platform for nanophotonics, following reports of hyperbolicphonon-polaritons and optically stable, ultra-bright quantum emitters. However,exploitation of hBN in scalable, on-chip nanophotonic circuits, quantuminformation processing and cavity quantum electrodynamics (QED) experimentsrequires robust techniques for the fabrication of monolithic opticalresonators. In this letter, we design and engineer high quality photoniccrystal cavities from hBN. We employ two approaches based on a focused ion beammethod and a minimally-invasive electron beam induced etching (EBIE) techniqueto fabricate suspended two dimensional (2D) and one dimensional (1D) cavitieswith quality (Q) factors in excess of 2,000. Subsequently, we showdeterministic, iterative tuning of individual cavities by direct-write,single-step EBIE without significant degradation of the Q-factor. Thedemonstration of tunable, high Q cavities made from hBN is an unprecedentedadvance in nanophotonics based on van der Waals materials. Our results and hBNprocessing methods open up promising new avenues for solid-state systems withapplications in integrated quantum photonics, polaritonics and cavity QEDexperiments.

Kim, S, Toth, M & Aharonovich, I 2018, 'Design of photonic microcavities in hexagonal boron nitride', Beilstein Journal of Nanotechnology, vol. 9, no. 1, pp. 102-108.
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We propose and design photonic crystal cavities (PCCs) in hexagonal boron nitride (hBN) for diverse photonic and quantum applications. Two dimensional (2D) hBN flakes contain quantum emitters which are ultra-bright and photostable at room temperature. To achieve optimal coupling of these emitters to optical resonators, fabrication of cavities from hBN is therefore required to maximize the overlap between cavity optical modes and the emitters. Here, we design 2D and 1D PCCs using anisotropic indices of hBN. The influence of underlying substrates and material absorption are investigated, and spontaneous emission rate enhancements are calculated. Our results are promising for future quantum photonic experiments with hBN.

King, SR, Gentle, AR, Cortie, MB & McDonagh, AM 2018, 'On the Development of Optical Properties during Thermal Coarsening of Gold Nanoparticle Composites', The Journal of Physical Chemistry C, vol. 122, no. 22, pp. 12098-12105.
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© 2018 American Chemical Society. The changes in optical properties that occur as gold nanoparticles (AuNPs) are thermally converted to a continuous thin film were studied with the purpose of determining the roles of particle coarsening and temperature. In situ reflectance spectroscopy, electron microscopy, and synchrotron X-ray diffraction (XRD) were applied to provide complementary information on the changes in particle size and shape. The AuNPs studied were stabilized with 1-butanethiol, 1-octanethiol, oleylamine (OA), or 4-(pyren-1-yl)butane-1-thiol (PyBuSH). Initially, the films were dark brown or purple because of the plasmon resonance of the AuNPs. As the temperature was increased, the AuNPs started to coalesce and percolate, thereby changing the color of the films to that of bulk gold. Films of AuNPs stabilized with alkanethiols sintered very rapidly, measured as a rapid change in the reflectance spectrum. In contrast, films of AuNPs stabilized with OA or PyBuSH sintered more gradually and at a higher temperature. This permitted the transition to be studied in greater detail than for the alkanethiols. Red-shifted plasmon peaks and increased intensity in the reflectance data and XRD and electron microscopy measurements revealed that a prolonged process of nanoparticle coarsening occurred prior to sintering. The effect of temperature on the optical properties was isolated by monitoring samples as they cooled. The insulator-to-metal transition in these types of composites offers a very flexible platform for controlling spectral properties in the near-infrared region.

Klingberg, J, Shimmon, R, Philp, M, Tahtouh, M, Nic Daeid, N & Fu, S 2018, 'Evaluating the use of Differential Scanning Calorimetry for the analysis of illicit substances and their adulterants', Journal of Forensic Investigation, vol. 6, no. 1, pp. 8-8.

Knauer, J, Zaehle, S, Medlyn, BE, Reichstein, M, Williams, CA, Migliavacca, M, De Kauwe, MG, Werner, C, Keitel, C, Kolari, P, Limousin, J & Linderson, M 2018, 'Towards physiologically meaningful water‐use efficiency estimates from eddy covariance data', Global Change Biology, vol. 24, no. 2, pp. 694-710.
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AbstractIntrinsic water‐use efficiency (iWUE) characterizes the physiological control on the simultaneous exchange of water and carbon dioxide in terrestrial ecosystems. Knowledge of iWUE is commonly gained from leaf‐level gas exchange measurements, which are inevitably restricted in their spatial and temporal coverage. Flux measurements based on the eddy covariance (EC) technique can overcome these limitations, as they provide continuous and long‐term records of carbon and water fluxes at the ecosystem scale. However, vegetation gas exchange parameters derived from EC data are subject to scale‐dependent and method‐specific uncertainties that compromise their ecophysiological interpretation as well as their comparability among ecosystems and across spatial scales. Here, we use estimates of canopy conductance and gross primary productivity (GPP) derived from EC data to calculate a measure of iWUE (G1, “stomatal slope”) at the ecosystem level at six sites comprising tropical, Mediterranean, temperate, and boreal forests. We assess the following six mechanisms potentially causing discrepancies between leaf and ecosystem‐level estimates of G1: (i) non‐transpirational water fluxes; (ii) aerodynamic conductance; (iii) meteorological deviations between measurement height and canopy surface; (iv) energy balance non‐closure; (v) uncertainties in net ecosystem exchange partitioning; and (vi) physiological withi...

Kondaveeti, S, Bueno, PVDA, Carmona-Ribeiro, AM, Esposito, F, Lincopan, N, Sierakowski, MR & Petri, DFS 2018, 'Microbicidal gentamicin-alginate hydrogels', Carbohydrate Polymers, vol. 186, pp. 159-167.
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Kondaveeti, S, Semeano, ATS, Cornejo, DR, Ulrich, H & Petri, DFS 2018, 'Magnetic hydrogels for levodopa release and cell stimulation triggered by external magnetic field', Colloids and Surfaces B: Biointerfaces, vol. 167, pp. 415-424.
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Koolaji, N, Rawling, T, Bourget, K & Murray, M 2018, 'Carboxylate Analogues of Aryl‐Urea‐Substituted Fatty Acids That Target the Mitochondria in MDA‐MB‐231 Breast Cancer Cells to Promote Cell Death', ChemMedChem, vol. 13, no. 10, pp. 1036-1043.
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AbstractSelective targeting of the tumor cell mitochondrion is a viable approach for the development of anticancer agents because the organelle is functionally different from the mitochondria of normal cells. We recently developed a novel aryl‐urea fatty acid, 16({[4‐chloro‐3‐(trifluoromethyl)phenyl]carbamoyl}amino)hexadecanoic acid (1) that was found to disrupt mitochondria and to activate apoptosis in MDA‐MB‐231 breast cancer cells. However, there is currently little information on the structural requirements for the activity of compound 1 analogues. The present study evaluated the role of the carboxylic acid group on the anticancer activity of 1. Bioisosteric replacement of the carboxylate in 1 maintained activity. Thus, like 1, the sulfonic acid analogue 1‐SA and the oxo‐thiadiazole analogue 1‐OT were also found to target the mitochondrion and to activate cell killing capacity. The hydroxamic acid analogue 1‐HA also killed MDA‐MB‐231 cells, but its onset of action was slower than that of 1‐SA and 1‐OT. In contrast, replacement of the carboxylate with non‐bioisosteric amido and methylamido groups produced analogues that minimally altered mitochondrial function and showed little capacity to decrease tumor cell viability. These findings suggest that the carboxylate moiety in the novel mitochondrially targeted agent 1 is an important determinant of the kinetics and efficacy of anticancer cell activities of compound 1 analogues. Further development of carboxylate‐modified analogues of aryl‐urea fatty acids as potential anticancer agents could now be warranted.

Kordzakhia, NE, Kutoyants, YA, Novikov, AA & Hin, L-Y 2018, 'On limit distributions of estimators in irregular statistical models and a new representation of fractional Brownian motion', Statistics & Probability Letters, vol. 139, pp. 141-151.
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© 2018 Elsevier B.V. We provide new results concerning the limit distributions of Bayesian estimators (BE) and maximum likelihood estimators (MLE) of location parameters of cusp-type signals in “signal plus white noise” models. The limit distributions of BE and MLE are expressed in terms of fractional Brownian motion (fBm) with the Hurst parameter H, 0

Kota, A, Deshpande, DA, Haghi, M, Oliver, B & Sharma, P 2018, 'Autophagy and airway fibrosis: Is there a link?', F1000Research, vol. 6, pp. 409-409.
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In the past decade, an emerging process named “autophagy” has generated intense interest in many chronic lung diseases. Tissue remodeling and fibrosis is a common feature of many airway diseases, and current therapies do not prevent or reverse these structural changes. Autophagy has evolved as a conserved process for bulk degradation and recycling of cytoplasmic components to maintain basal cellular homeostasis and healthy organelle populations in the cell. Furthermore, autophagy serves as a cell survival mechanism and can also be induced by chemical and physical stress to the cell. Accumulating evidence demonstrates that autophagy plays an essential role in vital cellular processes, including tissue remodeling. This review will discuss some of the recent advancements made in understanding the role of this fundamental process in airway fibrosis with emphasis on airway remodeling, and how autophagy can be exploited as a target for airway remodeling in asthma and chronic obstructive pulmonary disease.

Kounalakis, M, Dickel, C, Bruno, A, Langford, NK & Steele, GA 2018, 'Tuneable hopping and nonlinear cross-Kerr interactions in a high-coherence superconducting circuit', npj Quantum Information, vol. 4, no. 1.
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AbstractAnalog quantum simulations offer rich opportunities for exploring complex quantum systems and phenomena through the use of specially engineered, well-controlled quantum systems. A critical element, increasing the scope and flexibility of such experimental platforms, is the ability to access and tune in situ different interaction regimes. Here, we present a superconducting circuit building block of two highly coherent transmons featuring in situ tuneable photon hopping and nonlinear cross-Kerr couplings. The interactions are mediated via a nonlinear coupler, consisting of a large capacitor in parallel with a tuneable superconducting quantum interference device (SQUID). We demonstrate the working principle by experimentally characterising the system in the single-excitation and two-excitation manifolds, and derive a full theoretical model that accurately describes our measurements. Both qubits have high coherence properties, with typical relaxation times in the range of 15 to 40 μs at all bias points of the coupler. Our device could be used as a scalable building block in analog quantum simulators of extended Bose-Hubbard and Heisenberg XXZ models, and may also have applications in quantum computing such as realising fast two-qubit gates and perfect state transfer protocols.

Kramer, T, Noack, M, Reimers, JR, Reinefeld, A, Rodríguez, M & Yin, S 2018, 'Energy flow in the Photosystem I supercomplex: Comparison of approximative theories with DM-HEOM', Chemical Physics, vol. 515, pp. 262-271.
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© 2018 Elsevier B.V. We analyze the exciton dynamics in Photosystem I from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Förster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results.

Krix, DW & Murray, BR 2018, 'Landscape variation in plant leaf flammability is driven by leaf traits responding to environmental gradients', Ecosphere, vol. 9, no. 2, pp. e02093-e02093.
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AbstractLandscape differences in environmental conditions select for divergences among plant species in strategically important leaf traits such as leaf mass per area (LMA) and leaf area (LA). Interspecific variation in some of these same leaf traits has been associated to varying degrees with differences among species in leaf flammability, including the attributes ignitibility, sustainability, and combustibility. Yet, how environmentally selected variation in leaf traits drives variation in leaf flammability at landscape scales remains largely unknown. Here, we compared leaf traits and flammability attributes between species of sheltered forest vegetation (low light, moist habitat) and plant species of exposed woodland vegetation (high light, dry habitat) in a fire‐prone landscape of south‐eastern Australia. We found that leaves of sheltered forest species were significantly more flammable via both higher ignitibility and combustibility compared with exposed woodland species. These significant differences in leaf ignitibility and combustibility were underpinned by sheltered forest species having leaves with significantly larger LA and lower LMA compared with exposed woodland species. Further, multiple regression analyses revealed that both LA and LMA were significantly and uniquely related to faster time to ignition (TTI; ignitibility) and higher mean mass loss rate (combustibility). Most notably, although significantly higher fuel moisture content (FMC) of leaves of sheltered forest species si...

Kroon, SJ, Ravel, J & Huston, WM 2018, 'Cervicovaginal microbiota, women's health, and reproductive outcomes', Fertility and Sterility, vol. 110, no. 3, pp. 327-336.
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© 2018 American Society for Reproductive Medicine The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.

Kumar, C, Verma, S, Singh, B, Haque, A, Satija, S & Vyas, M 2018, 'A review on conventional and modern techniques to develop Orodispersible films', Asian Journal of Pharmaceutics, vol. 12, pp. S433-S438.
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Nowadays, solubility of active pharmaceutical ingredient (API) is one of the biggest challenges faced by the researchers during the development of pharmaceutical oral dosage form. Developing a new molecule is very expensive than formulating a dosage form of existing API. Orodispersible film (ODF) is one of the alternatives for the conventional dosage form as it dissolves and directly absorbed from the mouth. It is suitable for the delivery of poorly soluble drugs. It does not require water for the administration and gives quick absorption and high bioavailability. There are various techniques that can be used to improve the solubility of poorly soluble drugs in ODFs, namely, surfactants, superdisintegrants, and printing technology. Water-soluble polymers are used as the film former, but the different concentration and different combination of polymers and use of various additives like surfactant; superdisintegrants can show the significant effect on the solubility. It can be used for both local and systemic action. ODFs are gaining popularity and are widely accepted by the consumers, but it is still lacking in some areas due to the absence of pharmacopoeial specifications for disintegration, mechanical properties, etc.

Kumar, R, Arjuna, A, Diksha, Gupta, R, Mahajan, S, Satija, S & Mehta, M 2018, 'In vitro antioxidant and antimicrobial activity of polyherbal formulation', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 80-84.
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Context: Antioxidants play a major role in protecting the body against oxidative stress that is associated with many chronic diseases and disorders including chronic wounds. Plants are the richest source for antioxidant and are effective in the management of oxidative stress, caused by free radical damage. Wound healing and antimicrobial potential are also attributed to the antioxidant potential of drugs. Aim: The aim of this study is to carry out the antioxidant and antimicrobial activity of given polyherbal formulation (PHF) to correlate with the wound healing potential of the formulation. Materials and Methods: Antioxidant potential of the PHF was evaluated by the 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method. Agar well diffusion method was used to determine its antimicrobial activity against the Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Klebsiella aerogenes. Results: Results of the study demonstrated that PHF exhibited significant antioxidant activity. Antibacterial activity of polyherbal formula was evaluated against the four pathogenic microorganisms in which it showed mild-to-moderate antimicrobial activity against the E. coli and K. aerogenes, while mild antimicrobial activity against the P. aeruginosa and P. vulgaris. Conclusion: Results of this study suggested that PHF can be used for the treatment of wound infections due to its marked antioxidant and antimicrobial activity.

Kumar, R, Kumar, R, Anand, A, Mahajan, R, Khatik, GL, Duggal, N, Mehta, M, Satija, S, Sharma, N & Khurana, N 2018, 'Potential of prediction of activity spectra of substances software to justify 3Rs ethics for in Vivo anti-Alzheimer’s studies of phytochemicals', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 66-72.
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Context: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder having important concern in today’s society. The prediction of activity spectra of substances (PASS) software allows prediction of the pharmacological activity on behalf of canonical simplified molecular-input line-entry system (SMILES) of the substance. PASS predicted the activity of substances in two manners, i.e. probable activity (Pa) and probable inactivity. Objective: In this study, we elaborated the benefit of PASS to define 3Rs ethics (replacement, reduction, and refinement) in animal study for anti-Alzheimer’s activities of phytochemicals. Materials and Methods: Pa values of different phytochemicals important for AD predicted using PASS. For the prediction of activity in the different targets of AD, canonical SMILES of phytochemicals was obtained from PubChem website. Results and Discussion: Based on these Pa values predicted for different target sites of AD, screening of pharmacologically important phytochemicals was performed so that those phytochemicals can be further explored for in vivo pharmacological activity against AD to justify the 3Rs ethics. Conclusion: PASS online software provides an informative data to support the reported activities of the phytochemicals.

Kumari, N & Srivastava, A 2018, 'Harmonization and comparative evaluation of evapotranspiration estimates in data scarce conditions', Indian Journal of Ecology, vol. 45, no. 2, pp. 305-310.
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For efficient irrigation water management and hydro-meteorological studies at both the field and catchment scales, a need exists to evaluate the existing évapotranspiration (ET) estimation methods under varied physiographical and data availability conditions. With the limited availability of meteorological variables at basin-scale in many remote areas, ET estimation is becoming a challenging task. There is a scope to test the ET methods by FAO-56 PM method, the benchmark method with Hargreaves raw model. All of them were inter-compared by taking its basin average. Further, FAO-56 PM and Hargreaves raw model were harmonized by daily and monthly correction factor (C, ) for five year period and was verified by using statistical indicators namely, index of agreement (d) and Pearson correlation coefficient (r) as well as graphical indicators. The harmonized estimators of less data intensive methods relative to FAO PM provides satisfactory results in all six stations after applying the correction factor.

Kuppusamy, R, Yasir, M, Berry, T, Cranfield, CG, Nizalapur, S, Yee, E, Kimyon, O, Taunk, A, Ho, KKK, Cornell, B, Manefield, M, Willcox, M, Black, DS & Kumar, N 2018, 'Design and synthesis of short amphiphilic cationic peptidomimetics based on biphenyl backbone as antibacterial agents', European Journal of Medicinal Chemistry, vol. 143, pp. 1702-1722.
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© 2017 Elsevier Masson SAS Antimicrobial peptides (AMPs) and their synthetic mimics have received recent interest as new alternatives to traditional antibiotics in attempts to overcome the rise of antibiotic resistance in many microbes. AMPs are part of the natural defenses of most living organisms and they also have a unique mechanism of action against bacteria. Herein, a new series of short amphiphilic cationic peptidomimetics were synthesized by incorporating the 3′-amino-[1,1′-biphenyl]-3-carboxylic acid backbone to mimic the essential properties of natural AMPs. By altering hydrophobicity and charge, we identified the most potent analogue 25g that was active against both Gram-positive Staphylococcus aureus (MIC = 15.6 μM) and Gram-negative Escherichia coli (MIC = 7.8 μM) bacteria. Cytoplasmic permeability assay results revealed that 25g acts primarily by depolarization of lipids in cytoplasmic membranes. The active compounds were also investigated for their cytotoxicity to human cells, lysis of lipid bilayers using tethered bilayer lipid membranes (tBLMs) and their activity against established biofilms of S. aureus and E. coli.

Kuriakose, S, Ahmed, T, Balendhran, S, Collis, GE, Bansal, V, Aharonovich, I, Sriram, S, Bhaskaran, M & Walia, S 2018, 'Effects of plasma-treatment on the electrical and optoelectronic properties of layered black phosphorus', Applied Materials Today, vol. 12, pp. 244-249.
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© 2018 Elsevier Ltd Exfoliated few-layer black-phosphorus (BP) has been explored for a variety of electrical and optoelectronic applications. Plasma-assisted thinning of BP has emerged as an exciting pathway to achieve BP crystals of desired thickness. However, to fully realise the true potential of plasma-assisted thinning of BP and other emerging 2D materials, it is critical to understand the effects of different plasma environments on the electrical and optoelectronic properties of the resultant material. Here, we investigate the influence of Ar and O2plasma on the electrical and optoelectronic properties of plasma-treated BP flakes. It is revealed that by manipulating the environment under which BP is exposed to the plasma, it is possible to engineer defects that lead to new photoluminescence (PL) emission peaks without compromising the switching ratios or carrier mobilities of BP-based field effect transistors (FETs). Overall, our study finds the use of O2plasma as a more suitable approach to retain and enrich the intrinsic (opto)electronic properties of BP. Additionally, our study, for the first time, experimentally reveals the ability of BP to respond to UV excitation.

Kusrini, E, Hashim, F, Gunawan, C, Mann, R, Azmi, WNNWN & Amin, NM 2018, 'Anti-amoebic activity of acyclic and cyclic-samarium complexes on Acanthamoeba', Parasitology Research, vol. 117, no. 5, pp. 1409-1417.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. This work investigated the anti-amoebic activity of two samarium (Sm) complexes, the acyclic complex [bis(picrato)(pentaethylene glycol)samarium(III)] picrate—referred to as [Sm(Pic)2(EO5)](Pic)—and the cyclic complex [bis(picrato)(18-crown-6)samarium(III)] picrate—referred to as [Sm(Pic)2(18C6)](Pic). Both Sm complexes caused morphological transformation of the protozoa Acanthamoeba from its native trophozoite form carrying a spine-like structure called acanthopodia, to round-shaped cells with loss of the acanthopodia structure, a trademark response to environmental stress. Further investigation, however, revealed that the two forms of the Sm complexes exerted unique cytotoxicity characteristics. Firstly, the IC50 of the acyclic complex (0.7 μg/mL) was ~ 10-fold lower than IC50 of the cyclic Sm complex (6.5 μg/mL). Secondly, treatment of the Acanthamoeba with the acyclic complex caused apoptosis of the treated cells, while the treatment with the cyclic complex caused necrosis evident by the leakage of the cell membrane. Both treatments induced DNA damage in Acanthamoeba. Finally, a molecular docking simulation revealed the potential capability of the acyclic complex to form hydrogen bonds with profilin—a membrane protein present in eukaryotes, including Acanthamoeba, that plays important roles in the formation and degradation of actin cytoskeleton. Not found for the cyclic complex, such potential interactions could be the underlying reason, at least in part, for the much higher cytotoxicity of the acyclic complex and also possibly, for the observed differences in the cytotoxicity traits. Nonetheless, with IC50 values of < 10 μg/mL, both the acyclic and cyclic Sm complexes feature a promising potential as cytotoxic agents to fight amoebic infections.

Kusrini, E, Wicaksono, B, Yulizar, Y, Prasetyanto, EA & Gunawan, C 2018, 'Textile Dye Removal from Aqueous Solution using Modified Graphite Waste/Lanthanum/Chitosan Composite', IOP Conference Series: Materials Science and Engineering, vol. 316, no. 1, pp. 012029-012029.
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© Published under licence by IOP Publishing Ltd. We investigated various pre-treatment processes of graphite waste using thermal, mechanical and chemical methods. The aim of this work is to study the performance of modified graphite waste/lanthanum/chitosan composite (MG) as adsorbent for textile dye removal from aqueous solution. Effect of graphite waste resources, adsorbent size and lanthanum concentration on the dye removal were studied in batch experiments. Selectivity of MG was also investigated. Pre-heated graphite waste (NMG) was conducted at 80°C for 1 h, followed by mechanical crushing of the resultant graphite to 75 μm particle size, giving adsorption performance of ∼58%, ∼67%, ∼93% and ∼98% of the model dye rhodamine B (concentration determined by UV-vis spectroscopy at 554 nm), methyl orange (464 nm), methylene blue (664 nm) and methyl violet (580 nm), respectively from aqueous solution. For this process, the system required less than ∼5 min for adsorbent material to be completely saturated with the adsorbate. Further chemical modification of the pre-treated graphite waste (MG) with lanthanum (0.01 - V 0.03 M) and chitosan (0.5% w/w) did not improve the performance of dye adsorption. Under comparable experimental conditions, as those of the 'thermal-mechanical-pre-treated-only' (NMG), modification of graphite waste (MG) with 0.03 M lanthanum and 0.5% w/w chitosan resulted in ∼14%, ∼47%, ∼72% and ∼85% adsorption of rhodamine B, methyl orange, methylene blue and methyl violet, respectively. Selective adsorption of methylene blue at most to ∼79%, followed by methyl orange, methyl violet and rhodamine B with adsorption efficiency ∼67, ∼38, and ∼9% sequentially using MG with 0.03 M lanthanum and 0.5% w/w chitosan.

Kusrini, E, Wicaksono, W, Gunawan, C, Daud, NZA & Usman, A 2018, 'Kinetics, mechanism, and thermodynamics of lanthanum adsorption on pectin extracted from durian rind', Journal of Environmental Chemical Engineering, vol. 6, no. 5, pp. 6580-6588.
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The rare-earth elements in aqueous waste streams have received great attention due to their potential to pollute the environment. Lanthanum is one of the most used rare-earth elements in industries and disposed as waste. Several efforts have been devoted to remove lanthanum from waste water systems. This study was focused on the adsorption of lanthanum from aqueous solutions by using pectin extracted from durian rind, which is home and industrial waste of durian fruit. Adsorption experiments were carried out in batch method, and the effects of contact time, initial concentration of lanthanum ion, pH of medium, pectin dosage, and temperature on the adsorption efficiency were investigated. The kinetics, mechanism, and thermodynamics of lanthanum adsorption on the pectin were also evaluated. The results demonstrated that the pectin as a cost-effective biosorbent could remove lanthanum with efficiency as high as 41.2 mg/g (at the optimum conditions: pH 4.0, 25 °C, 90 min). The adsorption process of lanthanum on the pectin is well described by either Freundlich or Temkin isotherm model, indicating that adsorption occurs mainly on multilayers and heterogeneous surfaces of pectin. Thermodynamic quantities suggested that the adsorption of lanthanum on the pectin was exothermic and spontaneous, and the reaction was feasible. We also showed that the spent adsorbent can be regenerated up to a limited number of times, upon strong base treatment.

Laiolo, L, Matear, R, Baird, ME, Soja-Woźniak, M & Doblin, MA 2018, 'Information content of in situ and remotely sensed chlorophyll-a: Learning from size-structured phytoplankton model', Journal of Marine Systems, vol. 183, pp. 1-12.
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© 2018 Chlorophyll-a measurements in the form of in situ observations and satellite ocean colour products are commonly used in data assimilation to calibrate marine biogeochemical models. Here, a two size-class phytoplankton biogeochemical model, with a 0D configuration, was used to simulate the surface chlorophyll-a dynamics (simulated surface Chl-a) for cyclonic and anticyclonic eddies off East Australia. An optical model was then used to calculate the inherent optical properties from the simulation and convert them into remote-sensing reflectance (Rrs). Subsequently, Rrs was used to produce a satellite-like estimate of the simulated surface Chl-a concentrations through the MODIS OC3M algorithm (simulated OC3M Chl-a). Identical parameter optimisation experiments were performed through the assimilation of the two separate datasets (simulated surface Chl-a and simulated OC3M Chl-a), with the purpose of investigating the contrasting information content of simulated surface Chl-a and remotely-sensed data sources. The results we present are based on the analysis of the distribution of a cost function, varying four parameters of the biogeochemical model. In our idealized experiments the simulated OC3M Chl-a product is a poor proxy for the total simulated surface Chl-a concentration. Furthermore, our result show the OC3M algorithm can underestimate the simulated chlorophyll-a concentration in offshore eddies off East Australia (Case I waters), because of the weak relationship between large-sized phytoplankton and remote-sensing reflectance. Although Case I waters are usually characteristic of oligotrophic environments, with a photosynthetic community typically represented by relatively small-sized phytoplankton, mesoscale features such as eddies can generate seasonally favourable conditions for a photosynthetic community with a greater proportion of large phytoplankton cells. Furthermore, our results show that in mesoscale features such as eddies, in situ ch...

Lan, C, Peng, H, McGowan, EM, Hutvagner, G & Li, J 2018, 'An isomiR expression panel based novel breast cancer classification approach using improved mutual information', BMC Medical Genomics, vol. 11, no. S6, pp. 118-118.
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BACKGROUND:Gene expression-based profiling has been used to identify biomarkers for different breast cancer subtypes. However, this technique has many limitations. IsomiRs are isoforms of miRNAs that have critical roles in many biological processes and have been successfully used to distinguish various cancer types. Biomarker isomiRs for identifying different breast cancer subtypes has not been investigated. For the first time, we aim to show that isomiRs are better performing biomarkers and use them to explain molecular differences between breast cancer subtypes. RESULTS:In this study, a novel method is proposed to identify specific isomiRs that faithfully classify breast cancer subtypes. First, as a null hypothesis method we removed the lowly expressed isomiRs from small sequencing data generated from diverse breast cancers types. Second, we developed an improved mutual information-based feature selection method to calculate the weight of each isomiR expression. The weight of isomiR measures the importance of a given isomiR in classifying breast cancer subtypes. The improved mutual information enables to apply the dataset in which the feature is continuous data and label is discrete data; whereby, the traditional mutual information cannot be applied in this dataset. Finally, the support vector machine (SVM) classifier is applied to find isomiR biomarkers for subtyping. CONCLUSIONS:Here we demonstrate that isomiRs can be used as biomarkers in the identification of different breast cancer subtypes, and in addition, they may provide new insights into the diverse molecular mechanisms of breast cancers. We have also shown that the classification of different subtypes of breast cancer based on isomiRs expression is more effective than using published gene expression profiling. The proposed method provides a better performance outcome than Fisher method and Hellinger method for discovering biomarkers to distinguish different breast cancer subtypes. This novel techniqu...

Larkin, BP, Glastras, SJ, Chen, H, Pollock, CA & Saad, S 2018, 'DNA methylation and the potential role of demethylating agents in prevention of progressive chronic kidney disease', The FASEB Journal, vol. 32, no. 10, pp. 5215-5226.
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© 2018 American Society for Biochemistry and Molecular Biology Inc. All rights reserved. Chronic kidney disease (CKD) is a global epidemic, and itsmajor risk factors include obesity and type 2 diabetes. Obesity not only promotes metabolic dysregulation and the development of diabetic kidney disease but alsomay independently lead to CKD by a variety ofmechanisms, including endocrine andmetabolic dysfunction, inflammation, oxidative stress, altered renal hemodynamics, and lipotoxicity. Deleterious renal effects of obesity can also be transmitted from one generation to the next, and it is increasingly recognized that offspring of obese mothers are predisposed to CKD. Epigenetic modifications are changes that regulate gene expression without altering theDNAsequence.Of these,DNAmethylation is the most studied. Epigenetic imprints, particularlyDNA methylation, are laid down during critical periods of fetal development, and they may provide a mechanism by whichmaternal-fetal transmissionof chronic diseaseoccurs.Ourcurrent review explores the evidence for the role of DNAmethylationinthedevelopment ofCKD,diabetickidneydisease,diabetes, andobesity.DNAmethylationhas been implicated in renal fibrosis-the final pathophysiologic pathway in the development of end-stage kidney disease-which supports the notion that demethylating agentsmay play a potential therapeutic role in preventing development and progression of CKD.

Larkum, AWD, Ritchie, RJ & Raven, JA 2018, 'Living off the Sun: chlorophylls, bacteriochlorophylls and rhodopsins', Photosynthetica, vol. 56, no. SPECIAL ISSUE, pp. 11-43.
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Larsson, M, Laczka, O, Harwood, D, Lewis, R, Himaya, S, Murray, S & Doblin, M 2018, 'Toxicology of Gambierdiscus spp. (Dinophyceae) from Tropical and Temperate Australian Waters', Marine Drugs, vol. 16, no. 1, pp. 7-7.
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Ciguatera Fish Poisoning (CFP) is a human illness caused by the consumption of marine fish contaminated with ciguatoxins (CTX) and possibly maitotoxins (MTX), produced by species from the benthic dinoflagellate genus Gambierdiscus. Here, we describe the identity and toxicology of Gambierdiscus spp. isolated from the tropical and temperate waters of eastern Australia. Based on newly cultured strains, we found that four Gambierdiscus species were present at the tropical location, including G. carpenteri, G. lapillus and two others which were not genetically identical to other currently described species within the genus, and may represent new species. Only G. carpenteri was identified from the temperate location. Using LC-MS/MS analysis we did not find any characterized microalgal CTXs (P-CTX-3B, P-CTX-3C, P-CTX-4A and P-CTX-4B) or MTX-1; however, putative maitotoxin-3 (MTX-3) was detected in all species except for the temperate population of G. carpenteri. Using the Ca2+ influx SH-SY5Y cell Fluorescent Imaging Plate Reader (FLIPR) bioassay we found CTX-like activity in extracts of the unidentified Gambierdiscus strains and trace level activity in strains of G. lapillus. While no detectable CTX-like activity was observed in tropical or temperate strains of G. carpenteri, all species showed strong maitotoxin-like activity. This study, which represents the most comprehensive analyses of the toxicology of Gambierdiscus strains isolated from Australia to date, suggests that CFP in this region may be caused by currently undescribed ciguatoxins and maitotoxins.

Larsson, ME, Laczka, OF, Suthers, IM, Ajani, PA & Doblin, MA 2018, 'Hitchhiking in the East Australian Current: rafting as a dispersal mechanism for harmful epibenthic dinoflagellates', Marine Ecology Progress Series, vol. 596, pp. 49-60.
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© Inter-Research 2018. Due to their small size, planktonic marine microorganisms have large dispersal capacity in the global ocean. However, it is not known how epibenthic microalgae disperse across long distances because they are generally associated with a substrate. In this study, we examined a long-term data series (~50 yr) of microalgal composition from a coastal station in southeast Australia for the presence of epibenthic dinoflagellates in the plankton. In addition, we collected drifting macrophytes (i.e. macroalgae and seagrass) and plastic debris from the East Australian Current, identified the associated microalgal assemblage, assessed their viability, and used phylogenetic analyses to taxonomically identify cryptic harmful epibenthic dinoflagellate species. We found no occurrences of epibenthic dinoflagellates from the genera Gambierdiscus, Fukuyoa, Ostreopsis, and Coolia at the long-term coastal station, concluding that entrainment of cells in ocean currents is an unlikely mechanism for transport of these taxa. The epibenthic microalgal communities associated with macrophyte rafts and plastic debris were primarily comprised of diatom taxa. However, intact cells of potentially harmful epibenthic dinoflagellates from the genera Coolia, Amphidinium, and Prorocentrum were also observed, and their viability was confirmed by division of isolated cells and establishment into clonal cultures. Phylogenetic analyses confirmed the presence of C. palmyrensis on a drifting Sargassum sp. raft, the first report of this potentially harmful epibenthic species in temperate Australian waters. This study shows that epibenthic dinoflagellates can attach to, and remain viable, when associated with macrophyte fragments that drift in the open ocean, therefore revealing rafting as a potential vector for dispersal of these organisms.

Lawson, CA, Raina, J, Kahlke, T, Seymour, JR & Suggett, DJ 2018, 'Defining the core microbiome of the symbiotic dinoflagellate, Symbiodinium', Environmental Microbiology Reports, vol. 10, no. 1, pp. 7-11.
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SummaryDinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α‐proteobacterium Labrenzia and the γ‐proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.

Lebender, LF, Prünte, L, Rumzhum, NN & Ammit, AJ 2018, 'Selectively targeting prostanoid E (EP) receptor-mediated cell signalling pathways: Implications for lung health and disease', Pulmonary Pharmacology & Therapeutics, vol. 49, pp. 75-87.
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Arachidonic acid is metabolized by cyclooxygenases (COX-1 and COX-2) into various prostanoids which exert different functions in mammalian physiology. One of these prostanoids, prostaglandin E2 (PGE2), interacts with four different G protein-coupled receptors, named EP1, EP2, EP3 and EP4, to initiate different downstream signalling pathways. Prostanoid receptors are diversely expressed throughout different tissues all over the body and PGE2 is responsible for a large variety of beneficial and disadvantageous effects. We have recently achieved a greater understanding of the biology of prostanoid E receptors and the potential for specific drug targeting with the advent of potent and selective EP receptor agonists and antagonists. This has important implications for lung health and disease as PGE2-mediated EP receptor activation impacts upon migration of airway smooth muscle cells, airway microvascular leak, tone regulation of pulmonary blood vessels, mast cell degranulation, bronchodilatation, cough, angiogenesis and airway inflammation, to name a few. In this review, we overview the EP receptor family and the related signalling pathways, summarize a variety of EP1-4 receptor agonists and antagonists, provide an overview of pharmacological tools used to implicate EP receptor function in the context of respiratory health and disease and finally highlight some of the more selective pharmacological reagents that have recently been developed. The availability of selective pharmacological agonists and antagonists for the distinct EP receptors, as well as the development of specific prostanoid receptor knock-out mice, offer hitherto unattainable opportunities for achieving an in depth understanding of the role and function of PGE2 in respiratory disease and the exciting potential of targeting EP receptors more broadly.

Leclaire, NA, Li, M, Véron, AC, Neels, A, Heier, J, Reimers, JR & Nüesch, FA 2018, 'Cyanine platelet single crystals: growth, crystal structure and optical spectra', Physical Chemistry Chemical Physics, vol. 20, no. 46, pp. 29166-29173.
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Micro transmittance spectroscopy of ultrathin crystalline organic salt semiconductors reveals strong low-energy and weak high-energy bands polarized along the crystallographic b- and c-axis. While the excitonic coupling pattern explains the occurrence of polarized bands, the observed intensities are opposite of expectations based on chromophore alignment within the crystal.

Lee, AS, White, E, Monahan, LG, Jensen, SO, Chan, R & van Hal, SJ 2018, 'Defining the Role of the Environment in the Emergence and Persistence of vanA Vancomycin-Resistant Enterococcus (VRE) in an Intensive Care Unit: A Molecular Epidemiological Study', Infection Control & Hospital Epidemiology, vol. 39, no. 6, pp. 668-675.
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OBJECTIVETo describe the transmission dynamics of the emergence and persistence of vanA vancomycin-resistant enterococcus (VRE) in an intensive care unit (ICU) using whole-genome sequencing of patient and environmental isolates.DESIGNRetrospective cohort study.SETTINGICU in a tertiary referral center.PARTICIPANTSPatients admitted to the ICU over an 11-month period.METHODSVanA VRE isolated from patients (n=31) were sequenced using the Illumina MiSeq platform. Environmental samples from bed spaces, equipment, and waste rooms were collected. All vanA VRE-positive environmental samples (n=14) were also sequenced. Data were collected regarding patient ward and bed movements.RESULTSThe 31 patient vanA VRE isolates were from screening (n=19), urine (n=4), bloodstream (n=3), skin/wound (n=3), and intra-abdominal (n=2) sources. The phylogeny from sequencing data confirmed several VRE clusters, with 1 group accounting for 38 of 45 isolates (84%). Within this cluster, cross-transmission was extensive and complex across the ICU. Directionality indicated that colonized patients contaminated environmental sites. Similarly, environmental sources not only led to patient colonization but also to infection. Notably, shared equipment acte...

Lees, T, Shad-Kaneez, F, Simpson, AM, Nassif, NT, Lin, Y & Lal, S 2018, 'Heart Rate Variability as a Biomarker for Predicting Stroke, Post-stroke Complications and Functionality', Biomarker Insights, vol. 13, pp. 117727191878693-117727191878693.
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Background: Heart rate variability (HRV) is a non-invasive measure of the function of the autonomic nervous system, and its dynamic nature may provide a means through which stroke and its associated complications may be predicted, monitored, and managed. Objective: The objective of this review is to identify and provide a critique on the most recent uses of HRV in stroke diagnosis/management and highlight areas that warrant further research. Methods: The MEDLINE, CINAHL, and OVID MEDLINE databases were canvassed using a systematic search strategy, for articles investigating the use of HRV in stroke diagnosis and management. Initial paper selections were based on title alone, and final paper inclusion was informed by a full-text critical appraisal. Results: The systematic search returned 98 records, of which 51 were unique. Following screening, 22 records were included in the final systematic review. The included papers provided some information regarding predicting incident stroke, which largely seems to be best predicted by time- and frequency-domain HRV parameters. Furthermore, post-stroke complications and functionality are similarly predicted by time- and frequency-domain parameters, as well as non-linear parameters in some instances. Conclusions: Current research provides good evidence that HRV parameters may have utility as a biomarker for stroke and for post-stroke complications and/or functionality. Future research would benefit from the integration of non-linear, and novel parameters, the hybridisation of HRV parameters, and the expansion of the utilisation of predictive regression and hazard modelling.

Leiper, I, Zander, KK, Robinson, CJ, Carwadine, J, Moggridge, BJ & Garnett, ST 2018, 'Quantifying current and potential contributions of Australian indigenous peoples to threatened species management', Conservation Biology, vol. 32, no. 5, pp. 1038-1047.
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AbstractFormal engagement of indigenous peoples in conservation is increasing globally and leads to multiple benefits to communities while contributing to national and international biodiversity goals and obligations. This and ongoing declines in biodiversity have led to calls to increase opportunities for indigenous people to engage in managing their estates. However, there is no overarching understanding of indigenous peoples’ involvement in conservation, which limits the identification of new opportunities. We amalgamated information across governments and large nongovernmental organizations in the megadiverse country of Australia to quantify the involvement of indigenous people in management of threatened species. We identified 153 Australian‐based projects undertaken by different indigenous groups around the nation in 2015 and 2016 that included explicit funds for management of threatened species or threatened ecosystems. Most were in remote parts of western and northern Australia. Almost one‐quarter of all threatened animals and 2% of threatened plants were the subject of some formal conservation action by indigenous people. Occurrence records for 1574 threatened species showed that 823 (89.2%) of 923 species recorded on indigenous peoples’ lands were not listed in management projects. This gap may represent new opportunities for conservation initiatives. Because at least 59.5% of Australia's threatened species occur on indigenous peoples’ lands, efforts to build appropriate and effective indigenous conservation alliances are vital. However, it is also important to recognize that threatened species are part of complex social, ecological, economic and cultural systems, and to achieve successful outcomes requires consideration of indigenous peoples’ priorities, rights, and obligations and relationships with their traditionally owned land and sea.

Lenzini, F, Poddubny, AN, Titchener, J, Fisher, P, Boes, A, Kasture, S, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 2018, 'Direct characterization of a nonlinear photonic circuit’s wave function with laser light', Light: Science & Applications, vol. 7, no. 1, pp. 17143-17143.
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AbstractIntegrated photonics is a leading platform for quantum technologies including nonclassical state generation1, 2, 3, 4, demonstration of quantum computational complexity5 and secure quantum communications6. As photonic circuits grow in complexity, full quantum tomography becomes impractical, and therefore an efficient method for their characterization7, 8 is essential. Here we propose and demonstrate a fast, reliable method for reconstructing the two-photon state produced by an arbitrary quadratically nonlinear optical circuit. By establishing a rigorous correspondence between the generated quantum state and classical sum-frequency generation measurements from laser light, we overcome the limitations of previous approaches for lossy multi-mode devices9, 10. We applied this protocol to a multi-channel nonlinear waveguide network and measured a 99.28±0.31% fidelity between classical and quantum characterization. This technique enables fast and precise evaluation of nonlinear quantum photonic networks, a crucial step towards complex, large-scale, device production.

Li, C, Zang, R, Li, P, Man, Z, Wang, S, Li, X, Wu, Y, Liu, S & Wang, G 2018, 'High Crystalline Prussian White Nanocubes as a Promising Cathode for Sodium‐ion Batteries', Chemistry – An Asian Journal, vol. 13, no. 3, pp. 342-349.
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AbstractPrussian blue and its analogues (PBAs) have been recognized as one of the most promising cathode materials for room‐temperature sodium‐ion batteries (SIBs). Herein, we report high crystalline and Na‐rich Prussian white Na2CoFe(CN)6 nanocubes synthesized by an optimized and facile co‐precipitation method. The influence of crystallinity and sodium content on the electrochemical properties was systematically investigated. The optimized Na2CoFe(CN)6 nanocubes exhibited an initial capacity of 151 mA h g−1, which is close to its theoretical capacity (170 mA h g−1). Meanwhile, the Na2CoFe(CN)6 cathode demonstrated an outstanding long‐term cycle performance, retaining 78 % of its initial capacity after 500 cycles. Furthermore, the Na2CoFe(CN)6 Prussian white nanocubes also achieved a superior rate capability (115 mA h g−1 at 400 mA g−1, 92 mA h g−1 at 800 mA g−1). The enhanced performances could be attributed to the robust crystal structure and rapid transport of Na ions through large channels in the open‐framework. Most noteworthy, the as‐prepared Na2CoFe(CN)6 nanocubes are not only low‐cost in raw materials but also contain a rich sodium content (1.87 Na ions per lattice unit cell), which will be favorable for full cell fabrication and large‐scale electric storage applications.

Li, D, Wen, S, Sun, W, Zhang, J, Jin, D, Peng, C, Shen, M & Shi, X 2018, 'One-Step Loading of Gold and Gd₂O₃ Nanoparticles within PEGylated Polyethylenimine for Dual Mode Computed Tomography/Magnetic Resonance Imaging of Tumors', ACS Applied Bio Materials, vol. 1, no. 2, pp. 221-225.
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We report here a facile method for one-step loading of gold (Au) and gadolinium oxide (Gd2O3) nanoparticles (NPs) within polyethylenimine (PEI) premodified with polyethtylene glycol (PEG) for dual mode computed tomography (CT) and magnetic resonance (MR) imaging of tumors. PEGylated PEI was used as a template to complex Au(III) and Gd(III) salts, followed by sodium borohydride reduction and acetylation of remaining PEI surface amines to generate the hybrid PEI@Au/Gd2O3 NPs. The hybrid NPs exhibit a remarkable colloidal stability and cytocompatibility and possess a high X-ray attenuation efficacy and r1 relaxivity, enabling their uses for dual mode CT/MR imaging of tumors.

Li, G, Saad, S, Oliver, BG & Chen, H 2018, 'Heat or Burn? Impacts of Intrauterine Tobacco Smoke and E-Cigarette Vapor Exposure on the Offspring’s Health Outcome', Toxics, vol. 6, no. 3, pp. 43-43.
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Maternal smoking during pregnancy leads to gestational complications and organ disorders in the offspring. As nicotine replacement therapy is often ineffective for smoking cessation, pregnant women turn to alternatives such as heat-not-burn tobacco and e-cigarettes. Recently, the popularly of e-cigarettes has been increasing especially among the youth and pregnant women, mainly due to the advertisements claiming their safety. This has even led to some clinicians recommending their use during pregnancy. E-cigarettes heat e-liquid to produce an aerosol (e-vapor), delivering flavorings and nicotine to the user. However, e-vapor also contains toxins such as formaldehyde along with heavy metals and carcinogenic nitrosamines. In addition, specific flavoring compounds such as diacetyl can be toxic themselves or decompose into toxic compounds such as benzaldehydes. These compounds can induce toxicity, inflammation and oxidative stress in the mothers and can accumulate in the developing fetus, affecting intrauterine development. Recent animal studies suggest that maternal e-vapor exposure during pregnancy could cause respiratory and neurological disorders in the offspring. This review will examine the available literature to shed light on the current understanding of this problem-to-be from lessons learned in animal models.

Li, H, Staudenmayer, J, Wang, T, Keadle, SK & Carroll, RJ 2018, 'Three‐part joint modeling methods for complex functional data mixed with zero‐and‐one–inflated proportions and zero‐inflated continuous outcomes with skewness', Statistics in Medicine, vol. 37, no. 4, pp. 611-626.
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We take a functional data approach to longitudinal studies with complex bivariate outcomes. This work is motivated by data from a physical activity study that measured 2 responses over time in 5‐minute intervals. One response is the proportion of time active in each interval, a continuous proportions with excess zeros and ones. The other response, energy expenditure rate in the interval, is a continuous variable with excess zeros and skewness. This outcome is complex because there are 3 possible activity patterns in each interval (inactive, partially active, and completely active), and those patterns, which are observed, induce both nonrandom and random associations between the responses. More specifically, the inactive pattern requires a zero value in both the proportion for active behavior and the energy expenditure rate; a partially active pattern means that the proportion of activity is strictly between zero and one and that the energy expenditure rate is greater than zero and likely to be moderate, and the completely active pattern means that the proportion of activity is exactly one, and the energy expenditure rate is greater than zero and likely to be higher. To address these challenges, we propose a 3‐part functional data joint modeling approach. The first part is a continuation‐ratio model to reorder the ordinal valued 3 activity patterns. The second part models the proportions when they are in interval (0,1). The last component specifies the skewed continuous energy expenditure rate with Box‐Cox transformations when they are greater than zero. In this 3‐part model, the regression structures are specified as smooth curves measured at various time points with random effects that have a correlation structure. The smoothed random curves for each variable are summarized using a few important principal components, and the association of the 3 longitudinal components is modeled through the association of the principal component scores. The di...

Li, L, Wang, Y, Arora, VK, Eamus, D, Shi, H, Li, J, Cheng, L, Cleverly, J, Hajima, T, Ji, D, Jones, C, Kawamiya, M, Li, W, Tjiputra, J, Wiltshire, A, Zhang, L & Yu, Q 2018, 'Evaluating Global Land Surface Models in CMIP5: Analysis of Ecosystem Water- and Light-Use Efficiencies and Rainfall Partitioning', Journal of Climate, vol. 31, no. 8, pp. 2995-3008.
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AbstractWater and carbon fluxes simulated by 12 Earth system models (ESMs) that participated in phase 5 of the Coupled Model Intercomparison Project (CMIP5) over several recent decades were evaluated using three functional constraints that are derived from both model simulations, or four global datasets, and 736 site-year measurements. Three functional constraints are ecosystem water-use efficiency (WUE), light-use efficiency (LUE), and the partitioning of precipitation P into evapotranspiration (ET) and runoff based on the Budyko framework. Although values of these three constraints varied significantly with time scale and should be quite conservative if being averaged over multiple decades, the results showed that both WUE and LUE simulated by the ensemble mean of 12 ESMs were generally lower than the site measurements. Simulations by the ESMs were generally consistent with the broad pattern of energy-controlled ET under wet conditions and soil water-controlled ET under dry conditions, as described by the Budyko framework. However, the value of the parameter in the Budyko framework ω, obtained from fitting the Budyko curve to the ensemble model simulation (1.74), was larger than the best-fit value of ω to the observed data (1.28). Globally, the ensemble mean of multiple models, although performing better than any individual model simulations, still underestimated the observed WUE and LUE, and overestimated the ratio of ET to P, as a result of overestimation in ET and underestimation in gross primary production (GPP). The results suggest that future model development should focus on improving the algorithms of the partitioning of precipitation into ecosystem ET and runoff, and the coupling of water and carbon cycles for different land-use types.

Li, M, Cortie, DL, Liu, J, Yu, D, Islam, SMKN, Zhao, L, Mitchell, DRG, Mole, RA, Cortie, MB, Dou, S & Wang, X 2018, 'Ultra-high thermoelectric performance in graphene incorporated Cu2Se: Role of mismatching phonon modes', Nano Energy, vol. 53, pp. 993-1002.
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© 2018 Elsevier Ltd A thermoelectric material consisting of Cu2Se incorporated with up to 0.45 wt% of graphene nanoplates is reported. The carbon-reinforced Cu2Se exhibits an ultra-high thermoelectric figure-of-merit of zT = 2.44 ± 0.25 at 870 K. Microstructural characterization reveals dense, nanostructured grains of Cu2Se with multilayer-graphene and graphite agglomerations located at grain boundaries. High temperature X-ray diffraction shows that the graphene incorporated Cu2Se matrix retains a cubic structure and the composite microstructure is chemically stable. Based on the experimental structure, density functional theory was used to calculate the formation energy of carbon point defects and the associated phonon density of states. The isolated carbon inclusion is shown to have a high formation energy in Cu2Se whereas graphene and graphite phases are enthalpically stable relative to the solid solution. Neutron spectroscopy proves that there is a frequency mismatch in the phonon density of states between the carbon honeycomb phases and cubic Cu2Se. This provides a mechanism for the strong scattering of phonons at the composite interfaces, which significantly impedes the conduction of heat and enhances thermoelectric performance.

Li, M, Reimers, JR, Dobson, JF & Gould, T 2018, 'Faraday cage screening reveals intrinsic aspects of the van der Waals attraction', Proceedings of the National Academy of Sciences, vol. 115, no. 44, pp. E10295-E10302.
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Significance How the van der Waals dispersion interaction relates to chemical electron-correlation effects presents a critical challenge to density functional theory development. Here, recently observed screening of the dispersion force between two insulating objects caused by the insertion of an intermediary graphene layer is explained in terms of Dobson’s general description of dispersion. This then provides a much-needed handle concerning how density functional approaches relate such long-range dispersion interactions to the subtleties of covalent bonding. Screening at intermediate distances appears to change the London expression from r −6 to r −7 , an effect that becomes antiscreening (dispersion enhancement) at distances shorter than van der Waals contact. This provides basic insight into modern revelations that dispersion forces can outcompete covalent forces to control chemical structure.

Li, X, Wang, C, Cao, Y & Wang, G 2018, 'Functional MXene Materials: Progress of Their Applications', Chemistry – An Asian Journal, vol. 13, no. 19, pp. 2742-2757.
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AbstractNowadays, two‐dimensional materials have many applications in materials science. As a novel two‐dimensional layered material, MXene possesses distinct structural, electronic, and chemical properties; thus, it has potential applications in many fields, including battery electrodes, energy storage materials, sensors, and catalysts. Up to now, more than 70 MAX phases have been reported. However, in contrast to the variety of MAX phases, the existing MXene family merely includes Ti2C, Ti3C2, (Ti1/2, Nb1/2)2C, (V1/2, Cr1/2)3C2, Nb2C, Ti3CN, Ta4C3, V2C, and Nb4C3. Among these materials, the Ti3C2Tx MXene exhibits prominently high volumetric capacitance, and the rate at which it transports electron is suitable for electrode materials in batteries and supercapacitors. Hence, Ti3C2Tx is commonly utilized as an electrode material in ion batteries such as Li+, Na+, K+, Mg2+, Ca2+, and Al3+ batteries. What is more, Ti2C has the biggest specific surface area among all of these potential MXene phases, and therefore, Ti2C has remarkably high gravimetric hydrogen storage capacities. In addition, Ti2CO2 materials display extremely high activity for CO oxidation, which makes it possible to design c...

Li, Y, Shi, H, Zhou, L, Eamus, D, Huete, A, Li, L, Cleverly, J, Hu, Z, Harahap, M, Yu, Q, He, L & Wang, S 2018, 'Disentangling Climate and LAI Effects on Seasonal Variability in Water Use Efficiency Across Terrestrial Ecosystems in China', Journal of Geophysical Research: Biogeosciences, vol. 123, no. 8, pp. 2429-2443.
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AbstractWater use efficiency (WUE), the ratio of gross primary productivity (GPP) over evapotranspiration (ET), is a critical ecosystem function. However, it is difficult to distinguish the individual effects of climatic variables and leaf area index (LAI) on WUE, mainly due to the high collinearity among these factors. Here we proposed a partial least squares regression‐based sensitivity algorithm to confront the issue, which was first verified at seven ChinaFlux sites and then applied across China. The results showed that across all biomes in China, monthly GPP (0.42–0.65), ET (0.33–0.56), and WUE (0.01–0.31) showed positive sensitivities to air temperature, particularly in croplands in northeast China and forests in southwest China. Radiation exerted stronger effects on ET (0.55–0.78) than GPP (0.19–0.65), resulting in negative responses (−0.44 to 0.04) of WUE to increased radiation among most biomes. Increasing precipitation stimulated both GPP (0.06–0.17) and ET (0.05–0.12) at the biome level, but spatially negative effects of excessive precipitation were also found in some grasslands. Both monthly GPP (−0.01 to 0.29) and ET (0.02–0.12) showed weak or moderate responses to vapor pressure deficit among biomes, resulting in weak response of monthly WUE to vapor pressure deficit (−0.04 to 0.08). LAI showed positive effects on GPP (0.18–0.60), ET (0–0.23), and WUE (0.13–0.42) across biomes, particularly on WUE in grasslands (0.42 ± 0.30). Our results highlighted the importance of LAI in influencing WUE against climatic variables. Furthermore, the sensitivity algorithm can be used to inform the design of manipulative experiments and compare with factorial simulations for discerning effects of various variables on ecosystem functions.

Li, Z, Liu, X, Causer, GL, Lin, K-W, Pong, P, Holt, SA, Klose, F & Li, YY 2018, 'Structural evolution of a Ni/NiOx based supercapacitor in cyclic charging-discharging: A polarized neutron and X-ray reflectometry study', Electrochimica Acta, vol. 290, pp. 118-127.
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Liana, AE, Marquis, CP, Gunawan, C, Justin Gooding, J & Amal, R 2018, 'Antimicrobial activity of T4 bacteriophage conjugated indium tin oxide surfaces', Journal of Colloid and Interface Science, vol. 514, pp. 227-233.
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We report the antimicrobial activity of bare and surface functionalized indium tin oxide (ITO) conjugated with T4 bacteriophage towards E. coli. A ∼ 103-fold reduction (99.9%) in the bacterial concentration was achieved within 2 h exposure of E. coli to the bare as well as the amine, carboxylic and methyl functionalized ITO/T4 surfaces. Despite the known differences in bacteriophage loading of these ITO/T4 systems, the almost identical extent of antimicrobial activity of all of the ITO/T4 systems resulted from the release of a comparable amount of infective T4 from the systems. As anticipated, a single dose of immobilized bacteriophage was sufficient to eliminate further surge of bacterial population. Upon the 2 h eradication of the '1st batch' of E. coli population, all of the ITO/T4 systems, each system with 102-fold more suspended bacteriophage (due to propagation of the phage at the expense of the '1st batch' E. coli death), reduced the '2nd batch' of E. coli concentration by ∼104-fold in just 30 min, suggesting the potential of immobilized bacteriophage systems as solution to the issues of antimicrobial agent depletion. All of the ITO/T4 systems maintained their antimicrobial activity in the presence of model food components. The antimicrobial activity was however, affected by pH; at pH 5 whereby the bacteria's growth was physiologically inhibited, generally no reduction in E. coli concentration was detected. The present work provides an understanding of the mode of antimicrobial activity exhibited by an immobilized bacteriophage based substrate and demonstrates efficacy in the presence of food components.

Liang, L, Carroll, R & Ma, Y 2018, 'Dimension reduction and estimation in the secondary analysis of case-control studies', Electronic Journal of Statistics, vol. 12, no. 1, pp. 1782-1821.
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© 2018, Institute of Mathematical Statistics. All rights reserved. Studying the relationship between covariates based on retrospective data is the main purpose of secondary analysis, an area of increasing interest. We examine the secondary analysis problem when multiple covariates are available, while only a regression mean model is specified. Despite the completely parametric modeling of the regression mean function, the case-control nature of the data requires special treatment and semiparametric efficient estimation generates various nonparametric estimation problems with multivariate covariates. We devise a dimension reduction approach that fits with the specified primary and secondary models in the original problem setting, and use reweighting to adjust for the case-control nature of the data, even when the disease rate in the source population is unknown. The resulting estimator is both locally efficient and robust against the misspecification of the regression error distribution, which can be heteroscedastic as well as non-Gaussian. We demonstrate the advantage of our method over several existing methods, both analytically and numerically.

Liang, L, Ma, Y, Wei, Y & Carroll, RJ 2018, 'Semiparametrically Efficient Estimation in Quantile Regression of Secondary Analysis', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 80, no. 4, pp. 625-648.
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SummaryAnalysing secondary outcomes is a common practice for case–control studies. Traditional secondary analysis employs either completely parametric models or conditional mean regression models to link the secondary outcome to covariates. In many situations, quantile regression models complement mean-based analyses and provide alternative new insights on the associations of interest. For example, biomedical outcomes are often highly asymmetric, and median regression is more useful in describing the ‘central’ behaviour than mean regressions. There are also cases where the research interest is to study the high or low quantiles of a population, as they are more likely to be at risk. We approach the secondary quantile regression problem from a semiparametric perspective, allowing the covariate distribution to be completely unspecified. We derive a class of consistent semiparametric estimators and identify the efficient member. The asymptotic properties of the resulting estimators are established. Simulation results and a real data analysis are provided to demonstrate the superior performance of our approach with a comparison with the only existing approach so far in the literature.

Liao, Y, Ithurbide, S, de Silva, RT, Erdmann, S & Duggin, IG 2018, 'Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope', Emerging Topics in Life Sciences, vol. 2, no. 4, pp. 547-559.
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The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.

Lin, G & Jin, D 2018, 'Taking upconversion to lase in microcavity', Nature Nanotechnology, vol. 13, no. 7, pp. 534-536.
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© 2018 The Publisher. Stable, sharp-bandwidth and upconverted stimulated emissions are generated from a 5-μm polystyrene cavity pumped by a low-power continuous-wave excitation.

Lin, G, Baker, MAB, Hong, M & Jin, D 2018, 'The Quest for Optical Multiplexing in Bio-discoveries', Chem, vol. 4, no. 5, pp. 997-1021.
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© 2018 Elsevier Inc. Optical multiplexing has significantly boosted our capacity to acquire and process information in the modern era. This review surveys new methods for coding optical information to move from the macroscopic to the nanoscale. We highlight that advances in new materials, fabrication methods, super-resolution imaging tools, and microfluidic devices are the enabling technologies for many recent breakthroughs in micro- and nanoscale biophotonics. Multidimensional optical coding has been developed to assign addressable molecular probes for multiplexed molecular and cellular sensing. While illustrating the principles of coding information in multiple dimensions, we discuss prospective opportunities in material design and technological advancement and identify the challenges for eventually integrating and translating these biophotonic tools into cellular insights. Recent discoveries in luminescent materials, the advent of lasers, and high-resolution microscopy offer improvements to bio-discovery processes and better reporting that will ultimately boost healthcare efficiency. However, slow analysis of the screening process has limited the delivery of improved patient care. Analysis of one or two molecular or cellular targets is no longer sufficient for characterizing a disease or biochemical process, and cellular imaging typically generates significant amounts of information from even a single cell, let alone larger interacting biological systems. By developing optical multiplexing into multiple dimensions, we can significantly increase the throughput of imaging, allowing simultaneous tracking of multiple targets. The eventual goal of optical multiplexing is to synchronize developments in materials and platforms to boost the throughput of bio-discovery to enable us to mine the enormous amounts of information buried inside living organisms. Analysis of one or two molecular or cellular targets is no longer sufficient for characterizing a diseas...

Lin, S, Li, J, Liu, Q, Huete, A & Li, L 2018, 'Effects of Forest Canopy Vertical Stratification on the Estimation of Gross Primary Production by Remote Sensing', Remote Sensing, vol. 10, no. 9, pp. 1329-1329.
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Gross primary production (GPP) in forests is the most important carbon flux in terrestrial ecosystems. Forest ecosystems with high leaf area index (LAI) values have diverse species or complex forest structures with vertical stratifications that influence the carbon–water–energy cycles. In this study, we used three light use efficiency (LUE) GPP models and site-level experiment data to analyze the effects of the vertical stratification of dense forest vegetation on the estimates of remotely sensed GPP during the growing season of two forest sites in East Asia: Dinghushan (DHS) and Tomakomai (TMK). The results showed that different controlling environmental factors of the vertical layers, such as temperature and vapor pressure deficit (VPD), produce different responses for the same LUE value in the different sub-ecosystems (defined as the tree, shrub, and grass layers), which influences the GPP estimation. Air temperature and VPD play important roles in the effects of vertical stratification on the GPP estimates in dense forests, which led to differences in GPP uncertainties from −50% to 30% because of the distinct temperature responses in TMK. The unequal vertical LAI distributions in the different sub-ecosystems led to GPP variations of 1–2 gC/m2/day with uncertainties of approximately −30% to 20% because sub-ecosystems have unique absorbed fractions of photosynthetically active radiation (APAR) and LUE. A comparison with the flux tower-based GPP data indicated that the GPP estimations from the LUE and APAR values from separate vertical layers exhibited better model performance than those calculated using the single-layer method, with 10% less bias in DHS and more than 70% less bias in TMK. The precision of the estimated GPP in regions with thick understory vegetation could be effectively improved by considering the vertical variations in environmental parameters and the LAI values of different sub-ecosystems as separate factors when calculating...

Linton, A, Cheng, YY, Griggs, K, Schedlich, L, Kirschner, MB, Gattani, S, Srikaran, S, Chuan-Hao Kao, S, McCaughan, BC, Klebe, S, van Zandwijk, N & Reid, G 2018, 'Erratum: An RNAi-based screen reveals PLK1, CDK1 and NDC80 as potential therapeutic targets in malignant pleural mesothelioma', British Journal of Cancer, vol. 118, no. 6, pp. e13-e13.
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Liu, C, Liew, CW, Wong, YH, Tan, ST, Poh, WH, Manimekalai, MSS, Rajan, S, Xin, L, Liang, Z-X, Grüber, G, Rice, SA & Lescar, J 2018, 'Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa', Journal of Bacteriology, vol. 200, no. 3.
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ABSTRACT RbdA is a positive r egulator of b iofilm d ispersal of Pseudomonas aeruginosa . Its cytoplasmic region (cRbdA) comprises an N-terminal Per-ARNT-Sim (PAS) domain followed by a diguanylate cyclase (GGDEF) domain and an EAL domain, whose phosphodiesterase activity is allosterically stimulated by GTP binding to the GGDEF domain. We report crystal structures of cRbdA and of two binary complexes: one with GTP/Mg 2+ bound to the GGDEF active site and one with the EAL domain bound to the c-di-GMP substrate. These structures unveil a 2-fold symmetric dimer stabilized by a closely packed N-terminal PAS domain and a noncanonical EAL dimer. The autoinhibitory switch is formed by an α-helix (S-helix) immediately N-terminal to the GGDEF domain that interacts with the EAL dimerization helix (α 6-E ) of the other EAL monomer and maintains the protein in a locked conformation. We propose that local conformational changes in cRbdA upon GTP binding lead to a structure with the PAS domain and S-helix shifted away from the GGDEF-EAL domains, as suggested by small-angle X-ray scattering (SAXS) experiments. Domain reorientation should be facilitated by the presence of an α-helical lever (H-helix) that tethers the GGDEF and EAL regions, allowing the EAL domain to rearrange into an active dimeric conformation. IMPORTANCE Biofilm formation by bacterial pathogens increases resistance to antibiotics. RbdA positively regulates biofilm dispersal of Journal of Alloys and Compounds, vol. 745, pp. 155-163.
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© 2018 Elsevier B.V. Graphitic carbon nitride nanosheets (g-C3N4 NS) were prepared and used for self-templated electrodeposition of copper and copper oxide nanostructures. The as-prepared g-C3N4 NS can provide a lot of anchoring sites for copper ions in the process of electrodeposition. The electrodeposited CuO@Cu demonstrates high density and good uniformity. During the electrodeposition, the addition of nickel ions had enabled to entrap Ni ions in the lattice of CuO. The CeO2-CuO@Cu/g-C3N4 NS composites have been prepared by the addition of Ce ions in the process of electrodepositing CuO@Cu onto g-C3N4 NS. The cerium and nickel ions, as the additives, can effectively improve the density and uniformity of the electrodeposited CuO@Cu. Furthermore, the successful entrapment of CeO2 and Ni ions greatly improve electrochemical performance of CuO@Cu/g-C3N4 NS/ITO in the non-enzymatic detection of glucose. The Ce and Ni ion additives showed a synergistic effect on improving uniformity and density of the electrodeposited CuO@Cu and electro-catalytic properties of as-prepared composites. The as-prepared CuO@Cu/g-C3N4 NS/ITO, CeO2-CuO@Cu/g-C3N4 NS/ITO and Ni-doped CuO@Cu/g-C3N4 NS/ITO have been respectively used for non-enzymatic detection of glucose. These three proposed electrodes all demonstrate good electrochemical performance in the non-enzymatic detection of glucose. The CeO2−CuO@Cu/g-C3N4 NS/ITO and Ni-doped CuO@Cu/g-C3N4 NS/ITO appear to greatly improve the electro-catalytic activity toward the oxidation of glucose. Among these three electrodes, the Ni-doped CuO@Cu/g-C3N4 NS/ITO demonstrated the best electrochemical performance in the detection of glucose. These three proposed electrodes all demonstrated good stability and anti-interference performance.

Liu, MY, Cokcetin, NN, Lu, J, Turnbull, L, Carter, DA, Whitchurch, CB & Harry, EJ 2018, 'Rifampicin-Manuka Honey Combinations Are Superior to Other Antibiotic-Manuka Honey Combinations in Eradicating Staphylococcus aureus Biofilms', Frontiers in Microbiology, vol. 8, no. JAN, pp. 1-12.
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© 2018 Liu, Cokcetin, Lu, Turnbull, Carter, Whitchurch and Harry. Chronic wound infections are a major burden to both society and the health care industry. Bacterial biofilms are the major cause of chronic wound infections and are notoriously recalcitrant to treatments with antibiotics, making them difficult to eradicate. Thus, new approaches are required to combat biofilms in chronic wounds. One possible approach is to use drug combination therapies. Manuka honey has potent broad-spectrum antibacterial activity and has previously shown synergistic activity in combination with antibiotics against common wound pathogens, including Staphylococcus aureus. In addition, manuka honey exhibits anti-biofilm activity, thereby warranting the investigation of its potential as a combination therapy with antibiotics for the topical treatment of biofilm-related infections. Here we report the first use of MacSynergy II to investigate the response of established S. aureus (strain NCTC 8325) biofilms to treatment by combinations of Medihoney (medical grade manuka honey) and conventional antibiotics that are used for preventing or treating infections: rifampicin, oxacillin, fusidic acid, clindamycin, and gentamicin. Using checkerboard microdilution assays, viability assays and MacSynergy II analysis we show that the Medihoney-rifampicin combination was more effective than combinations using the other antibiotics against established staphylococcal biofilms. Medihoney and rifampicin were strongly synergistic in their ability to reduce both biofilm biomass and the viability of embedded S. aureus cells at a level that is likely to be significant in vivo. Other combinations of Medihoney and antibiotic produced an interesting array of effects: Medihoney-fusidic acid treatment showed minor synergistic activity, and Medihoney-clindamycin, -gentamicin, and -oxacillin combinations showed overall antagonistic effects when the honey was used at sub-inhibitory concentration, due to e...

Liu, SH, Bobb, JF, Claus Henn, B, Schnaas, L, Tellez‐Rojo, MM, Gennings, C, Arora, M, Wright, RO, Coull, BA & Wand, MP 2018, 'Modeling the health effects of time‐varying complex environmental mixtures: Mean field variational Bayes for lagged kernel machine regression', Environmetrics, vol. 29, no. 4.
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There is substantial interest in assessing how exposure to environmental mixtures, such as chemical mixtures, affects child health. Researchers are also interested in identifying critical time windows of susceptibility to these complex mixtures. A recently developed method, called lagged kernel machine regression (LKMR), simultaneously accounts for these research questions by estimating the effects of time‐varying mixture exposures and by identifying their critical exposure windows. However, LKMR inference using Markov chain Monte Carlo (MCMC) methods (MCMC‐LKMR) is computationally burdensome and time intensive for large data sets, limiting its applicability. Therefore, we develop a mean field variational approximation method for Bayesian inference (MFVB) procedure for LKMR (MFVB‐LKMR). The procedure achieves computational efficiency and reasonable accuracy as compared with the corresponding MCMC estimation method. Updating parameters using MFVB may only take minutes, whereas the equivalent MCMC method may take many hours or several days. We apply MFVB‐LKMR to Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS), a prospective cohort study in Mexico City. Results from a subset of PROGRESS using MFVB‐LKMR provide evidence of significant and positive association between second trimester cobalt levels and z‐scored birth weight. This positive association is heightened by cesium exposure. MFVB‐LKMR is a promising approach for computationally efficient analysis of environmental health data sets, to identify critical windows of exposure to complex mixtures.

Liu, T, Zhang, W, McLean, P, Ueland, M, Forbes, SL & Su, SW 2018, 'Electronic Nose-Based Odor Classification using Genetic Algorithms and Fuzzy Support Vector Machines', International Journal of Fuzzy Systems, vol. 20, no. 4, pp. 1309-1320.
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© 2018, Taiwan Fuzzy Systems Association and Springer-Verlag GmbH Germany, part of Springer Nature. Electronic nose devices consisting of a matrix of sensors to sense the smell of various target gases have received considerable attention during the past two decades. This paper presents an efficient classification algorithm for a self-designed electronic nose, which integrates both genetic algorithms (GAs) and fuzzy support vector machines (FSVMs) to detect the target odor. GAs are applied to select the informative features and the optimal model parameters of FSVMs. FSVMs are adopted as fitness evaluation criterion and the sequent odor classifier, which can reduce the outlier effects and provide a robust and accurate classification. This proposed algorithm has been compared with some commonly used learning algorithms, such as support vector machine, the k-nearest neighbors and other combination algorithms. This study is based on experimental data collected from the response of the UTS NOS.E, which is the electronic nose system developed by the University of Technology Sydney NOS.E team. In comparison with other approaches, the experiment results show that the proposed odor classification algorithm can significantly improve the classification accuracy by selecting high-quality features and reach to 92.05% classification accuracy.

Liu, X, Zhou, J, Zhou, S, Yue, Y & Qiu, J 2018, 'Transparent glass-ceramics functionalized by dispersed crystals', Progress in Materials Science, vol. 97, pp. 38-96.
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© 2018 Elsevier Ltd Transparent glass ceramics (TGCs) with minimized scattering loss offer the combined characteristics of both glasses and (transparent) ceramics. The functionalities of the dispered crystals make TGCs a new generation of tailorable optical materials with a wide range of applications from optics to photonics. Most of conventional glass ceramics (GCs), e.g., silicate glass ceramics, contain crystals involving both network formers and modifiers, and they are known for their superior mechanical/thermal performances. In this paper, we pay more attention to those TGCs containing crystalline phases composed of only network modifiers, including nanocrystals of noble metals, metal fluorides, oxides, chalcogenides, etc. We review recent advances in conventional fabrication methods as well as in emerging techniques for the production of TGCs, such as solid state reaction, sol–gel and laser–induced crystallization. We then discuss the applications of TGCs, particularly the TGCs functionalized by crystals that exhibit various optical functionalities, including photoluminescence, optical nonlinearity, plasmonic absorption, etc. Experimental advances in the use of TGCs for lasers, optical amplifiers and different spectral converters are highlighted. We also anticipate that TGCs will find new applications, and the investigations into TGCs will unravel the mechanism of crystal formation, and hence, lead to the discovery of novel TGC systems.

Liu, YY, van Dijk, AIJM, Miralles, DG, McCabe, MF, Evans, JP, de Jeu, RAM, Gentine, P, Huete, A, Parinussa, RM, Wang, L, Guan, K, Berry, J & Restrepo-Coupe, N 2018, 'Enhanced canopy growth precedes senescence in 2005 and 2010 Amazonian droughts', Remote Sensing of Environment, vol. 211, pp. 26-37.
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© 2018 Unprecedented droughts hit southern Amazonia in 2005 and 2010, causing a sharp increase in tree mortality and carbon loss. To better predict the rainforest's response to future droughts, it is necessary to understand its behavior during past events. Satellite observations provide a practical source of continuous observations of Amazonian forest. Here we used a passive microwave-based vegetation water content record (i.e., vegetation optical depth, VOD), together with multiple hydrometeorological observations as well as conventional satellite vegetation measures, to investigate the rainforest canopy dynamics during the 2005 and 2010 droughts. During the onset of droughts in the wet-to-dry season (May–July) of both years, we found large-scale positive anomalies in VOD, leaf area index (LAI) and enhanced vegetation index (EVI) over the southern Amazonia. These observations are very likely caused by enhanced canopy growth. Concurrent below-average rainfall and above-average radiation during the wet-to-dry season can be interpreted as an early arrival of normal dry season conditions, leading to enhanced new leaf development and ecosystem photosynthesis, as supported by field observations. Our results suggest that further rainfall deficit into the subsequent dry season caused water and heat stress during the peak of 2005 and 2010 droughts (August–October) that exceeded the tolerance limits of the rainforest, leading to widespread negative VOD anomalies over the southern Amazonia. Significant VOD anomalies were observed mainly over the western part in 2005 and mainly over central and eastern parts in 2010. The total area with significant negative VOD anomalies was comparable between these two drought years, though the average magnitude of significant negative VOD anomalies was greater in 2005. This finding broadly agrees with the field observations indicating that the reduction in biomass carbon uptake was stronger in 2005 than 2010. The enhanced canopy...

Llewelyn, J, Choyce, NC, Phillips, BL, Webb, JK, Pearson, DJ, Schwarzkopf, L & Shine, R 2018, 'Behavioural responses of an Australian colubrid snake (Dendrelaphis punctulatus) to a novel toxic prey item (the Cane Toad Rhinella marina)', Biological Invasions, vol. 20, no. 9, pp. 2507-2516.
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© 2018, Springer International Publishing AG, part of Springer Nature. The invasion of a toxic prey type can differentially affect closely related predator species. In Australia, the invasive Cane Toad (Rhinella marina) kills native anurophagous predators that cannot tolerate the toad’s toxins; but predators that are physiologically resistant (i.e., belong to lineages that entered Australia recently from Asia, where toads of other species are common) have been more resilient. In the current study, we examine the case of an Asian-derived predator lineage that relies on behavioural not physiological adaptations to deal with toads. Despite their Asian origins, Common Tree Snakes (Dendrelaphis punctulatus) are highly sensitive to toad toxins; yet this snake has not declined in abundance due to toads. We exposed captive (field-collected) snakes to toads of different sizes and ontogenetic stages, to quantify feeding responses and outcomes. Tree Snakes were less likely to attack toads than to attack native frogs, and rarely retained their hold on large toads. Tree Snakes ingested frogs of a wide range of body sizes but only ingested very small toads (< 1 g vs. up to 30 g for frogs). Behavioural responses were virtually identical between Tree Snakes from invaded versus yet-to-be-invaded areas, suggesting that preadaptation (from Asia) rather than adaptation (within Australia) is the key to successful utilisation of this novel but potentially toxic prey resource. Nonetheless, a previously-documented shift in relative head sizes of Tree Snakes coincident with toad invasion suggests that the ancestral behavioural tactic may have been reinforced by a recent morphological shift that further reduces maximal prey size, and hence the risk of fatal poisoning.

Loyeung, B, Lee, J, Michaeil, C & Zaslawski, C 2018, 'An experimental study in distinguishing an authentic herbal substance from sham herbal substances', Complementary Therapies in Medicine, vol. 39, pp. 92-96.
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An unblinded randomised trial can result in biased treatment effect estimates and lead to erroneous conclusions on the efficacy of the therapeutic intervention. Unlike pharmaceutical substances, Chinese herbal medicines have special characteristics including texture, colour, odour and taste as the origin of these constituents are different. In addition, its distinctive odour makes blinding of Chinese herbal medicine RCTs very difficult, as the placebo substance needs to match the special characteristics of the herbal substance being investigated. For these reasons, two studies were undertaken to evaluate whether a participant could distinguish a herbal intervention capsule (Ganopoly combination) when compared to three types of capsules containing culinary materials following a visual, odour and taste evaluation.Study One, was a pilot involving eleven participants (n = 11) while Study Two, involved eighty one participants (n = 81) and was conducted to make improvements on Study One. For both studies, participants were asked to identify which of four capsules were a herbal substance following a visual, smell and taste evaluation.For study One it was found that for both odour (p = .484) and visual appearance (p = .077) the number of participants selecting the herbal substance was not significantly different from what may have been selected by chance. This was not the case for taste where significantly more participants selected capsule B as the herbal substance (p = .004). For Study Two test it was found that all three evaluations for odour, visual appearance and taste significantly more participants selected the herbal substance (p < .0001 in all cases). This indicates that the participant guesses were not evenly distributed across the four choices and suggests a failure to blind.The failure to blind participants highlights the difficulties in preparing sham herbal substances that look, smell and taste like the real herbal substance.

Lun, JH, Hewitt, J, Sitabkhan, A, Eden, J-S, Enosi Tuipulotu, D, Netzler, NE, Morrell, L, Merif, J, Jones, R, Huang, B, Warrilow, D, Ressler, K-A, Ferson, MJ, Dwyer, DE, Kok, J, Rawlinson, WD, Deere, D, Crosbie, ND & White, PA 2018, 'Emerging recombinant noroviruses identified by clinical and waste water screening', Emerging Microbes & Infections, vol. 7, no. 1, pp. 1-14.
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Luo, Q, O’Leary, G, Cleverly, J & Eamus, D 2018, 'Effectiveness of time of sowing and cultivar choice for managing climate change: wheat crop phenology and water use efficiency', International Journal of Biometeorology, vol. 62, no. 6, pp. 1049-1061.
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Luo, Y, Liu, Z, Hau, SC-K, Yeung, YY, Wong, K-L, Shiu, KK, Chen, X, Zhu, H, Bao, G & Tanner, PA 2018, 'Electronic Spectra of Cs₂NaYb(NO₂)₆: Is There Quantum Cutting?', The Journal of Physical Chemistry A, vol. 122, no. 17, pp. 4381-4388.
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© 2018 American Chemical Society. The crystal structure and electronic spectra of the Th symmetry hexanitritoytterbate(III) anion have been studied in Cs2NaY0.96Yb0.04(NO2)6, which crystallizes in the cubic space group Fm3. The emission from Yb3+ can be excited via the NO2- antenna. The latter electronic transition is situated at more than twice the energy of the former, but at room temperature, one photon absorbed at 470 nm in the triplet state produces no more than one photon emitted. Some degree of quantum cutting is observed at 298 K under 420 nm excitation into the singlet state and at 25 K using excitation into either state. The quantum efficiency is ∼10% at 25 K. The energy level scheme of Yb3+ has been deduced from excitation and emission spectra and calculated by crystal field theory. New improved energy level calculations are also reported for the Cs2NaLn(NO2)6 (Ln = Pr, Eu, Tb) series using the f-Spectra package. The neat crystal Cs2NaYb(NO2)6 has also been studied, but results were unsatisfactory due to sample decomposition, and this chemical instability makes it unsuitable for applications.

Luong, S, Forbes, SL, Wallman, JF & Roberts, RG 2018, 'Monitoring the extent of vertical and lateral movement of human decomposition products through sediment using cholesterol as a biomarker', Forensic Science International, vol. 285, pp. 93-104.
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Due to the lack of human decomposition research facilities available in different geographical regions, the extent of movement of human decomposition products from a cadaver into various sedimentary environments, in different climates, has not been able to be studied in detail. In our study, a human cadaver was placed on the surface of a designated plot at the Australian Facility for Taphonomic Experimental Research (AFTER), the only human decomposition facility in Australia, where the natural process of decomposition was allowed to progress over 14days in the Australian summer. Sediment columns (approximately 1m deep) were collected at lateral distances of 0.25m, 0.5m, 1.0m and 2.5m in each of four directions from the centre of the torso. Plot elevation and weather data were also collected. Each sediment column was subdivided, dried and homogenised. A sample was isolated from each sediment subdivision, extracted with hexane, and the hexane extract cleaned with citrate buffer (pH 3), filtered and spiked with cholesterol-D7 internal standard. After derivatisation with BSTFA+1% TMCS, cholesterol was monitored in the samples using targeted gas chromatography tandem mass spectrometry analysis. A positive result for decomposition products was given if the cholesterol abundance in the test sample was higher than that detected in the 'control' samples of a similar substrate type collected prior to cadaver placement. Within the confines of the experimental design and the measured parameters, lateral leaching was observed over distances of up to 2.5m from the centre of the torso, which was the maximum distance tested in the study. Vertical leaching was detected to depths of up to 49cm below the ground surface. Such data can aid the development of policies related to plot sizing and sediment renewal and regeneration at other human decomposition facilities and at cemeteries. The density and distribution of cholesterol surrounding the cadaver in this study can also help fore...

Luthi, F, Stavenga, T, Enzing, OW, Bruno, A, Dickel, C, Langford, NK, Rol, MA, Jespersen, TS, Nygård, J, Krogstrup, P & DiCarlo, L 2018, 'Evolution of Nanowire Transmon Qubits and Their Coherence in a Magnetic Field', Physical Review Letters, vol. 120, no. 10.
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We present an experimental study of flux- and gate-tunable nanowire transmons with state-of-the-art relaxation time allowing quantitative extraction of flux and charge noise coupling to the Josephson energy. We evidence coherence sweet spots for charge, tuned by voltage on a proximal side gate, where first order sensitivity to switching two-level systems and background 1/f noise is minimized. Next, we investigate the evolution of a nanowire transmon in a parallel magnetic field up to 70 mT, the upper bound set by the closing of the induced gap. Several features observed in the field dependence of qubit energy relaxation and dephasing times are not fully understood. Using nanowires with a thinner, partially covering Al shell will enable operation of these circuits up to 0.5 T, a regime relevant for topological quantum computation and other applications.

Luts, J, Wang, SSJ, Ormerod, JT & Wand, MP 2018, 'Semiparametric Regression Analysis via Infer.NET', Journal of Statistical Software, vol. 87, no. 2.
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© 2018, American Statistical Association. All rights reserved. We provide several examples of Bayesian semiparametric regression analysis via the Infer.NET package for approximate deterministic inference in Bayesian models. The examples are chosen to encompass a wide range of semiparametric regression situations. Infer.NET is shown to produce accurate inference in comparison with Markov chain Monte Carlo via the BUGS package, but to be considerably faster. Potentially, this contribution represents the start of a new era for semiparametric regression, where large and complex analyses are performed via fast Bayesian inference methodology and software, mainly being developed within Machine Learning.

Luu, LDW, Octavia, S, Zhong, L, Raftery, MJ, Sintchenko, V & Lan, R 2018, 'Comparison of the Whole Cell Proteome and Secretome of Epidemic Bordetella pertussis Strains From the 2008–2012 Australian Epidemic Under Sulfate-Modulating Conditions', Frontiers in Microbiology, vol. 9, no. NOV, p. 2851.
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Sulfate is an important modulator for virulence factor expression in Bordetella pertussis, the causative organism for whooping cough. During infection, sulfate is released when respiratory epithelial cells are damaged which can affect gene expression. The current predominant strains in Australia are found in single nucleotide polymorphism (SNP) cluster I (ptxP3/prn2). It has been reported that ptxP3 strains have higher mRNA expression of virulence genes than ptxP1 strains under intermediate sulfate-modulating conditions (5 mM MgSO4). Our previous proteomic study compared L1423 (cluster I, ptxP3) and L1191 (cluster II, ptxP1) in Thalen-IJssel (THIJS) media without sulfate modulation and identified an upregulation of transport proteins and a downregulation of immunogenic proteins. To determine whether proteomic differences exist between cluster I and cluster II strains in intermediate modulating conditions, this study compared the whole cell proteome and secretome between L1423 and L1191 grown in THIJS media with 5 mM MgSO4 using iTRAQ and high-resolution multiple reaction monitoring (MRM-hr). Two proteins (BP0200 and BP1175) in the whole cell were upregulated in L1423 [fold change (FC) >1.2, false discovery rate (FDR) <0.05]. In the secretome, four proteins from the type III secretion system (T3SS) effectors were downregulated (FC < 0.8, FDR < 0.05) while six proteins, including two adhesins, pertactin (Prn) and tracheal colonization factor A (TcfA), were upregulated which were consistent with our previous proteomic study. The upregulation of Prn and TcfA in SNP cluster I may result in improved adhesion while the downregulation of the T3SS and other immunogenic proteins may reduce immune recognition, which may contribute to the increased fitness of cluster I B. pertussis strains.

Luu, LDW, Octavia, S, Zhong, L, Raftery, MJ, Sintchenko, V & Lan, R 2018, 'Proteomic Adaptation of Australian Epidemic Bordetella pertussis', PROTEOMICS, vol. 18, no. 8, pp. 1-12.
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AbstractBordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non‐ptxP3/non‐prn2). Cluster I was mostly responsible for the 2008–2012 Australian epidemic and was found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunization status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using isobaric tags for relative and absolute quantification (iTRAQ), and high‐resolution multiple reaction monitoring (MRM‐hr). A few key differences in the whole cell and secretome were identified between the cluster I and II strains tested. In the whole cell, nine proteins were upregulated (>1.2 fold change, q < 0.05) and three were downregulated (<0.8 fold change, q < 0.05) in cluster I. One downregulated protein was BP1569, a TLR2 agonist for Th1 immunity. In the secretome, 12 proteins were upregulated and 1 was downregulated which was Bsp22, a type III secretion system (T3SS) protein. Furthermore, there was a trend of downregulation in three T3SS effectors and other virulence factors. Three proteins were upregulated in both whole cell and supernatant: BP0200, molybdate ABC transporter (ModB), and tracheal colonization factor A (TcfA). Important expression differences in lipoprotein, T3SS, and transport proteins between the cluster I and II strains were identified. These differences may affect immune evasion, virulence and metabolism, and play a role in increased fitness of cluster I.

Lv, H, Teng, Z, Wang, S, Feng, K, Wang, X, Wang, C & Wang, G 2018, 'Voltammetric simultaneous ion flux measurements platform for Cu2+, Pb2+ and Hg2+ near rice root surface: Utilizing carbon nitride heterojunction film modified carbon fiber microelectrode', Sensors and Actuators B: Chemical, vol. 256, pp. 98-106.
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© 2017 Elsevier B.V. Developing an available analysis platform for simultaneous heavy metal ion flux measurement at trace level is urgent for understanding the mechanisms of phytoremediation. Herein, oxygenous functionalized carbon nitride nanosheets assembled porous films on multi-walled carbon nanotube formed nano frameworks was firstly prepared on a carbon fiber disk microelectrode by an advanced drop-casting method. The as-prepared electrode shows low detection limit (The 1.0 × 10−13 mol L−1 for Cu2+, 1.8 × 10−11 mol L−1 for Pb2+ and 8.0 × 10−12 mol L−1 for Hg2+), acceptable linear range (6.6 × 10−12 ∼ 8.5 × 10−6 mol L−1 for Cu2+, 8.1 × 10−10 ∼ 8.5 × 10−6 mol L−1 for Pb2+ and 2.2 × 10−11 ∼ 8.5 × 10−6 mol L−1 for Hg2+) and fine selectivity in simultaneous determination. The improved accumulation ability of modifier is attributed to improved conductivity and the porous morphology of the film, which may improve useful rate of the chelation groups. Based on the as-prepared electrode and a stepper motor, the voltammetric platform for simultaneous heavy metal ion flux measurement at trace level is fabricated for the first time. This platform can be utilized for mechanism investigation of simultaneous metal uptake on the surface of rice roots at trace level.

Lv, Y, Huang, C, Xu, H, Han, X, Zhang, L, Mao, W, Ji, Y, Jin, D, Lou, W & Xu, X 2018, 'Clinicopathological Characteristics of the primary and metastatic Hepatic Neuroendocrine Tumors and the relevant Prognosis-Related Factors: A Retrospective Study of 81 Cases in a Single Chinese Center', Journal of Cancer, vol. 9, no. 3, pp. 479-487.
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Lv, Y, Pu, N, Mao, W-L, Chen, W-Q, Wang, H-Y, Han, X, Ji, Y, Zhang, L, Jin, D-Y, Lou, W-H & Xu, X-F 2018, 'Development of predictive prognostic nomogram for NECs of rectum on population-based exploration', Endocrine Connections, vol. 7, no. 11, pp. 1178-1185.
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AimWe aim to investigate the clinical characteristics of the rectal NECs and the prognosis-related factors and construct a nomogram for prognosis prediction.MethodsThe data of 41 patients and 1028 patients with rectal NEC were retrieved respectively from our institution and SEER database. OS or PFS was defined as the major study outcome. Variables were compared by chi-square test and t-test when appropriate. Kaplan–Meier analysis with log-rank test was used for survival analysis and the Cox regression analysis was applied. The nomogram integrating risk factors for predicting OS was constructed by R to achieve superior discriminatory ability. Predictive utility of the nomogram was determined by concordance index (C-index) and calibration curve.ResultsIn the univariate and multivariate analyses, tumor differentiation, N stage, M stage and resection of primary site were identified as independent prognostic indicators. The linear regression relationship was found between the value of Ki-67 index and the duration of OS (P < 0.05). Furthermore, the independent prognostic factors were added to formulate prognostic nomogram. The constructed nomogram showed good performance according to the C-index.ConclusionsContrary to WHO classification guideline, we found that the rectal NEC diseases are heterogeneous and should be divided as different categories according to the pathological differentiation. Besides, the nomogram formulated in this study showed excellent discriminative capability to predict OS for those patients. More advanced predictive model for this disease is required to assist risk stratification via the formulated nomogram.

Ma, K, Zhang, F, Sayyadi, N, Chen, W, Anwer, AG, Care, A, Xu, B, Tian, W, Goldys, EM & Liu, G 2018, '“Turn-on” Fluorescent Aptasensor Based on AIEgen Labeling for the Localization of IFN-γ in Live Cells', ACS Sensors, vol. 3, no. 2, pp. 320-326.
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Macha, IJ & Ben-Nissan, B 2018, 'Marine Skeletons: Towards Hard Tissue Repair and Regeneration', Marine Drugs, vol. 16, no. 7, pp. 225-225.
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Musculoskeletal disorders in the elderly have significantly increased due to the increase in an ageing population. The treatment of these diseases necessitates surgical procedures, including total joint replacements such as hip and knee joints. Over the years a number of treatment options have been specifically established which are either permanent or use temporary natural materials such as marine skeletons that possess unique architectural structure and chemical composition for the repair and regeneration of bone tissue. This review paper will give an overview of presently used materials and marine structures for hard tissue repair and regeneration, drugs of marine origin and other marine products which show potential for musculoskeletal treatment.

Machaalani, R & Chen, H 2018, 'Brain derived neurotrophic factor (BDNF), its tyrosine kinase receptor B (TrkB) and nicotine', NeuroToxicology, vol. 65, pp. 186-195.
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Nicotine is the major neurotoxicant in cigarettes that affects many transmitter systems within the brain as well as other factors, including the growth factors. Brain derived neurotrophic factor (BDNF), is the most abundant growth factor in the brain and plays a critical role in early new neuron differentiation, development and synapsis growth, and the survival of fully developed neurons and synaptic activity. Over the past 3 decades, data has emerged on the effects of nicotine and cigarette smoke exposure on the expression of BDNF and its primary specific receptor tyrosine kinase receptor B (TrkB). This review summarizes data regarding the changes in brain BDNF expression after nicotine or cigarette smoke exposure, and discusses their implications considering BDNF's functional roles.

MacMillan, CP, Birke, H, Chuah, A, Brill, E, Tsuji, Y, Ralph, J, Dennis, ES, Llewellyn, D & Pettolino, FA 2018, 'Correction to: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls', BMC Genomics, vol. 19, no. 1.
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Macreadie, PI, McLean, DL, Thomson, PG, Partridge, JC, Jones, DOB, Gates, AR, Benfield, MC, Collin, SP, Booth, DJ, Smith, LL, Techera, E, Skropeta, D, Horton, T, Pattiaratchi, C, Bond, T & Fowler, AM 2018, 'Eyes in the sea: Unlocking the mysteries of the ocean using industrial, remotely operated vehicles (ROVs)', Science of The Total Environment, vol. 634, pp. 1077-1091.
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© 2018 For thousands of years humankind has sought to explore our oceans. Evidence of this early intrigue dates back to 130,000 BCE, but the advent of remotely operated vehicles (ROVs) in the 1950s introduced technology that has had significant impact on ocean exploration. Today, ROVs play a critical role in both military (e.g. retrieving torpedoes and mines) and salvage operations (e.g. locating historic shipwrecks such as the RMS Titanic), and are crucial for oil and gas (O&G) exploration and operations. Industrial ROVs collect millions of observations of our oceans each year, fueling scientific discoveries. Herein, we assembled a group of international ROV experts from both academia and industry to reflect on these discoveries and, more importantly, to identify key questions relating to our oceans that can be supported using industry ROVs. From a long list, we narrowed down to the 10 most important questions in ocean science that we feel can be supported (whole or in part) by increasing access to industry ROVs, and collaborations with the companies that use them. The questions covered opportunity (e.g. what is the resource value of the oceans?) to the impacts of global change (e.g. which marine ecosystems are most sensitive to anthropogenic impact?). Looking ahead, we provide recommendations for how data collected by ROVs can be maximised by higher levels of collaboration between academia and industry, resulting in win-win outcomes. What is clear from this work is that the potential of industrial ROV technology in unravelling the mysteries of our oceans is only just beginning to be realised. This is particularly important as the oceans are subject to increasing impacts from global change and industrial exploitation. The coming decades will represent an important time for scientists to partner with industry that use ROVs in order to make the most of these ‘eyes in the sea’.

Maes, WH, Huete, AR, Avino, M, Boer, MM, Dehaan, R, Pendall, E, Griebel, A & Steppe, K 2018, 'Can UAV-Based Infrared Thermography Be Used to Study Plant-Parasite Interactions between Mistletoe and Eucalypt Trees?', Remote Sensing, vol. 10, no. 12, pp. 2062-2062.
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Some of the remnants of the Cumberland Plain woodland, an endangered dry sclerophyllous forest type of New South Wales, Australia, host large populations of mistletoe. In this study, the extent of mistletoe infection was investigated based on a forest inventory. We found that the mistletoe infection rate was relatively high, with 69% of the Eucalyptus fibrosa and 75% of the E. moluccana trees being infected. Next, to study the potential consequences of the infection for the trees, canopy temperatures of mistletoe plants and of infected and uninfected trees were analyzed using thermal imagery acquired during 10 flights with an unmanned aerial vehicle (UAV) in two consecutive summer seasons. Throughout all flight campaigns, mistletoe canopy temperature was 0.3–2 K lower than the temperature of the eucalypt canopy it was growing in, suggesting higher transpiration rates. Differences in canopy temperature between infected eucalypt foliage and mistletoe were particularly large when incoming radiation peaked. In these conditions, eucalypt foliage from infected trees also had significantly higher canopy temperatures (and likely lower transpiration rates) compared to that of uninfected trees of the same species. The study demonstrates the potential of using UAV-based infrared thermography for studying plant-water relations of mistletoe and its hosts.

Maestrini, L & Wand, MP 2018, 'Variational message passing for skew t regression', Stat, vol. 7, no. 1, pp. e196-e196.
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We extend recent work concerning variational approximations via message passing to accommodate approximate fitting and inference for skew t regression models. Derivation of variational message passing is challenging owing to the presence of non‐standard exponential families and numerical integration being needed. Nevertheless, the factor graph fragment approach means that algorithm updates only need to be derived once for a particular response model, which can be integrated in an arbitrarily complex model. Another advantage of our work is that all skew t parameters are inferred, rather than being held fixed. Furthermore, we show that posterior dependence arising in an auxiliary variable representation of a skew t model may lead to poor performances in terms of variational message passing approximation when using simple auxiliary variable representations of the likelihood fragment and convenient factorizations of the approximating densities. © 2018 John Wiley & Sons, Ltd.

Maheshwari, R, Sharma, P, Tekade, M, Atneriya, U, Dua, K, Hansbro, PM & Tekade, RK 2018, 'Microsponge Embedded Tablets for Sustained Delivery of Nifedipine', Pharmaceutical Nanotechnology, vol. 5, no. 3, pp. 192-202.
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Nifedipine is a potential therapeutic agent for the treatment of cardiovascular disturbances, although it suffers from short half-life (t1/2, 2 hr).To address the problem, we first prepared nifedipine loaded sustained release microsponges and then formulated tablets for effective clinical application and patient compliance.Preparations of microsponges were carried out using different compositions of nifedipine and polymer (1:1, 1:2 and 1:3 % molar ratio) using emulsion solvent diffusion technique.The microsponges with molar ratio 1:3 (formulation code: MF-3) found optimized as revealed by analyzing surface morphology, better powder flow properties (angle of repose; 28.80 ± 0.9, Hausner ratio 1.15 ± 0.2, % compressibility 15.28 ± 0.5% and higher % drug content (80 ± 1.9 %). Different batches of tablets were then formulated incorporating MF-3 microsponges and different proportions (10-50 %) of microcrystalline cellulose and starch as additives. Among tablet formulations, batch composed of 48% of MF-3, 30% of MCC, 20 % of starch and 2 % of talc (TF-33), showed 92.73 ± 2.19 % drug release during 24 hr in vitro release study in comparison to other batches including commercial formulation which was found to be released completely in 20 hr. Further, stability analysis revealed good drug retention of loaded nifedipine as well as consistent in vitro release pattern over a period of 90 days at 40°C and 75% RH.The microsponge tablet delivery system was found to be superior concerning the therapeutic advantage as well as manufacturing feasibility of nifedipine.

Mahmodi, H, Hashim, MR, Soga, T, Alrokayan, S, Khan, HA & Rusop, M 2018, 'Synthesis of Ge1−xSnx Alloy Thin Films by Rapid Thermal Annealing of Sputtered Ge/Sn/Ge Layers on Si Substrates', Materials, vol. 11, no. 11, pp. 2248-2248.
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In this work, nanocrystalline Ge1−xSnx alloy formation from a rapid thermal annealed Ge/Sn/Ge multilayer has been presented. The multilayer was magnetron sputtered onto the Silicon substrate. This was followed by annealing the layers by rapid thermal annealing, at temperatures of 300 °C, 350 °C, 400 °C, and 450 °C, for 10 s. Then, the effect of thermal annealing on the morphological, structural, and optical characteristics of the synthesized Ge1−xSnx alloys were investigated. The nanocrystalline Ge1−xSnx formation was revealed by high-resolution X-ray diffraction (HR-XRD) measurements, which showed the orientation of (111). Raman results showed that phonon intensities of the Ge-Ge vibrations were improved with an increase in the annealing temperature. The results evidently showed that raising the annealing temperature led to improvements in the crystalline quality of the layers. It was demonstrated that Ge-Sn solid-phase mixing had occurred at a low temperature of 400 °C, which led to the creation of a Ge1−xSnx alloy. In addition, spectral photo-responsivity of a fabricated Ge1−xSnx metal-semiconductor-metal (MSM) photodetector exhibited its extending wavelength into the near-infrared region (820 nm).

Mahmood, A, Tabassum, H, Zhao, R, Guo, W, Aftab, W, Liang, Z, Sun, Z & Zou, R 2018, 'Fe₂N/S/N Codecorated Hierarchical Porous Carbon Nanosheets for Trifunctional Electrocatalysis', Small, vol. 14, no. 49, pp. 1803500-1803500.
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AbstractConstruction of multifunctional highly active earth‐abundant electrocatalysts on a large scale is a great challenge due to poor control over nanostructural features and limited active sites. Here, a simple methodology to tailor metal–organic frameworks (MOFs) to extract highly active multifunctional electrocatalysts on a large scale for oxygen reduction (ORR), oxygen evolution (OER), and hydrogen evolution reaction (HER) is presented. The N, S codoped Fe2N decorated highly porous and defect‐rich carbon nanosheets are grown using MOF xerogels, melamine, and polyvinylpyrollidone. The resulting catalyst exhibits excellent activity for ORR with an onset (0.92 V) and half‐wave (0.81 V) potential similar to state‐of‐the‐art Pt/C catalysts. The catalyst also shows outstanding OER and HER activities with a small overpotential of 360 mV in 1 m KOH and −123 mV in 0.5 m H2SO4 at a current density of 10 mA cm−2, respectively. Excellent catalytic properties are further supported by theoretical calculations where relevant models are built and various possible activation sites are identified by first‐principles calculations. The results suggest that the carbon atoms adjacent to heteroatoms as well as Fe2–N sites present the active sites for improved catalytic response, which is in agreement with the experimental results.

Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2018, 'Environmental sustainability assessment of hydropower plant in Europe using life cycle assessment', IOP Conference Series: Materials Science and Engineering, vol. 351, pp. 012006-012006.
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Mai, HT, Tran, TS, Ho-Le, TP, Pham, TT, Center, JR, Eisman, JA & Nguyen, TV 2018, 'Low-trauma rib fracture in the elderly: Risk factors and mortality consequence', Bone, vol. 116, pp. 295-300.
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© 2018 Elsevier Inc. Purpose: Low trauma rib fracture (hereinafter, rib fracture) is common in the elderly, but its risk factors and mortality consequence are rarely studied. We sought to define the epidemiology of rib fracture and the association between rib fracture and postfracture mortality. Methods: The study was part of the Dubbo Osteoporosis Epidemiology Study, which was designed as a population-based prospective study, and consisted of 2041 women and men (aged ≥ 60). The incidence of rib fracture was ascertained from X-ray reports. Bone mineral density (BMD) was measured by DXA (GE-Lunar). The time-dependent Cox model was used to access the relationship between rib fracture and mortality. Results: During the median follow-up of 13 years, 59 men and 78 women had sustained a rib fracture, making the annual incidence of 4.8/1000 person-years. Each SD (0.15 g/cm 2 ) lower in femoral neck BMD was associated with ~2-fold increase in the hazard of fracture (hazard ratio [HR] 1.9; 95% CI, 1.4 to 2.6 in men; and HR 2.1; 95% CI, 1.6 to 2.8 in women). Among those with a rib fracture, the incidence of subsequent fractures was 10.2/100 person-years. Compared with those without a fracture, the risk of mortality among those with a fracture was increased by ~7.8-fold (95% CI, 2.7 to 22.5) in men and 4.9-fold (95% CI 2.0 to 11.8) in women within the first year postfracture. Conclusions: A rib fracture signifies an increased risk of subsequent fractures and mortality. The increased risk of mortality during the first 2.5 years postfracture suggests a window of opportunity for treatment.

Main, BJ & Rodgers, KJ 2018, 'Assessing the Combined Toxicity of BMAA and Its Isomers 2,4-DAB and AEG In Vitro Using Human Neuroblastoma Cells', Neurotoxicity Research, vol. 33, no. 1, pp. 33-42.
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The non-protein amino acid (NPAA) ß-methylamino-L-alanine (BMAA) is produced by a diverse range of cyanobacteria, diatoms and dinoflagellates, and is present in both aquatic and terrestrial ecosystems globally. Exposure to BMAA has been implicated in the development of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD) and Parkinson's disease (PD). BMAA is often found in nature along with its structural isomers 2,4-diaminobutyric acid (2,4-DAB) and aminoethylglycine (AEG); however, the toxicity of these NPAAs in combination has not been examined. We have previously demonstrated that BMAA induces endoplasmic reticulum (ER) stress and increases caspase and cathepsin activity in human neuroblastoma cells (SH-SY5Y), effects consistent with proteotoxic stress due to disturbances in protein synthesis, folding or turnover. The current study investigates whether 2,4-DAB and AEG share a similar mechanism of toxicity to BMAA, and if simultaneous exposure of cells to BMAA and its isomers results in increased toxicity in vitro. We show that a 48-h treatment with both 500 μM BMAA and 2,4-DAB decreases cell viability in vitro whereas AEG was not cytotoxic under the same conditions. Treatment of SH-SY5Y cells with 2,4-DAB did not increase expression of ER stress markers. Combined treatment of cells with BMAA and 2,4-DAB resulted in increased caspase activity and increased apoptosis above that of BMAA or 2,4-DAB on their own. These results suggest that 2,4-DAB does not share the same mechanism of toxicity as BMAA but the presence of 2,4-DAB increases the toxicity of BMAA to human cells in vitro.

Main, BJ, Bowling, LC, Padula, MP, Bishop, DP, Mitrovic, SM, Guillemin, GJ & Rodgers, KJ 2018, 'Detection of the suspected neurotoxin β-methylamino- l -alanine (BMAA) in cyanobacterial blooms from multiple water bodies in Eastern Australia', Harmful Algae, vol. 74, pp. 10-18.
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© 2018 The emerging toxin β-methylamino-L-alanine (BMAA) has been linked to the development of a number of neurodegenerative diseases in humans including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, and Parkinson's disease. BMAA has been found to be produced by a range of cyanobacteria, diatoms, and dinoflagellates worldwide, and is present in freshwater, saltwater, and terrestrial ecosystems. Surface scum samples were collected from waterways in rural and urban New South Wales, Australia and algal species identified. Reverse phase liquid chromatography-tandem mass spectrometry was used to analyse sixteen cyanobacterial scum for the presence of BMAA as well as its toxic structural isomer 2,4-diaminobutyric acid (2,4-DAB). BMAA was detected in ten of the samples analysed, and 2,4-DAB in all sixteen. The presence of these toxins in water used for agriculture raises concerns for public health and food security in Australia.

Main, BJ, Italiano, CJ & Rodgers, KJ 2018, 'Investigation of the interaction of β-methylamino-l-alanine with eukaryotic and prokaryotic proteins', Amino Acids, vol. 50, no. 3-4, pp. 397-407.
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There is a strong body of evidence linking the non-protein amino acid (NPAA) β-methylamino-L-alanine (BMAA) to the development of a number of neurodegenerative diseases. BMAA has been found globally, is produced by a number of organisms including cyanobacteria, diatoms, and dinoflagellates; and has been shown to biomagnify through trophic levels. The role of BMAA in neurodegenerative disease is highlighted by its presence in the brains of a number of neurodegenerative disease patients, where it was found in a protein-bound form. We have previously shown that BMAA is bound to cell proteins, and results in the upregulation of the unfolded protein response, an endoplasmic reticulum stress response activated by the presence of misfolded proteins within the cell. Structurally aberrant proteins are features of a number of neurodegenerative diseases, and further investigation of how BMAA interacts with proteins is crucial to our understanding of its toxicity. Here we use radiolabelled BMAA to investigate the interaction and binding of BMAA to eukaryotic and prokaryotic proteins. We found differences in the presence and distribution of protein-bound BMAA between E. coli and neuroblastoma cells, with an increase in binding over time only seen in the eukaryotic cells. We also found that BMAA was unable to bind to pure proteins, or cell lysate in native or denaturing conditions, indicating that biological processing is required for BMAA to bind to proteins.

Maire, E, Villéger, S, Graham, NAJ, Hoey, AS, Cinner, J, Ferse, SCA, Aliaume, C, Booth, DJ, Feary, DA, Kulbicki, M, Sandin, SA, Vigliola, L & Mouillot, D 2018, 'Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1883, pp. 20181167-20181167.
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Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.

Maitre, M, Horder, M, Kirkbride, KP, Gassner, A-L, Weyermann, C, Roux, C & Beavis, A 2018, 'A forensic investigation on the persistence of organic gunshot residues', Forensic Science International, vol. 292, pp. 1-10.
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© 2018 Elsevier B.V. Gunshot residues (GSR) are a potential form of forensic traces in firearm-related events. In most forensic laboratories, GSR analyses focus on the detection and characterisation of the inorganic components (IGSR), which are mainly particles containing mixtures of lead, barium and antimony originating from the primer. The increasing prevalence of heavy metal-free ammunition challenges the current protocols used for IGSR analysis. To provide complementary information to IGSR particles, the current study concentrated on the organic components (OGSR) arising from the combustion of the propellant. The study focused on four compounds well-known as being part of OGSR: ethylcentralite (EC), methylcentralite (MC), diphenylamine (DPA), N-nitrosodiphenylamine (N-nDPA). This study assessed the retention of these OGSR traces on a shooter's hands. The overall project aim was to provide appropriate information regarding OGSR persistence, which can be suitable to be integrated into the interpretation framework of OGSR as recommended by the recent ENFSI Guideline for Evaluative Reporting in Forensic Science. The persistence was studied through several intervals ranging from immediately after discharge to four hours and two ammunition calibres were chosen:.40 S&W calibre, used by the NSW Police Force; and.357 Magnum, which is frequently encountered in Australian casework. This study successfully detected the compounds of interest up to four hours after discharge. The trends displayed a large decrease in the amount detected during the first hour. A large variability was also observed due to numerous factors involved in the production, deposition and collection of OGSR.

Maitre, M, Kirkbride, KP, Horder, M, Roux, C & Beavis, A 2018, 'Thinking beyond the lab: organic gunshot residues in an investigative perspective', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-7.
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© 2018, © 2018 Australian Academy of Forensic Sciences. Gunshot residues (GSR) are a common form of evidence in cases involving questions related to the association of a person of interest (POI) to a firearm-related event. GSR analyses currently focus on the detection and characterisation of the inorganic components of GSR (IGSR), which are typically particles composed of lead, barium and antimony originating from the primer. However, certain particles cannot be assigned to IGSR with a high degree of confidence due to possibility of being derived from industrial or domestic sources. Moreover, the increasing prevalence of the use of heavy metal-free ammunition challenges the current protocols used for IGSR analysis. In order to provide complementary evidence to IGSR particles, the current study focused on detecting the organic components (OGSR) arising from ammunition propellant. As the study focuses on the persistence of OGSR, three compounds well known as being part of OGSR were selected: ethyl centralite (EC), diphenylamine (DPA) and N-nitrosodiphenylamine (NnDPA). The study assessed the retention of OGSR traces on a person’s hands up to 1 h after they had discharged a firearm.

Maixner, F, Turaev, D, Cazenave-Gassiot, A, Janko, M, Krause-Kyora, B, Hoopmann, MR, Kusebauch, U, Sartain, M, Guerriero, G, O’Sullivan, N, Teasdale, M, Cipollini, G, Paladin, A, Mattiangeli, V, Samadelli, M, Tecchiati, U, Putzer, A, Palazoglu, M, Meissen, J, Lösch, S, Rausch, P, Baines, JF, Kim, BJ, An, H-J, Gostner, P, Egarter-Vigl, E, Malfertheiner, P, Keller, A, Stark, RW, Wenk, M, Bishop, D, Bradley, DG, Fiehn, O, Engstrand, L, Moritz, RL, Doble, P, Franke, A, Nebel, A, Oeggl, K, Rattei, T, Grimm, R & Zink, A 2018, 'The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals', Current Biology, vol. 28, no. 14, pp. 2348-2355.e9.
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The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.

Majeed, I, Manzoor, U, Kanodarwala, FK, Nadeem, MA, Hussain, E, Ali, H, Badshah, A, Stride, JA & Nadeem, MA 2018, 'Pd–Ag decorated g-C₃N₄as an efficient photocatalyst for hydrogen production from water under direct solar light irradiation', Catalysis Science & Technology, vol. 8, no. 4, pp. 1183-1193.
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Pd–Ag bimetallic and monometallic nanoparticles were decorated on g-C₃N₄and evaluated for their ability to produce H₂through water splitting reactions.

Malik, S, Afzal, I, Mehmood, MA, Al Doghaither, H, Rahimuddin, SA, Gull, M & Nahid, N 2018, 'Heterologous Synthesis and Recovery of Advanced Biofuels from Bacterial Cell Factories', Protein & Peptide Letters, vol. 25, no. 2, pp. 120-128.
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BACKGROUND: Microbial engineering to produce advanced biofuels is currently the most encouraging approach in renewable energy. Heterologous synthesis of biofuels and other useful industrial chemicals using bacterial cell factories has radically diverted the attentions from the native synthesis of these compounds. However, recovery of biofuels from the media and cellular toxicity are the main hindrances to successful commercialization of advanced biofuels. Therefore, membrane transporter engineering is gaining increasing attentions from all over the world. OBJECTIVE: The main objective of this review is to explore the ways to increase the microbial production of biofuels by counteracting the cellular toxicity and facilitating their easier recovery from media. CONCLUSION: Microbial synthesis of industrially viable compounds such as biofuels has been increased due to genomic revolution. Moreover, advancements in protein engineering, gene regulation, pathway portability, metabolic engineering and synthetic biology led the focus towards the development of robust and cost-effective systems for biofuel production. The most convenient way to combat cellular toxicity and to secrete biofuels is the use of membrane transport system. The use of membrane transporters is currently a serious oversight as do not involve chemical changes and contribute greatly to efflux biofuels in extracellular milieu. However, overexpression of transport systems can also be detrimental to cell, so, in future, structure-based engineering of transporters can be employed to evaluate optimum expression range, to increase biofuel specificity and transport rate through structural studies of biofuel molecules.

Mallick, K, Toivonen, E, Trebs, I, Boegh, E, Cleverly, J, Eamus, D, Koivusalo, H, Drewry, D, Arndt, SK, Griebel, A, Beringer, J & Garcia, M 2018, 'Bridging Thermal Infrared Sensing and Physically‐Based Evapotranspiration Modeling: From Theoretical Implementation to Validation Across an Aridity Gradient in Australian Ecosystems', Water Resources Research, vol. 54, no. 5, pp. 3409-3435.
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AbstractThermal infrared sensing of evapotranspiration (E) through surface energy balance (SEB) models is challenging due to uncertainties in determining the aerodynamic conductance (gA) and due to inequalities between radiometric (TR) and aerodynamic temperatures (T0). We evaluated a novel analytical model, the Surface Temperature Initiated Closure (STIC1.2), that physically integrates TR observations into a combined Penman‐Monteith Shuttleworth‐Wallace (PM‐SW) framework for directly estimating E, and overcoming the uncertainties associated with T0 and gA determination. An evaluation of STIC1.2 against high temporal frequency SEB flux measurements across an aridity gradient in Australia revealed a systematic error of 10–52% in E from mesic to arid ecosystem, and low systematic error in sensible heat fluxes (H) (12–25%) in all ecosystems. Uncertainty in TR versus moisture availability relationship, stationarity assumption in surface emissivity, and SEB closure corrections in E were predominantly responsible for systematic E errors in arid and semi‐arid ecosystems. A discrete correlation (r) of the model errors with observed soil moisture variance (r = 0.33–0.43), evaporative index (r = 0.77–0.90), and climatological dryness (r = 0.60–0.77) explained a strong association between ecohydrological extremes and T

Manandhar, B, Paudel, KR, Sharma, B & Karki, R 2018, 'Phytochemical profile and pharmacological activity of Aegle marmelos Linn.', Journal of Integrative Medicine, vol. 16, no. 3, pp. 153-163.
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© 2018 Aegle marmelos Linn. (Rutaceae), commonly known as “bael” in Nepal and India, is a valuable medicinal plant and is considered sacred by the Hindus. It is used to cure several diseases in the Indian traditional medicine system of Ayurveda and has had similar uses among many ethnic communities residing in Indian subcontinent for over 5000 years. Its leaves, bark, stem, fruits and seeds have been used for various medicinal purposes. Bael fruits are especially effective in the treatment of chronic diarrhea, dysentery and peptic ulcers, while they are also useful as a laxative and cure for respiratory infections. Scientific studies have validated many of the ethnomedicinal uses of A. marmelos, which include antibacterial, antiviral, antidiarrheal, gastroprotective, anti-ulcerative colitis, hepatoprotective, antidiabetic, cardioprotective and radioprotective effects. Recently, this plant has also received attention as an anticancer agent for the treatment of various types of cancers. Thus, this review focuses on scientific evidence verifying the important pharmacological activity such as antioxidant, antidiabetic, antimicrobial, hepatoprotective, cardioprotective and anticancer activity of A. marmelos.

Manshare, K, Anand, A, Mahajan, S, Satija, S, Sharma, N, Khurana, N, Duggal, N & Mehta, M 2018, 'Evaluation of nephroprotective activity of gallic acid in gentamicin-induced rat model of nephrotoxicity', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 48-52.
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Introduction: Renal damage due to gentamicin is associated with oxidative stress. Gallic acid is a phenolic compound that possesses antioxidant and anti-inflammatory properties. Hence, an attempt was made to explore the nephroprotective activity of gallic acid in gentamicin-induced nephrotoxicity. Materials and Methods: Wistar albino rats of either sex were used. Experimental nephrotoxicity was produced by intraperitoneal administration of gentamicin for 8 days. Rats were divided into five groups: Group I - normal control (normal Saline), Group II - gentamicin only treated group (100 mg/kg), Group III - gentamicin (s100 mg/kg) + Vitamin C (200 mg/kg), Group IV (treatment group) - gentamicin (100 mg/kg) + gallic acid (200 mg/kg), and Group V - gentamicin (100 mg/kg) + gallic acid (400 mg/kg). The period of drug administration was of 8 days, in which animals were treated with Vitamin C and gallic acid. After the treatment for 8 days, the animals were sacrificed for the investigation of biochemical parameters and histopathological examination. Results: Gentamicin-induced nephrotoxicity was successfully reproduced. Concurrent administration of gallic acid along with gentamicin significantly prevented the rise in level of serum creatinine, serum urea, blood urea nitrogen, and total protein. Administration of gallic acid also leads to increase glutathione and superoxide dismutase level in the kidney. Therefore, gallic acid had significantly prevented nephrotoxicity as compared to the group receiving gentamicin drug alone. Conclusion: These results showed that gallic acid is effective as nephroprotective agent.

Mao, W, Lyu, Y, Pu, N, Li, J, Xin, B, Chen, W, Jin, D, Lou, W & Xu, X 2018, '[Prognostic analysis and clinicopathological features of 20 patients with appendiceal neuroendocrine neoplasms].', Zhonghua Wei Chang Wai Ke Za Zhi, vol. 21, no. 5, pp. 564-568.
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OBJECTIVE: To investigate clinicopathological features and prognostic factors of appendiceal neuroendocrine neoplasms(a-NEN). METHODS: Clinical data of 20 patients diagnosed with a-NEN at Zhongshan Hospital of Fudan University between January 2000 and December 2016 were retrospectively analyzed. Pathological diagnosis was based on the WHO classification criteria of digestive system tumors (2010 edition). Based on the mitotic count and Ki-67 index, a-NENs were divided into grade 1 neuroendocrine tumor (NET G1), grade 2(G2) NET G2) and grade 3 (neuroendocrine carcinoma, NEC). Some special types of a-NEN (e.g. goblet cell carcinoid) and mixed adenoneuroendocrine neoplasms were classified as mixed adenoneuroendocrine carcinoma (MANEC). Follow-up was conducted by telephone or return visits. Univariate analysis was carried out using the Kaplan-Meier method, and the log-rank test was used to draw survival curves. RESULTS: Of 20 patients, 14 were male and 6 were female with median age of 54 years. Seventeen cases presented acute right lower quadrant abdominal pain, 1 chronic right lower quadrant abdominal pain, 1 persistent abdominal discomfort with outburst whole abdominal pain and 1 was found during body check without symptoms. Twenty cases comprised 8 G1 patients, 4 G2 patients, 3 G3 patients, and 5 MANEC patients. When diagnosed, there was 1 patient with liver metastasis, 1 patient with abdominal and pelvic metastases, and 2 patients with postoperative pathological findings of lymph node metastasis. Six patients underwent appendectomy, 12 underwent right hemicolectomy, 1 underwent right hemicolectomy plus small intestine resection, and 1 underwent partial hepatectomy plus right hemicolectomy. The follow-up time was 7-187 months(average, 36 months). The total 1- and 3-year survival rates were 94.7% and 60.2%, respectively. Univariate analysis showed that age >50 years (χ2=7.036, P=0.008), pathology grade as MANEC (χ2=5.297, P=0.021), and metastasis (χ2=6.558...

Marsili, E, Kjelleberg, S & Rice, SA 2018, 'Mixed community biofilms and microbially influenced corrosion', Microbiology Australia, vol. 39, no. 3, pp. 152-152.
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Metals are used in most marine infrastructures for energy extraction and production. Metal corrosion is a serious concern, due to the environmental, safety, and replacement costs associated with it. Microbially influenced corrosion (MIC) contributes to the overall corrosion process, through several chemical, electrochemical and biochemical mechanisms, particularly in the presence of microbial biofilms. In this short article, we discuss briefly recent advances in MIC research, comparing corrosion in single species and mixed species biofilms, and outline possible strategies for biofilm and corrosion control.

Mateer, SW, Mathe, A, Bruce, J, Liu, G, Maltby, S, Fricker, M, Goggins, BJ, Tay, HL, Marks, E, Burns, G, Kim, RY, Minahan, K, Walker, MM, Callister, RC, Foster, PS, Horvat, JC, Hansbro, PM & Keely, S 2018, 'IL-6 Drives Neutrophil-Mediated Pulmonary Inflammation Associated with Bacteremia in Murine Models of Colitis', The American Journal of Pathology, vol. 188, no. 7, pp. 1625-1639.
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© 2018 American Society for Investigative Pathology Inflammatory bowel disease (IBD) is associated with several immune-mediated extraintestinal manifestations. More than half of all IBD patients have some form of respiratory pathology, most commonly neutrophil-mediated diseases, such as bronchiectasis and chronic bronchitis. Using murine models of colitis, we aimed to identify the immune mechanisms driving pulmonary manifestations of IBD. We found increased neutrophil numbers in lung tissue associated with the pulmonary vasculature in both trinitrobenzenesulfonic acid– and dextran sulfate sodium–induced models of colitis. Analysis of systemic inflammation identified that neutrophilia was associated with bacteremia and pyrexia in animal models of colitis. We further identified IL-6 as a systemic mediator of neutrophil recruitment from the bone marrow of dextran sulfate sodium animals. Functional inhibition of IL-6 led to reduced systemic and pulmonary neutrophilia, but it did not attenuate established colitis pathology. These data suggest that systemic bacteremia and pyrexia drive IL-6 secretion, which is a critical driver for pulmonary manifestation of IBD. Targeting IL-6 may reduce neutrophil-associated extraintestinal manifestations in IBD patients.

Matis, PA, Donelson, JM, Bush, S, Fox, RJ & Booth, DJ 2018, 'Temperature influences habitat preference of coral reef fishes: Will generalists become more specialised in a warming ocean?', Global Change Biology, vol. 24, no. 7, pp. 3158-3169.
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AbstractClimate change is expected to pose a significant risk to species that exhibit strong behavioural preferences for specific habitat types, with generalist species assumed to be less vulnerable. In this study, we conducted habitat choice experiments to determine how water temperature influences habitat preference for three common species of coral reef damselfish (Pomacentridae) that differ in their levels of habitat specialisation. The lemon damselfish Pomacentrus moluccensis, a habitat specialist, consistently selected complex coral habitat across all temperature treatments (selected based on local average seasonal temperatures naturally experienced in situ: ambient winter 22°C; ambient summer 28°C; and elevated 31°C). Unexpectedly, the neon damselfish Pomacentrus coelestis and scissortail sergeant Abudefduf sexfasciatus, both of which have more generalist habitat associations, developed strong habitat preferences (for complex coral and boulder habitat, respectively) at the elevated temperature treatment (31°C) compared to no single preferred habitat at 22°C or 28°C. The observed shifts in habitat preference with temperature suggest that we may be currently underestimating the vulnerability of some habitat generalists to climate change and highlight that the ongoing loss of complex live coral through coral bleaching could further exacerbate resource overlap and species competition in ways not currently considered in climate change models.

MATTHEWS, CE, KOZEY KEADLE, S, MOORE, SC, SCHOELLER, DS, CARROLL, RJ, TROIANO, RP & SAMPSON, JN 2018, 'Measurement of Active and Sedentary Behavior in Context of Large Epidemiologic Studies', Medicine & Science in Sports & Exercise, vol. 50, no. 2, pp. 266-276.
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Copyright © 2017 by the American College of Sports Medicine Introduction/Purpose: To assess the utility of measurement methods that may be more accurate and precise than traditional questionnaire-based estimates of habitual physical activity and sedentary behavior we compared the measurement properties of a past year questionnaire (AARP) and more comprehensive measures: an internet-based 24-h recall (ACT24), and a variety of estimates from an accelerometer (ActiGraph). Methods: Participants were 932 adults (50-74 yr) in a 12-month study that included reference measures of energy expenditure from doubly labeled water (DLW) and active and sedentary time via activPAL. Results: Accuracy at the group level (mean differences) was generally better for both ACT24 and ActiGraph than the AARP questionnaire. The AARP accuracy for energy expenditure ranged from j4% to j13% lower than DLW, but its accuracy was poorer for physical activity duration (j48%) and sedentary time (j18%) versus activPAL. In contrast, ACT24 accuracy was within 3% to 10% of DLW expenditure measures and within 1% to 3% of active and sedentary time from activPAL. For ActiGraph, accuracy for energy expenditure was best for the Crouter 2-regression method (j2% to j7%), and for active and sedentary time the 100 counts per minute cutpoint was most accurate (j1% to 2%) at the group level. One administration of the AARP questionnaire was significantly correlated with long-term average from the reference measures (Q TX = 0.16-0.34) overall, but four ACT24 recalls had higher correlations (Q TX = 0.48-0.60), as did 4 d of ActiGraph assessment (Q TX = 0.54-0.87). Conclusions: New exposure assessments suitable for use in large epidemiologic studies (ACT24, ActiGraph) were more accurate and had higher correlations than a traditional questionnaire. Use of better more comprehensive measures in future epidemiologic studies could yield new etiologic discoveries and possibly new opportunities for prevention.

Matthews, JL, Oakley, CA, Lutz, A, Hillyer, KE, Roessner, U, Grossman, AR, Weis, VM & Davy, SK 2018, 'Partner switching and metabolic flux in a model cnidarian–dinoflagellate symbiosis', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1892, pp. 20182336-20182336.
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Metabolite exchange is fundamental to the viability of the cnidarian–Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13 C stable-isotope labelling coupled to gas chromatography–mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii . Relative to anemones containing B. minutum , D. trenchii -colonized hosts exhibited a 4.5-fold reduction in 13 C-labelled glucose and reduced abundance and diversity of 13 C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii- colonized hosts exhibited a 40-fold reduction in 13 C-labelled scyllo -inositol, a potential interpartner signalling molecule in symbiosis specificity. 13 C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses ...

McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2018, 'Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)', Algal Research, vol. 35, pp. 586-594.
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© 2018 Elsevier B.V. In consideration that, fatty acids bound within phospholipids may exhibit greater levels of bioavailability than neutral lipids, we investigated the effect of nutrient starvation on the phospholipid content and composition of cultivated Ulva biomass. Furthermore, we explored the simultaneous effects on the pigment and phenolic profiles and then correlation analysis to anti-oxidant and anti-inflammatory activity. High nutrient cultivation (nitrogen replete) provided a biomass with desirable n-6/n-3 (0.3) and 18:2n-6/18:3n-3 (0.5) ratios and beneficial 18:4n-3, 20:5n-3, 22:5n-3 fatty acids. These fatty acids dominated the abundant neutral lipid fraction, which comprised 62% of the lipid extract. The remaining phospholipids (38%) were characterised by high 16:0 (49.6%), 18:1n-7 (14.6%) and 18:3n-3 (13.6%) fatty acids. Nutrient-depleted samples had a 3-fold higher total fatty acid (TFA) content (12.05 mg·g−1 d.w, p < 0.0001) compared to nutrient replete samples (3.35 mg·g−1 d.w.). This occurred mostly within the neutral fraction, which represented 88% of the total lipids and the fatty acids 16:0 (4.02 ± 0.15 mg·g−1), 18:1n-7 (1.79 ± 0.06 mg·g−1), 18:2n-6 (2.30 ± 0.08 mg·g−1) and 18:3n-3 (1.09 ± 0.03 mg·g−1 d.w). Nutrient replete biomass yielded 1.5 mg·g−1 total chlorophyll, 0.1 mg·g−1 carotenoids and 1.6 mg·g−1 phenolics, whilst low nutrient growth conditions reduced the presence of pigments by 98%, phenolics by 34% and anti-oxidant activity by 87%. Significantly higher yields of pigment and phenolics were obtained using 95% ethanol for the extraction process, whilst acetone extracts were characterised by a higher proportion of carotenoids. All extracts from cultivated Ulva samples inhibited nitric oxide (NO) (≥81%) with acetone extracts demonstrating higher inhibition (94–97%) than 95% ethanol extracts (81–90%) with no significant effects observed between the two treatments. Thus, Ulva cultivated under high nutrients offers a sustainable source ...

McDonagh, J, Martin, L, Ferguson, C, Jha, SR, Macdonald, PS, Davidson, PM & Newton, PJ 2018, 'Frailty assessment instruments in heart failure: A systematic review', European Journal of Cardiovascular Nursing, vol. 17, no. 1, pp. 23-35.
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Background: Frailty is an independent predictor of mortality across many conditions. Reported rates of frailty in heart failure range from 15% to 74%. There are several instruments available to assess frailty; however, to date there has been no consensus on the most appropriate instrument for use in individuals with heart failure. Aims: To identify how frailty is assessed in individuals with heart failure and to elucidate which domains of frailty are most frequently assessed. Methods: Key electronic databases were searched (MEDLINE, COCHRANE Central and CINAHL) to identify studies that assessed frailty in individuals with heart failure using a formal frailty instrument. Results: Twenty studies published in 24 articles were included, for which a total of seven unique frailty instruments were identified. The most commonly used instrument was the Frailty Phenotype ( n= 11), with the majority of studies using a modified version of the Frailty Phenotype ( n= 8). The second most commonly used instrument identified was the Comprehensive Geriatric Assessment ( n= 4). Conclusion: There is an increasing interest in the assessment of frailty, but, to date, there is no frailty instrument validated specifically in the heart failure population.

McGowan, EM, Lin, Y & Hatoum, D 2018, 'Good Guy or Bad Guy? The Duality of Wild-Type p53 in Hormone-Dependent Breast Cancer Origin, Treatment, and Recurrence', Cancers, vol. 10, no. 6, pp. 172-172.
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“Lactation is at one point perilously near becoming a cancerous process if it is at all arrested”, Beatson, 1896. Most breast cancers arise from the milk-producing cells that are characterized by aberrant cellular, molecular, and epigenetic translation. By understanding the underlying molecular disruptions leading to the origin of cancer, we might be able to design novel strategies for more efficacious treatments or, ambitiously, divert the cancerous process. It is an established reality that full-term pregnancy in a young woman provides a lifetime reduction in breast cancer risk, whereas delay in full-term pregnancy increases short-term breast cancer risk and the probability of latent breast cancer development. Hormonal activation of the p53 protein (encode by the TP53 gene) in the mammary gland at a critical time in pregnancy has been identified as one of the most important determinants of whether the mammary gland develops latent breast cancer. This review discusses what is known about the protective influence of female hormones in young parous women, with a specific focus on the opportune role of wild-type p53 reprogramming in mammary cell differentiation. The importance of p53 as a protector or perpetrator in hormone-dependent breast cancer, resistance to treatment, and recurrence is also explored.

McGrath, KCY, Gangoda, SVS, Li, X-H, McRobb, LS & Heather, AK 2018, 'Corrigendum to “Inhibitory Effect of a French Maritime Pine Bark Extract‐Based Nutritional Supplement on TNF‐α‐Induced Inflammation and Oxidative Stress in Human Coronary Artery Endothelial Cells”', Evidence-Based Complementary and Alternative Medicine, vol. 2018, no. 1, pp. 1-1.
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[This corrects the article DOI: 10.1155/2015/260530.].

McIlroy, DJ, Minahan, K, Keely, S, Lott, N, Hansbro, P, Smith, DW & Balogh, ZJ 2018, 'Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome', Journal of Trauma and Acute Care Surgery, vol. 85, no. 2, pp. 354-358.
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BACKGROUND Cell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients’ plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA. METHODS Two-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30–59 years]; injury severity score, 18 [interquartile range, 12–26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples. RESULTS Increased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with he...

McIlroy, DJ, Minahan, K, Keely, S, Lott, N, Hansbro, P, Smith, DW & Balogh, ZJ 2018, 'Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome.', J Trauma Acute Care Surg, vol. 85, no. 2, pp. 354-358.
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BACKGROUND: Cell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients' plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA. METHODS: Two-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30-59 years]; injury severity score, 18 [interquartile range, 12-26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples. RESULTS: Increased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with healthy controls (DNAse: 0.17 ± 0.03U/mL). There was no correlation between DNAse and perioperative DNA concentrations. Elevated mtDNA (but not nDNA) correlated with the development of systemic inflammatory response syndrome (SIRS) (p = 0.026) but not multiple organ failure. CONCLUSIONS: The significant perioperative elevation in plasma-free mtDNA concentration is associated with the development of SIRS. The fa...

McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2018, 'Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis', International Journal of Antimicrobial Agents, vol. 52, no. 3, pp. 430-435.
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© 2018 Sequence type 58 (ST58) phylogroup B1 Escherichia coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multidrug-resistant E. coli ST58 strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing. Both ST58 strains were clonal and were characterised as serotype O8:H25, phylogroup B1 and carried a complex resistance locus/loci (CRL) that featured an atypical class 1 integron with a dfrA5 (trimethoprim resistance) gene cassette followed by only 24 bp of the 3ʹ-CS. CRL that carry this particular integron have been described previously in E. coli from cattle, pigs and humans in Australia. The integron abuts a copy of Tn6029, an IS26-flanked composite transposon encoding blaTEM, sul2 and strAB genes that confer resistance to ampicillin, sulfathiazole and streptomycin, respectively. The CRL resides within a novel Tn2610-like hybrid Tn1721/Tn21 transposon on an IncF, ColV plasmid (pSDJ2009-52F) of 138 553 bp that encodes virulence associated genes implicated in life-threatening extraintestinal pathogenic E. coli (ExPEC) infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 strain from a patient with blood sepsis from a hospital in San Francisco. These data suggest that extraintestinal infections caused by E. coli carrying ColV-like plasmids, irrespective of their phylogroup or ST, may pose a potential threat to human health, particularly to the elderly and immunocompromised.

McNevin, D 2018, 'Bayesian interpretation of discrete class characteristics', Forensic Science International, vol. 292, pp. 125-130.
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Bayesian interpretation of forensic evidence has become dominated by the likelihood ratio (LR) with a large LR generally considered favourable to the prosecution hypothesis, HP, over the defence hypothesis, HD. However, the LR simply quantifies by how much the prior odds ratio of the probability of HP relative to HD has been improved by the forensic evidence to provide a posterior ratio. Because the prior ratio is mostly neglected, the posterior ratio is largely unknown, regardless of the LR used to improve it. In fact, we show that the posterior ratio will only favour HP when LR is at least as large as the number of things that could possibly be the source of that evidence, all being equally able to contribute. This restriction severely limits the value of evidence to the prosecution when only a single, discrete class characteristic is used to match a subset of these things to the evidence. The limitation can be overcome by examining more than one individual characteristic, as long as they are independent of each other, as they are for the genotypes at multiple loci combined for DNA evidence. We present a criterion for determining how many such characteristics are required. Finally, we conclude that a frequentist interpretation is inappropriate as a measure of the strength of forensic evidence precisely because it only estimates the denominator of the LR.

Mediati, DG, Burke, CM, Ansari, S, Harry, EJ & Duggin, IG 2018, 'High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division', BMC Genomics, vol. 19, no. 1.
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© 2018 The Author(s). Background: Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. Results: We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. Conclusions: The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation.

Mehta, M, Garg, M, Dua, K & Satija, S 2018, 'Simultaneous HPTLC Densitometric Estimation of KBA and AKBA from Boswellia serrata', Current Analytical Chemistry, vol. 15, no. 1, pp. 84-91.
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Background: Boswellic acids (BAs) are extracted from oleo gum of Boswellia serrata andare utilized as potential anti-inflammatory, hypolipidemic, immunomodulatory and antitumor specialists.The present examination was meant to assess KBA and AKBA in Boswellia serrata separate byHigh-Performance Thin Layer Chromatography (HPTLC).Methods:The separation of bioactive compounds was performed utilizing mobile phase glacial aceticacid, n-hexane, ethyl acetate and toluene (0.3: 1: 8: 2) (v/v/v/v) and distinguished at wavelength 254nm. The technique was approved for linearity, precision, accuracy, limit of detection (LOD), limit ofquantification (LOQ), and so forth by International Conference on Harmonization guidelines.Results: The calibration range was observed to be 2- 14 μg/band for both the bioactive compounds.KBA was isolated with an Rf estimation of 0.39 ± 0.02 and AKBA with an Rf estimation of0.42 ± 0.02. The accuracy was seen to be as high as 99.17% and 97.42 for KBA and KBA, respectively.The percentage RSD value for intra-day and between day varieties was under 2%. The system indicatedhigh affectability and specificity.Conclusion: The developed HPTLC method was simple, precise, robust, specific, rapid, and costeffectiveand could be used for quality control analysis and quantification of KBA and AKBA in differentherbal formulations containing the plant species.

Mehta, M, Kalsi, V, Sharma, N, Khurana, N, Duggal, N, Khatik, GL, Singh, D, Mahajan, S, Singh, A, Satija, S, Gupta, R & Verma, S 2018, 'Pharmacognostic and pharmacological screening of Psidium guajava stem extract for its analgesic potential', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 53-57.
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Context: The search for biologically active compounds from natural source has always been of great interest to researchers looking for new source of drugs useful in infectious diseases. Higher plants have played a vital role as the source of important therapeutic agents. Objective: The present investigation was aimed to find novel analgesic agent from herbal origin. For the purpose, Psidium guajava stem extracts was screened for its analgesic potential. Materials and Methods: Animal model of acetic acid induced writhing was followed. Three different extracts were used to study the activity. Results: The methanolic extract at the dose tested was shown to possess analgesic activity. The significant reduction in acetic acid-induced writhings suggests that the analgesic effect may be peripherally mediated via the inhibition of synthesis and release of prostaglandins (PGs) and other endogenous substances. Discussion: The abdominal constriction response induced by acetic acid is a sensitive procedure to evaluate peripherally acting analgesics. In general acetic acid causes pain by liberating endogenous substances such as serotonin, histamine, PGs bradykinins and substance P, which stimulate nerve endings. Local peritoneal receptors are postulated to be involved in the abdominal constrictions response. Conclusion: It can be concluded that the crude extract of stem of P. guajava have given positive results for analgesic activity. These medicinal herbs may afford lead compounds which could be beneficial for future drug development.

Mehta, M, Neeta, Pandey, P, Mahajan, S & Satija, S 2018, 'Gastro retentive drug delivery systems: An overview', Research Journal of Pharmacy and Technology, vol. 11, no. 5, pp. 2157-2157.
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© RJPT All right reserved. Orally administered gastro retentive dosage forms draws great attention in the pharmaceutical research industry. These systems improved patient compliance with increased therapeutic index of drugs increase importance of gastro-retentive drug delivery systems (GRDDS). Numerous physiological constraints associated with gastroretentive dosage forms such as short gastric retentive time, variations in gastric emptying time can be reduced by various technological advanced utilized in the design and fabrication of gastroretentive dosage. Currently different development approaches are utilized to increase gastric retention time, including High density systems, Expanding systems, Unfoldable and Swellable systems and Superporous hydrogels. The present review briefly addresses various gastroretentive dosage forms for prolongation gastric residence time.

Mehta, M, Shukla, B, Khurana, N, Arora, P, Sharma, N, Mahajan, S, Khatik, GL, Verma, S, Vyas, M & Satija, S 2018, 'Recent patent technologies of boswellic acids: A short review', Drug Invention Today, vol. 10, no. 8, pp. 1446-1449.
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Boswellic acids (BAs) are pentacyclic triterpenoids and have potent biological properties that resulted in a number of protocols being developed for their synthesis. During the past 28 years (1990-2018), a number of synthetic BAs have been prepared. Both natural BAs and their synthetic derivatives can be used to treat various cancers as well as inflammatory diseases. This review covers patents on therapeutic activities of natural BAs and their synthetic derivatives published in past 28 years (1990-2018). BAs possess excellent anticancer and anti-inflammatory properties. A large number of BAs and their analogs have been prepared through modification at functional groups. Most importantly, the C-24 amide and amino derivatives demonstrated increased anticancer and anti-inflammatory activity compared with other BA derivatives. Furthermore, BAs have the potential to form conjugates with other anticancer drugs that will synergistically enhance their anticancer effects, and we believe that to get lead compounds, there needs to be a greater focus on the synthesis of halo derivatives of BAs.

Meiklejohn, KA, Wallman, JF & Pape, T 2018, 'Sarcophaga maxima sp. nov. (Diptera: Sarcophagidae: Sarcophaginae), a new Australian flesh fly recognised by morphology and DNA barcoding', Austral Entomology, vol. 57, no. 1, pp. 17-24.
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AbstractA new species, Sarcophaga (Sarcorohdendorfia) maxima sp. nov., supported by both morphological and DNA barcoding data, is described from Queensland and New South Wales, Australia. The major morphological features of the new species are listed, and the male terminalia are documented with both photography and scanning electron microscopy. Sarcophaga alcicornis Hardy, 1932 is transferred from subgenus Lioproctia Enderlein to Sarcorohdendorfia Baranov.

Mena, J, Brito, B, Moreira, R, Tadich, T, González, I, Cruces, J, Ortega, R, van Bakel, H, Rathnasinghe, R, Pizarro-Lucero, J, Medina, R & Neira, V 2018, 'Reemergence of H3N8 Equine Influenza A virus in Chile, 2018', Transboundary and Emerging Diseases, vol. 65, no. 6, pp. 1408-1415.
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© 2018 Blackwell Verlag GmbH A new outbreak of equine Influenza A virus (IAV) was reported in Chile in January 2018, 6 years after its last report in 2012. Equine IAV was detected by rtRT-PCR, followed by virus isolation and full genome sequencing. Genetic characterization of equine IAV classified the virus within clade 1 of the Florida sublineage. Although this is the same sublineage that caused an outbreak in Chile in 2012, the virus has a high similarity to other cocirculating viruses that were recently identified in Europe and Asia. The Chilean 2018 equine influenza (EI) outbreak was caused by an H3N8 strain circulating globally that spread through horse movements.

Meng, Z, Tan, X, Zhang, S, Ying, H, Yan, X, Tian, H, Wang, G & Han, W-Q 2018, 'Ultra-stable binder-free rechargeable Li/I₂ batteries enabled by “Betadine” chemical interaction', Chemical Communications, vol. 54, no. 87, pp. 12337-12340.
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ACC/PVP–I₂ was employed as a cathode for Li/I₂ batteries. The synergistic effect in the cathode enabled superior electrochemical performance of the cells.

Miles, NG, Butler, GL, Diamond, SL, Bishop, DP, van der Meulen, DE, Reinfelds, I & Walsh, CT 2018, 'Combining otolith chemistry and telemetry to assess diadromous migration in pinkeye mullet, Trachystoma petardi (Actinopterygii, Mugiliformes)', Hydrobiologia, vol. 808, no. 1, pp. 265-281.
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© 2017, Springer International Publishing AG, part of Springer Nature. This study examines the complex diadromous movements in pinkeye mullet (Trachystoma petardi) of south-eastern Australia. The techniques used to study these movements included LA-ICP-MS single line ablation transects and microchemical imaging as well as preliminary acoustic telemetry results which were used to aid in interpretation of chemical signatures related to complex movement patterns across salinity gradients. Ba:Ca and Sr:Ca from single ablation transects and microchemical images revealed differences between the otolith core and outer regions. Otolith Ba:Ca and Sr:Ca patterns were more easily distinguished in images compared to transects and these revealed that T. petardi spend their early life in saline waters. Movement patterns for adults varied, with a range of movements identified between fresh and saline waters. Telemetry data assisted in explaining the likely cause of the ambiguity in otolith microchemistry data, including identification of multiple rapid movements across salinity gradients. However, many movements through salinity gradients appear too brief to result in any clear Sr:Ca or Ba:Ca saline or mesohaline signature within the chemistry of the otolith. The combination of otolith chemistry and telemetry proved useful in providing information on this poorly understood species suggesting that T. petardi display a catadromous life history.

Mitchell, AB, Mourad, B, Buddle, L, Peters, MJ, Oliver, BGG & Morgan, LC 2018, 'Viruses in bronchiectasis: a pilot study to explore the presence of community acquired respiratory viruses in stable patients and during acute exacerbations', BMC Pulmonary Medicine, vol. 18, no. 1.
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© 2018 The Author(s). Background: Bronchiectasis is a chronic respiratory condition. Persistent bacterial colonisation in the stable state with increased and sometimes altered bacterial burden during exacerbations are accepted as key features in the pathophysiology. The extent to which respiratory viruses are present during stable periods and in exacerbations is less well understood. Methods: This study aimed to determine the incidence of respiratory viruses within a cohort of bronchiectasis patients with acute exacerbations at a teaching hospital and, separately, in a group of patients with stable bronchiectasis. In the group of stable patients, a panel of respiratory viruses were assayed for using real time quantitative PCR in respiratory secretions and exhaled breath. The Impact of virus detection on exacerbation rates and development of symptomatic infection was evaluated. Results: Routine hospital-based viral PCR testing was only requested in 28% of admissions for an exacerbation. In our cohort of stable bronchiectasis patients, viruses were detected in 92% of patients during the winter season, and 33% of patients during the summer season. In the 2-month follow up period, 2 of 27 patients presented with an exacerbation. Conclusions: This pilot study demonstrated that respiratory viruses are commonly detected in patients with stable bronchiectasis. They are frequently detected during asymptomatic viral periods, and multiple viruses are often present concurrently.

Mitchell, AB, Mourad, B, Morgan, LC, Oliver, BGG & Glanville, AR 2018, 'Transplanting the pulmonary virome: Dynamics of transient populations', The Journal of Heart and Lung Transplantation, vol. 37, no. 9, pp. 1111-1118.
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Mitchell, AB, Tang, B, Shojaei, M, Barnes, LS, Nalos, M, Oliver, BG & McLean, AS 2018, 'A novel sampling method to detect airborne influenza and other respiratory viruses in mechanically ventilated patients: a feasibility study', Annals of Intensive Care, vol. 8, no. 1.
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© 2018, The Author(s). Background: Respiratory viruses circulate constantly in the ambient air. The risk of opportunistic infection from these viruses can be increased in mechanically ventilated patients. The present study evaluates the feasibility of detecting airborne respiratory viruses in mechanically ventilated patients using a novel sample collection method involving ventilator filters. Methods: We collected inspiratory and expiratory filters from the ventilator circuits of mechanically ventilated patients in an intensive care unit over a 14-month period. To evaluate whether we could detect respiratory viruses collected in these filters, we performed a reverse transcription polymerase chain reaction on the extracted filter membrane with primers specific for rhinovirus, respiratory syncytial virus, influenza virus A and B, parainfluenza virus (type 1, 2 and 3) and human metapneumovirus. For each patient, we also performed a full virology screen (virus particles, antibody titres and virus-induced biomarkers) on respiratory samples (nasopharyngeal swab, tracheal aspirate or bronchoalveolar fluid) and blood samples. Results: Respiratory viruses were detected in the ventilator filters of nearly half the patients in the study cohort (n = 33/70). The most common virus detected was influenza A virus (n = 29). There were more viruses detected in the inspiratory filters (n = 18) than in the expiratory filters (n = 15). A third of the patients with a positive virus detection in the ventilator filters had a hospital laboratory confirmed viral infection. In the remaining cases, the detected viruses were different from viruses already identified in the same patient, suggesting that these additional viruses come from the ambient air or from cross-contamination (staff or visitors). In patients in whom new viruses were detected in the ventilator filters, there was no evidence of clinical signs of an active viral infection. Additionally, the levels of virus-induced...

Moheimani, F, Koops, J, Williams, T, Reid, AT, Hansbro, PM, Wark, PA & Knight, DA 2018, 'Influenza A virus infection dysregulates the expression of microRNA-22 and its targets; CD147 and HDAC4, in epithelium of asthmatics', Respiratory Research, vol. 19, no. 1.
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© 2018 The Author(s). Background: Specific microRNAs (miRNAs) play essential roles in airway remodeling in asthma. Infection with influenza A virus (IAV) may also magnify pre-existing airway remodeling leading to asthma exacerbation. However, these events remain to be fully defined. We investigated the expression of miRNAs with diverse functions including proliferation (miR-20a), differentiation (miR-22) or innate/adaptive immune responses (miR-132) in primary bronchial epithelial cells (pBECs) of asthmatics following infection with the H1N1 strain of IAV. Methods: pBECs from subjects (n = 5) with severe asthma and non-asthmatics were cultured as submerged monolayers or at the air-liquid-interface (ALI) conditions and incubated with IAV H1N1 (MOI 5) for up to 24 h. Isolated miRNAs were subjected to Taqman miRNAs assays. We confirmed miRNA targets using a specific mimic and antagomir. Taqman mRNAs assays and immunoblotting were used to assess expression of target genes and proteins, respectively. Results: At baseline, these miRNAs were expressed at the same level in pBECs of asthmatics and non-asthmatics. After 24 h of infection, miR-22 expression increased significantly which was associated with the suppression of CD147 mRNA and HDAC4 mRNA and protein expression in pBECs from non-asthmatics, cultured in ALI. In contrast, miR-22 remained unchanged while CD147 expression increased and HDAC4 remained unaffected in cells from asthmatics. IAV H1N1 mediated increases in SP1 and c-Myc transcription factors may underpin the induction of CD147 in asthmatics. Conclusion: The different profile of miR-22 expression in differentiated epithelial cells from non-asthmatics may indicate a self-defense mechanism against aberrant epithelial responses through suppressing CD147 and HDAC4, which is compromised in epithelial cells of asthmatics.

Moore, SJ, Sonar, K, Bharadwaj, P, Deplazes, E & Mancera, RL 2018, 'Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies', Molecules, vol. 23, no. 9, pp. 2142-2142.
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Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions.

Morelato, M, Broséus, J, De Grazia, A, Tahtouh, M, Esseiva, P & Roux, C 2018, 'Forensic drug intelligence and the rise of cryptomarkets. Part II: Combination of data from the physical and virtual markets', Forensic Science International, vol. 288, pp. 201-210.
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© 2018 Elsevier B.V. Technology provides new ways to access customers and suppliers while enhancing the security of off-line criminal activity. Since the first cryptomarket, Silk Road, in 2011, cryptomarkets have transformed the traditional drug sale by facilitating the creation of a global network of vendors and buyers. Due to the fragmented nature of traces that result from illegal activities, combining the results of concurrent processes based on traces of different nature should provide supplementary benefit to understand the drug market. This article compares the data of the Australian virtual market (in particular data extracted from cryptomarkets) to the data related to traditional market descriptors, namely national seizures and arrests, prevalence data, shipping countries of seized post shipments as well as outcomes of specific surveys targeting users’ behaviour online. Results revealed the domestic nature of the online illicit drug trade in Australia which is dominated by amphetamine-type substances (ATS), in particular methylamphetamine and cannabis. These illicit drugs were also the most seized drugs on the physical market. This article shows that the combination of different information offers a broader perspective of the illicit drug market in Australia and thus provides stronger arguments for policy makers. It also highlights the links between the virtual and physical markets.

Moreno-Torres, KI, Brito, BP, Branan, MA, Rodriguez, LL, Delgado, AH, Stenfeldt, C & Arzt, J 2018, 'Foot-and-Mouth Disease Infection Dynamics in Contact-Exposed Pigs Are Determined by the Estimated Exposure Dose', Frontiers in Veterinary Science, vol. 5, no. Jul.
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The quantitative relationship between the exposure dose of foot-and-mouth disease virus (FMDV) and subsequent infection dynamics has been demonstrated through controlled inoculation studies in various species. However, similar quantitation of viral doses has not been achieved during contact exposure experiments due to the intrinsic difficulty of measuring the virus quantities exchanged between animals. In the current study, novel modeling techniques were utilized to investigate FMDV infection dynamics in groups of pigs that had been contact-exposed to FMDV-infected donors shedding varying levels of virus, as well as in pigs inoculated via the intra-oropharyngeal (IOP) route. Estimated virus exposure doses were modeled and were found to be statistically significantly associated with the dynamics of FMDV RNA detection in serum and oropharyngeal fluid (OPF), and with the time to onset of clinical disease. The minimum estimated shedding quantity in OPF that defined infectiousness of donor pigs was 6.55 log10 genome copy numbers (GCN)/ml (95% CI 6.11, 6.98), which delineated the transition from the latent to infectious phase of disease which occurred during the incubation phase. This quantity corresponded to a minimum estimated exposure dose of 5.07 log10 GCN/ml (95% CI 4.25, 5.89) in contact-exposed pigs. Thus, we demonstrated that a threshold quantity of FMDV detection in donor pigs was necessary in order to achieve transmission by direct contact. The outcomes from this investigation demonstrate that variability of infection dynamics which occurs during the progression of FMD in naturally exposed pigs can be partially attributed to variations in exposure dose. Moreover, these modeling approaches for dose-quantitation may be retrospectively applied to contact-exposure experiments or field scenarios. Hence, robust information could be incorporated into models used to evaluate FMD spread and control.

Moret, S, Scott, E, Barone, A, Liang, K, Lennard, C, Roux, C & Spindler, X 2018, 'Metal-Organic Frameworks for fingermark detection — A feasibility study', Forensic Science International, vol. 291, pp. 83-93.
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© 2018 Elsevier B.V. Metal-Organic Frameworks (MOFs) are porous crystalline structures, currently used as sensors, separation membranes, and as catalysts. Due to their physicochemical and optical properties, they have been recently proposed for fingermark detection. This study further explored their potential for fingermark detection. Natural fingermarks, as well as charged and protein-enriched marks, were used to test the efficiency of the technique. Various parameters, such as precursor concentration, pH, immersion time and detection protocols, were investigated and optimised. The performance of the optimised MOF-based method was then compared to that of routinely used techniques. The results obtained indicated that MOFs can effectively detect fingermarks, especially protein-rich marks such as marks contaminated with body fluids. However, after comparison and evaluation against benchmark techniques, results were judged to be inferior to those from currently employed detection methods. However, with further research and optimisation MOFs may be promising as an alternative to current powder suspension techniques.

Moulder, DE, Hatoum, D, Tay, E, Lin, Y & McGowan, EM 2018, 'The Roles of p53 in Mitochondrial Dynamics and Cancer Metabolism: The Pendulum between Survival and Death in Breast Cancer?', Cancers, vol. 10, no. 6, pp. 189-189.
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Cancer research has been heavily geared towards genomic events in the development and progression of cancer. In contrast, metabolic regulation, such as aberrant metabolism in cancer, is poorly understood. Alteration in cellular metabolism was once regarded simply as a consequence of cancer rather than as playing a primary role in cancer promotion and maintenance. Resurgence of cancer metabolism research has identified critical metabolic reprogramming events within biosynthetic and bioenergetic pathways needed to fulfill the requirements of cancer cell growth and maintenance. The tumor suppressor protein p53 is emerging as a key regulator of metabolic processes and metabolic reprogramming in cancer cells—balancing the pendulum between cell death and survival. This review provides an overview of the classical and emerging non-classical tumor suppressor roles of p53 in regulating mitochondrial dynamics: mitochondrial engagement in cell death processes in the prevention of cancer. On the other hand, we discuss p53 as a key metabolic switch in cellular function and survival. The focus is then on the conceivable roles of p53 in breast cancer metabolism. Understanding the metabolic functions of p53 within breast cancer metabolism will, in due course, reveal critical metabolic hotspots that cancers advantageously re-engineer for sustenance. Illustration of these events will pave the way for finding novel therapeutics that target cancer metabolism and serve to overcome the breast cancer burden.

Mukherjee, M, Hu, Y, Tan, CH, Rice, SA & Cao, B 2018, 'Engineering a light-responsive, quorum quenching biofilm to mitigate biofouling on water purification membranes', Science Advances, vol. 4, no. 12.
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We engineered a light-responsive, quorum quenching biofilm and demonstrated its application in mitigating membrane biofouling.

Murray, BR, Martin, LJ, Brown, C, Krix, DW & Phillips, ML 2018, 'Selecting Low-Flammability Plants as Green Firebreaks within Sustainable Urban Garden Design', Fire, vol. 1, no. 1, pp. 15-15.
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In response to an increasing risk of property loss from wildfires at the urban–wildland interface[…]

Murray, M, Gillani, TB, Ghassabian, S, Edwards, RJ & Rawling, T 2018, 'Differential effects of hepatic cirrhosis on the intrinsic clearances of sorafenib and imatinib by CYPs in human liver', European Journal of Pharmaceutical Sciences, vol. 114, pp. 55-63.
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© 2017 Elsevier B.V. The tyrosine kinase inhibitors sorafenib and imatinib are important in the treatment of a range of cancers but adverse effects in some patients necessitate dosage modifications. CYP3A4 has a major role in the oxidation of sorafenib to its N-oxide and N-hydroxymethyl metabolites and also acts in concert with CYP2C8 to mediate imatinib N-demethylation. CYP3A4 expression and function are impaired in patients with advanced liver disease, whereas the functions of CYP2C enzymes are relatively preserved. We evaluated the biotransformation of sorafenib and imatinib in well-characterized microsomal fractions from 17 control subjects and 19 individuals with hepatic cirrhosis of varying severity. The principal findings were that liver disease impaired the microsomal oxidation of sorafenib to its major metabolites to 40–44% of control (P < 0.01), whereas the N-demethylation of imatinib was relatively unimpaired. The impairments in sorafenib biotransformation were correlated with decreased serum albumin concentrations and increased serum bilirubin concentrations in patients with liver disease, but not with the overall grade of liver disease according to the Child-Pugh system. In contrast, there was no relationship between imatinib N-demethylation and clinicopathologic factors in liver disease patients. These findings were accounted for in terms of the differential roles of CYPs 3A4 and 2C8 in the intrinsic clearance of the drugs. CYP3A4 has the major role in the intrinsic clearance of sorafenib but plays a secondary role to CYP2C8 in the intrinsic clearance of imatinib. In agreement with these findings CYP2C protein expression and CYP2C8-mediated paclitaxel 6α-hydroxylation were unimpaired in cirrhotic livers. This information could be adapted in individualized approaches such as in vivo CYP3A4 phenotyping to optimize sorafenib safety and efficacy in cancer patients with liver dysfunction.

Musumeci, G, Leggio, G, Marzagalli, R, Al-Badri, G, Drago, F & Castorina, A 2018, 'Identification of Dysregulated microRNA Networks in Schwann Cell-Like Cultures Exposed to Immune Challenge: Potential Crosstalk with the Protective VIP/PACAP Neuropeptide System', International Journal of Molecular Sciences, vol. 19, no. 4, pp. 981-981.
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Following peripheral nerve injury, dysregulations of certain non-coding microRNAs (miRNAs) occur in Schwann cells. Whether these alterations are the result of local inflammation and/or correlate with perturbations in the expression profile of the protective vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating polypeptide (PACAP) system is currently unknown. To address these issues, we aimed at profiling the expression of selected miRNAs in the rat RT4 Schwann cell line. Cells exposed to lipopolysaccharide (LPS), to mimic the local inflammatory milieu, were appraised by real-time qPCR, Western blot and ELISAs. We found that upon LPS treatment, levels of pro-inflammatory cytokines (IL-1β, -6, -18, -17A, MCP-1 and TNFα) increased in a time-dependent manner. Unexpectedly, the expression levels of VIP and PACAP were also increased. Conversely, levels of VPAC1 and VPAC2 receptors were reduced. Downregulated miRNAs included miR-181b, -145, -27a, -340 and -132 whereas upregulated ones were miR-21, -206, -146a, -34a, -155, -204 and -29a, respectively. Regression analyses revealed that a subset of the identified miRNAs inversely correlated with the expression of VPAC1 and VPAC2 receptors. In conclusion, these findings identified a novel subset of miRNAs that are dysregulated by immune challenge whose activities might elicit a regulatory function on the VIP/PACAP system.

Nair, PM, Starkey, MR, Haw, TJ, Ruscher, R, Liu, G, Maradana, MR, Thomas, R, O’Sullivan, BJ & Hansbro, PM 2018, 'RelB-Deficient Dendritic Cells Promote the Development of Spontaneous Allergic Airway Inflammation', American Journal of Respiratory Cell and Molecular Biology, vol. 58, no. 3, pp. 352-365.
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Copyright © 2018 by the American Thoracic Society RelB is a member of the NF-kB family, which is essential for dendritic cell (DC) function and maturation. However, the contribution of RelB to the development of allergic airway inflammation (AAI) is unknown. Here, we identify a pivotal role for RelB in the development of spontaneous AAI that is independent of exogenous allergen exposure. We assessed AAI in two strains of RelB-deficient (RelB2/2) mice: one with a targeted deletion and one expressing a major histocompatibility complex transgene. To determine the importance of RelB in DCs, RelB-sufficient DCs (RelB1/1 or RelB2/2) were adoptively transferred into RelB2/2 mice. Both strains had increased pulmonary inflammation compared with their respective wild-type (RelB1/1) and heterozygous (RelB1/2) controls. RelB2/2 mice also had increased inflammatory cell influx into the airways, levels of chemokines (CCL2/3/4/5/11/17 and CXCL9/10/13) and T-helper cell type 2-associated cytokines (IL-4/5) in lung tissues, serum IgE, and airway remodeling (mucus-secreting cell numbers, collagen deposition, and epithelial thickening). Transfer of RelB1/2 CD11c1 DCs into RelB2/2 mice decreased pulmonary inflammation, with reductions in lung chemokines, T-helper cell type 2-associated cytokines (IL-4/5/13/25/33 and thymic stromal lymphopoietin), serum IgE, type 2 innate lymphoid cells, myeloid DCs, gd T cells, lung Vb131 T cells, mucus-secreting cells, airway collagen deposition, and epithelial thickening. These data indicate that RelB deficiency may be a key pathway underlying AAI, and that DC-encoded RelB is sufficient to restore control of this inflammation.

Nedeljkovic, I, Carnero-Montoro, E, Lahousse, L, van der Plaat, DA, de Jong, K, Vonk, JM, van Diemen, CC, Faiz, A, van den Berge, M, Obeidat, M, Bossé, Y, Nickle, DC, Consortium, BIOS, Uitterlinden, AG, van Meurs, JJB, Stricker, BCH, Brusselle, GG, Postma, DS, Boezen, HM, van Duijn, CM & Amin, N 2018, 'Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics', European Journal of Human Genetics, vol. 26, no. 5, pp. 709-722.
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© 2018 European Society of Human Genetics. Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10-8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180:C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489). All four variants were significantly associated (P < 1.4 × 10-6) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in COPD cases and controls (P < 0.04). Further additive and multiplicative effects of smoking were evaluated and no significant effect was observed. To evaluate if these four genetic variants are expression quantitative trait loci, transcriptome-wide association analysis was performed in 1087 lung samples. All four variants were also significantly associated with differential expression of the IREB2 3'UTR in lung tissues (P < 5.4 × 10-95). We conclude that regulatory mechanisms affecting the expression of IREB2 gene, such as DNA methylation, may explain the association between genetic variants in chromosome 15q25.1 and COPD, largely independent of smoking.

Nedeljkovic, I, Lahousse, L, Carnero-Montoro, E, Faiz, A, Vonk, JM, de Jong, K, van der Plaat, DA, van Diemen, CC, van den Berge, M, Obeidat, M, Bossé, Y, Nickle, DC, Consortium, BIOS, Uitterlinden, AG, van Meurs, JBJ, Stricker, BHC, Brusselle, GG, Postma, DS, Boezen, HM, van Duijn, CM & Amin, N 2018, 'COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression', Human Molecular Genetics, vol. 27, no. 2, pp. 396-405.
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© The Author 2017. Chronic obstructive pulmonary disease (COPD) is among the major health burdens in adults. While cigarette smoking is the leading risk factor, a growing number of genetic variations have been discovered to influence disease susceptibility. Epigenetic modifications may mediate the response of the genome to smoking and regulate gene expression. Chromosome 19q13.2 region is associated with both smoking and COPD, yet its functional role is unclear. Our study aimed to determine whether rs7937 (RAB4B, EGLN2), a top genetic variant in 19q13.2 region identified in genome-wide association studies of COPD, is associated with differential DNA methylation in blood (N=1490) and gene expression in blood (N=721) and lungs (N=1087). We combined genetic and epigenetic data from the Rotterdam Study (RS) to perform the epigenome-wide association analysis of rs7937. Further, we used genetic and transcriptomic data from blood (RS) and from lung tissue (Lung expression quantitative trait loci mapping study), to perform the transcriptome-wide association study of rs7937. Rs7937 was significantly (FDR < 0.05) and consistently associated with differential DNA methylation in blood at 4 CpG sites in cis, independent of smoking. One methylation site (cg11298343-EGLN2) was also associated with COPD (P=0.001). Additionally, rs7937 was associated with gene expression levels in blood in cis (EGLN2), 42% mediated through cg11298343, and in lung tissue, in cis and trans (NUMBL, EGLN2, DNMT3A, LOC101929709 and PAK2). Our results suggest that changes of DNA methylation and gene expression may be intermediate steps between genetic variants and COPD, but further causal studies in lung tissue should confirm this hypothesis.

Neshev, D & Aharonovich, I 2018, 'Optical metasurfaces: new generation building blocks for multi-functional optics', Light: Science & Applications, vol. 7, no. 1.
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AbstractOptical metasurfaces (OMs) have emerged as promising candidates to solve the bottleneck of bulky optical elements. OMs offer a fundamentally new method of light manipulation based on scattering from resonant nanostructures rather than conventional refraction and propagation, thus offering efficient phase, polarization, and emission control. This perspective highlights state of the art OMs and provides a roadmap for future applications, including active generation, manipulation and detection of light for quantum technologies, holography and sensing.

New, EJ, Wimmer, VC & Hare, DJ 2018, 'Promises and Pitfalls of Metal Imaging in Biology', Cell Chemical Biology, vol. 25, no. 1, pp. 7-18.
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© 2017 Elsevier Ltd A picture may speak a thousand words, but if those words fail to form a coherent sentence there is little to be learned. As cutting-edge imaging technology now provides us the tools to decipher the multitude of roles played by metals and metalloids in molecular, cellular, and developmental biology, as well as health and disease, it is time to reflect on the advances made in imaging, the limitations discovered, and the future of a burgeoning field. In this Perspective, the current state of the art is discussed from a self-imposed contrarian position, as we not only highlight the major advances made over the years but use them as teachable moments to zoom in on challenges that remain to be overcome. We also describe the steps being taken toward being able to paint a completely undisturbed picture of cellular metal metabolism, which is, metaphorically speaking, the Holy Grail of the discipline. New technology has allowed visualization of metals in biology with unprecedented detail. New et al. discuss the potential and limitations for imaging metals in biological systems, and pose the question: how real are the pictures we create?

Newton, K, Jeffries, TC, Smith, RJ, Seymour, JR, Seuront, L & Mitchell, JG 2018, 'Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs', Journal of Oceanology and Limnology, vol. 36, no. 6, pp. 2033-2049.
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© 2018, Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature. The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates tha...

Ng, ZY, Wong, J-Y, Panneerselvam, J, Madheswaran, T, Kumar, P, Pillay, V, Hsu, A, Hansbro, N, Bebawy, M, Wark, P, Hansbro, P, Dua, K & Chellappan, DK 2018, 'Assessing the potential of liposomes loaded with curcumin as a therapeutic intervention in asthma', Colloids and Surfaces B: Biointerfaces, vol. 172, pp. 51-59.
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© 2018 Elsevier B.V. Curcumin a component of turmeric, which is derived from Curcuma longa is used as a colouring agent and as a dietary spice for centuries. Extensive studies have been done on the anti-inflammatory activity of curcumin along with its molecular mechanism involving different signalling pathways. However, the physicochemical and biological properties such as poor solubility and rapid metabolism of curcumin have led to low bioavailability and hence limits its application. Current therapies for asthma such as bronchodilators and inhaled corticosteroids (ICS) are aimed at controlling disease symptoms and prevent asthma exacerbation. However, this approach requires lifetime therapy and is associated with a constellation of side effects. This creates a clear unmet medical need and there is an urgent demand for new and more-effective treatments. The present study is aimed to formulate liposomes containing curcumin and evaluate for its anti-inflammatory effects on lipopolysaccharide (LPS)-induced inflammation on BCi-NS1.1 cell line. Curcumin and salbutamol liposomes were formulated using lipid hydration method. The prepared liposomes were characterized in terms of particle size, zeta potential, encapsulation efficiency and in-vitro release profile. The liposomes were tested on BCI-NS1.1 cell line to evaluate its anti-inflammatory properties. The various pro-inflammatory markers studied were Interleukin-6 (IL-6), Interleukin-8 (IL-8), Interleukin-1β (IL-1β) and Tumour Necrosis Factor-a (TNF-a). Additionally, molecular mechanics simulations were used to elucidate the positioning, energy minimization, and aqueous dispersion of the liposomal architecture involving lecithin and curcumin. The prepared curcumin formulation showed an average size and zeta potential of 271.3 ± 3.06 nm and −61.0 mV, respectively. The drug encapsulation efficiency of liposomal curcumin is 81.1%. Both curcumin-loaded liposomes formulation (1 μg/mL, 5 μg/mL) resulted in sign...

Nguyen, HT, Ma, X, Newbigin, E, Beggs, P, Davies, J & Huete, A 2018, 'Grassland Phenology and Meteorology Co-Influence Grass Pollen Counts in Victoria, Australia', ISEE Conference Abstracts, vol. 2018, no. 1.
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Nguyen, LT, Chen, H, Mak, C, Zaky, A, Pollock, C & Saad, S 2018, 'SRT1720 attenuates obesity and insulin resistance but not liver damage in the offspring due to maternal and postnatal high-fat diet consumption', American Journal of Physiology-Endocrinology and Metabolism, vol. 315, no. 2, pp. E196-E203.
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Recent studies indicate that sirtuin-1 (SIRT1), an important metabolic sensor and regulator of life span, plays a mechanistic role in maternal obesity-induced programming of metabolic disorders in the offspring. In this study we investigate whether SIRT1 activation in early childhood can mitigate metabolic disorders due to maternal and postnatal high-fat feeding in mice. Male offspring born to chow-fed (MC) or high fat diet-fed dams (MHF) were weaned onto postnatal chow or high-fat diet and treated with SRT1720 (25 mg/kg ip every 2 days) or vehicle control for 6 wk and examined for metabolic disorders. MHF exacerbated offspring body weight and insulin resistance in the offspring exposed to postnatal HFD (OHF). These metabolic changes were associated with reduced hepatic lipid droplet accumulation but increased plasma levels of alanine aminotransferase (ALT), a marker of liver damage. SRT1720 significantly decreased offspring body weight, adiposity, glucose intolerance, and hyperleptinemia due to OHF and reversed hyperinsulinemia and adipocyte hypertrophy due to the additive effects of MHF. Although SRT1720 suppresses liver lipogenesis, inflammation, and oxidative stress markers, it also reduces antioxidants and increased liver collagen deposition in OHF offspring independent of MHF. Hepatic steatosis was attenuated only in MC/OHF offspring in association with elevated plasma ALT levels. The study suggests that postnatal SRT1720 administration can mitigate obesity and insulin resistance in the offspring due to maternal and postnatal HFD exposure. However, the possibility of liver toxicity needs to be further examined.

Nguyen, M, Zhu, T, Kianinia, M, Massabuau, F, Aharonovich, I, Toth, M, Oliver, R & Bradac, C 2018, 'Effects of microstructure and growth conditions on quantum emitters in Gallium Nitride', APL Materials, vol. 7, no. 8.
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Single-photon emitters in gallium nitride (GaN) are gaining interest asattractive quantum systems due to the well-established techniques for growthand nanofabrication of the host material, as well as its remarkable chemicalstability and optoelectronic properties. We investigate the nature of suchsingle-photon emitters in GaN with a systematic analysis of various samplesproduced under different growth conditions. We explore the effect thatintrinsic structural defects (dislocations and stacking faults), doping andcrystal orientation in GaN have on the formation of quantum emitters. Weinvestigate the relationship between the position of the emitters (determinedvia spectroscopy and photoluminescence measurements) and the location ofthreading dislocations (characterised both via atomic force microscopy andcathodoluminescence). We find that quantum emitters do not correlate withstacking faults or dislocations; instead, they are more likely to originatefrom point defects or impurities whose density is modulated by the localextended defect density.

Nguyen, T, Li, GE, Chen, H, Cranfield, CG, McGrath, KC & Gorrie, CA 2018, 'Maternal E-Cigarette Exposure Results in Cognitive and Epigenetic Alterations in Offspring in a Mouse Model', Chemical Research in Toxicology, vol. 31, no. 7, pp. 601-611.
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© 2018 American Chemical Society. Electronic cigarette (e-cigarette) use is on the rise worldwide and is particularly attractive to young people and as a smoking substitute by pregnant woman. There is a perception in pregnant women and women of child-bearing age that the use of e-cigarettes (vaping) is safer than smoking tobacco cigarettes during pregnancy. However, there is little evidence to support this perception. Here, we examined the offspring from mouse dams that had been exposed during and after pregnancy to ambient air (sham) (n = 8), e-cigarette aerosols with nicotine (n = 8), or e-cigarette aerosols without nicotine (n = 8). Offspring underwent cognitive testing at 12 weeks of age and epigenetic testing of brain tissues at 1 day, 20 days, and 13 weeks after birth. The findings showed deficits in short-term memory, reduced anxiety, and hyperactivity in offspring following maternal e-cigarette exposure using the novel object recognition and elevated plus maze tests. In addition, global DNA methylation was increased in the brains of offspring soon after birth. Using a quantitative-PCR array specific to chromatin modification enzymes on genomic DNA and histones,13 key genes were identified to be significantly altered in the offspring brains from the e-cigarette groups compared to the nonexposed groups. The changes to genes Aurka, Aurkb, Aurkc, Kdm5c, Kdm6b, Dnmt3a, Dnmt3b, and Atf2, all associated with modulating neurological activity, were validated using RT-qPCR. In conclusion, in a mouse model, maternal exposure to e-cigarette aerosols resulted in both cognitive and epigenetic changes in offspring. This suggests that the use of e-cigarettes during pregnancy may have hitherto undetected neurological consequences on newborns.

Nielsen, DA, Petrou, K & Gates, RD 2018, 'Coral bleaching from a single cell perspective', The ISME Journal, vol. 12, no. 6, pp. 1558-1567.
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Abstract Ocean warming is resulting in increased occurrence of mass coral bleaching; a response in which the intracellular algal endosymbionts (Symbiodinium sp.) are expelled from the coral host due to physiological stress. This detrimental process is often attributed to overproduction of reactive oxygen species (ROS) that leak out of the endosymbionts and causes damage to the host cell, though direct evidence validating this link is limited. Here, for the first time, we used confocal microscopy and fluorescent dyes to investigate if endosymbiont ROS production significantly and predictably affects physiological parameters in its host cell. Heat treatment resulted in a 60% reduction in coral symbiont density, a ~70% increase in median endosymbiont ROS and a small reduction in photosystem efficiency (FV/FM, 11%), indicating absence of severe light stress. Notably, no other physiological parameters were affected in either endosymbionts or host cells, including reduced glutathione and ROS-induced lipid peroxidation. Taken together, the increase in endosymbiont ROS could not be linked to physiological damage in either partner, suggesting that oxidative stress is unlikely to have been the driver for symbiont expulsion in this study.

Nissen, G, Hollaender, H, Tang, FSM, Wegmann, M, Lunding, L, Vock, C, Bachmann, A, Lemmel, S, Bartels, R, Oliver, BG, Burgess, JK, Becker, T, Kopp, MV & Weckmann, M 2018, 'Tumstatin fragment selectively inhibits neutrophil infiltration in experimental asthma exacerbation', Clinical & Experimental Allergy, vol. 48, no. 11, pp. 1483-1493.
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SummaryBackgroundAsthma is a chronic inflammatory disease with structural changes present. Burgess and colleagues recently found tumstatin markedly reduced in adult asthmatic lung tissue compared with nonasthmatics. ECM fragments such as tumstatin are named matrikines and act independently of the parent molecule. The role of Col IV matrikines in neutrophil inflammation (eg. exacerbation in asthma) has not been investigated to date. Severe adult asthma phenotypes are dominated by neutrophilic inflammation and show a high frequency of severe exacerbations.ObjectiveThis study sought to investigate the role of a novel active region within tumstatin (CP17) and its implication in neutrophil inflammatory responses related to asthma exacerbation.MethodsFor reactive oxygen production, isolated neutrophils were preincubated with peptides or vehicle for 1 hour and stimulated (PMA). Luminescence signal was recorded (integration over 10 seconds) for 1.5 hours. Neutrophil migration was performed according to the SiMA protocol. Mice were sensitized to OVA/Alumn by intraperitoneal (i.p.) injections. Mice were then treated with CP17, vehicle (PBS) or scrambled peptide (SP17) after OVA

Nitschke, MR, Gardner, SG, Goyen, S, Fujise, L, Camp, EF, Ralph, PJ & Suggett, DJ 2018, 'Utility of Photochemical Traits as Diagnostics of Thermal Tolerance amongst Great Barrier Reef Corals', Frontiers in Marine Science, vol. 5, no. FEB.
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© 2018 Nitschke, Gardner, Goyen, Fujise, Camp, Ralph and Suggett. Light availability is considered a key factor regulating the thermal sensitivity of reef building corals, where excessive excitation of photosystem II (PSII) further exacerbates pressure on photochemical pathways already compromised by heat stress. Coral symbionts acclimate to changes in light availability (photoacclimation) by continually fine-tuning the photochemical operating efficiency of PSII. However, how this process adjusts throughout the warmest months in naturally heat-tolerant or sensitive species is unknown, and whether this influences the capacity to tolerate transient heat stress is untested. We therefore examined the PSII photophysiology of 10 coral species (with known thermal tolerances) from shallow reef environments at Heron Island (Great Barrier Reef, Australia), in spring (October-November, 2015) vs. summer (February-March, 2016). Corals were maintained in flow-through aquaria and rapid light curve (RLC) protocols using pulse amplitude modulated (PAM) fluorometry captured changes in the PSII photoacclimation strategy, characterized as the minimum saturating irradiance (Ek), and the extent of photochemical ([1-C], operating efficiency) vs. non-photochemical ([1-Q]) energy dissipation. Values of Ek across species were > 2-fold higher in all coral species in spring, consistent with a climate of higher overall light exposure (i.e., higher PAR from lower cloud cover, rainfall and wind speed) compared with summer. Summer decreases in Ek were combined with a shift toward preferential photochemical quenching in all species. All coral species were subsequently subjected to thermal stress assays. An equivalent temperature-ramping profile of 1°C increase per day and then maintenance at 32°C was applied in each season. Despite the significant seasonal photoacclimation, the species hierarchy of thermal tolerance [maximum quantum yields of PSII (Fv/Fm), monitored at dawn and dusk] d...

Nixon, GL, McEntee, L, Johnson, A, Farrington, N, Whalley, S, Livermore, J, Natal, C, Washbourn, G, Bibby, J, Berry, N, Lestner, J, Truong, M, Owen, A, Lalloo, D, Charles, I & Hope, W 2018, 'Repurposing and Reformulation of the Antiparasitic Agent Flubendazole for Treatment of Cryptococcal Meningoencephalitis, a Neglected Fungal Disease', Antimicrobial Agents and Chemotherapy, vol. 62, no. 4.
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ABSTRACT Current therapeutic options for cryptococcal meningitis are limited by toxicity, global supply, and emergence of resistance. There is an urgent need to develop additional antifungal agents that are fungicidal within the central nervous system and preferably orally bioavailable. The benzimidazoles have broad-spectrum antiparasitic activity but also have in vitro antifungal activity that includes Cryptococcus neoformans . Flubendazole (a benzimidazole) has been reformulated by Janssen Pharmaceutica as an amorphous solid drug nanodispersion to develop an orally bioavailable medicine for the treatment of neglected tropical diseases such as onchocerciasis. We investigated the in vitro activity, the structure-activity-relationships, and both in vitro and in vivo pharmacodynamics of flubendazole for cryptococcal meningitis. Flubendazole has potent in vitro activity against Cryptococcus neoformans , with a modal MIC of 0.125 mg/liter using European Committee on Antimicrobial Susceptibility Testing (EUCAST) methodology. Computer models provided an insight into the residues responsible for the binding of flubendazole to cryptococcal β-tubulin. Rapid fungicidal activity was evident in a hollow-fiber infection model of cryptococcal meningitis. The solid drug nanodispersion was orally bioavailable in mice with higher drug exposure in the cerebrum. The maximal dose of flubendazole (12 mg/kg of body weight/day) orally resulted in an ∼2 log 10

Nolan, LM, Whitchurch, CB, Barquist, L, Katrib, M, Boinett, CJ, Mayho, M, Goulding, D, Charles, IG, Filloux, A, Parkhill, J & Cain, AK 2018, 'A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa', Microbial Genomics, vol. 4, no. 11.
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Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.

Nolan, RH, Tarin, T, Rumman, R, Cleverly, J, Fairweather, KA, Zolfaghar, S, Santini, NS, O'Grady, AP & Eamus, D 2018, 'Contrasting ecophysiology of two widespread arid zone tree species with differing access to water resources', Journal of Arid Environments, vol. 153, pp. 1-10.
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© 2018 Elsevier Ltd Arid environments can support the seemingly unlikely coexistence of species tolerant of, or sensitive to, dry soil moisture. Here, we examine water-use and carbon-gain traits in two widespread tree species in central Australia: Acacia aptaneura and Eucalyptus camaldulensis. The former has a shallow root distribution and relies on soil moisture, while the latter is groundwater dependent. We hypothesised that A. aptaneura would exhibit a suite of characteristics that confer tolerance to low soil moisture, in contrast to E. camaldulensis. Consistent with our hypotheses A. aptaneura was relatively more anisohydric than E. camaldulensis (seasonal leaf water potential of −7.2 to −0.8 MPa cf. −1.4 to −0.3 MPa). Additionally, compared to E. camaldulensis, A. aptaneura had lower water potential at turgor loss (−2.5 cf. −1.1 MPa); a larger Huber value; smaller, narrower and thicker phyllodes/leaves; and larger photosynthetic capacity (Jmax); and larger water-use efficiency. Further, water-use efficiency for E. camaldulensis was similar to species receiving annual rainfall of 1500 mm, despite annual rainfall of 348 mm. We conclude that mean annual rainfall is the dominant determinant of water and carbon relations for A. aptaneura, but not E. camaldulensis. This has important implications for ecosystem-scale transpiration and primary productivity across this arid zone.

Noorian, P, Sun, S & McDougald, D 2018, 'Complete Genome Sequence of Oyster Isolate Vibrio vulnificus Env1', Genome Announcements, vol. 6, no. 20.
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ABSTRACT Vibrio vulnificus , a ubiquitous inhabitant of coastal marine environments, has been isolated from a variety of sources. It is an opportunistic pathogen of both marine animals and humans. Here, the genome sequence of V. vulnificus Env1, an environmental isolate resistant to predation by the ciliate Tetrahymena pyriformis , is reported.

O’Neil, JD, Ammit, AJ & Clark, AR 2018, 'MAPK p38 regulates inflammatory gene expression via tristetraprolin: Doing good by stealth', The International Journal of Biochemistry & Cell Biology, vol. 94, pp. 6-9.
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Tristetraprolin (TTP) is an RNA-destabilizing protein that exerts profound anti-inflammatory effects by inhibiting the expression of tumour necrosis factor and many other inflammatory mediators. The mitogen-activated protein kinase (MAPK) p38 signaling pathway controls the strength and duration of inflammatory responses by regulating both the expression and function of TTP. The kinase MK2 (MAPK activated kinase 2) is activated by MAPK p38, and in turn phosphorylates TTP at two critical serine residues. One consequence of these phosphorylations is the protection of TTP from proteasome-mediated degradation. Another consequence is the loss of mRNA destabilizing activity. The control of TTP expression and function by the MAPK p38 pathway provides an elegant mechanism for coupling the on and off phases of inflammatory responses, and dictating the precise kinetics of expression of individual inflammatory mediators.

O’Rourke, MB, Raymond, BBA, Djordjevic, SP & Padula, MP 2018, 'The Effect of Collimating Lens Focusing on Laser Beam Shape in Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)', Journal of the American Society for Mass Spectrometry, vol. 29, no. 3, pp. 512-515.
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© 2018, American Society for Mass Spectrometry. Tissue imaging using matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a well-established technique that, in recent years, has seen wider adoption and novel application. Applications such imaging mass spectrometry (IMS) and biotyping are beginning to gain greater exposure and use; however, with limitations in optimization methods, producing the best result often relies on the ability to customize the physical characteristics of the instrumentation, a task that is challenging for most mass spectrometry laboratories. With this in mind, we have described the effect of making simple adjustments to the laser optics at the final collimating lens area, to adjust the laser beam size and shape in order to allow greater customization of the instrument for improving techniques such as IMS. We have therefore been able to demonstrate that improvements can be made without requiring the help of an electrical engineer or external funding in a way that only costs a small amount of time. [Figure not available: see fulltext.].

Obeidat, M, Dvorkin-Gheva, A, Li, X, Bossé, Y, Brandsma, C-A, Nickle, DC, Hansbro, PM, Faner, R, Agusti, A, Paré, PD, Stampfli, MR & Sin, DD 2018, 'The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD', Scientific Reports, vol. 8, no. 1.
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AbstractGenome-wide mRNA profiling in lung tissue from human and animal models can provide novel insights into the pathogenesis of chronic obstructive pulmonary disease (COPD). While 6 months of smoke exposure are widely used, shorter durations were also reported. The overlap of short term and long-term smoke exposure in mice is currently not well understood, and their representation of the human condition is uncertain. Lung tissue gene expression profiles of six murine smoking experiments (n = 48) were obtained from the Gene Expression Omnibus (GEO) and analyzed to identify the murine smoking signature. The “human smoking” gene signature containing 386 genes was previously published in the lung eQTL study (n = 1,111). A signature of mild COPD containing 7 genes was also identified in the same study. The lung tissue gene signature of “severe COPD” (n = 70) contained 4,071 genes and was previously published. We detected 3,723 differentially expressed genes in the 6 month-exposure mice datasets (FDR <0.1). Of those, 184 genes (representing 48% of human smoking) and 1,003 (representing 27% of human COPD) were shared with the human smoking-related genes and the COPD severity-related genes, respectively. There was 4-fold over-representation of human and murine smoking-related genes (P = 6.7 × 10−26) and a 1.4 fold in the severe COPD -related genes (P = 2.3 × 10−12). There was no significant enrichment of the mice and human smoking-related genes in mild COPD signature. These data suggest that murine smoke models are strongly representative of molecular processes of human smoking but less of COPD.

O'Donoghue, SI, Baldi, BF, Clark, SJ, Darling, AE, Hogan, JM, Kaur, S, Maier-Hein, L, McCarthy, DJ, Moore, WJ, Stenau, E, Swedlow, JR, Vuong, J & Procter, JB 2018, 'Visualization of Biomedical Data', Annual Review of Biomedical Data Science, vol. 1, no. 1, pp. 275-304.
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The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.

Oh, B, Eade, T, Kneebone, A, Hruby, G, Lamoury, G, Pavlakis, N, Clarke, S, Zaslawski, C, Marr, I, Costa, D & Back, M 2018, 'Acupuncture in Oncology: The Effectiveness of Acupuncture May Not Depend on Needle Retention Duration', Integrative Cancer Therapies, vol. 17, no. 2, pp. 458-466.
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Background. Guidelines surrounding optimum needle retention duration in acupuncture have not been established, despite a growing evidence base for acupuncture over recent decades. This retrospective study explored the effect of varying acupuncture needle retention durations in cancer patients. Method. Patients received either 2 (n = 35), 10 (n = 53), or 20 minutes (n = 54) of acupuncture once a week for 6 weeks. Outcomes of anxiety and depression, stress, fatigue, and quality of life (QOL), with the Hospital Anxiety and Depression Scale, Perceived Stress Scale, Functional Assessment of Cancer Therapy–Fatigue, and European Organization for Research and Treatment of Cancer Quality of Life, were measured at baseline and at 6 weeks following the intervention. Results. The mean age of participants was 58 years (n = 152). The majority were female, diagnosed with breast cancer. Depression, stress, fatigue, and QOL were significantly improved in all 3 groups at 6 weeks postintervention. No significant differences in all outcomes were found between the 3 groups (≤2 vs 10 minutes vs 20 minutes). There were no differences with the satisfaction of the acupuncture services and perceived efficacy of acupuncture among the 3 groups. More than 95% of participants indicated that they would recommend acupuncture to other cancer patients, friends, and their family members. Conclusion. The efficacy of acupuncture may not only depend on needle retention duration, but may also be associated with multiple factors. Considering the limitations of this study design, robust randomized controlled studies are warranted to confirm the findings.

Oh, B, Yeung, A, Klein, P, Larkey, L, Ee, C, Zaslawski, C, Knobf, T, Payne, P, Stener-Victorin, E, Lee, R, Choi, W, Chun, M, Bonucci, M, Lang, H-D, Pavlakis, N, Boyle, F, Clarke, S, Back, M, Yang, P, Wei, Y, Guo, X, Weng, C-HD, Irwin, MR, Elfiky, AA & Rosenthal, D 2018, 'Accreditation Standard Guideline Initiative for Tai Chi and Qigong Instructors and Training Institutions', Medicines, vol. 5, no. 2, pp. 51-51.
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Evidence of the health and wellbeing benefits of Tai Chi and Qigong (TQ) have emerged in the past two decades, but TQ is underutilized in modern health care in Western countries due to lack of promotion and the availability of professionally qualified TQ instructors. To date, there are no government regulations for TQ instructors or for training institutions in China and Western countries, even though TQ is considered to be a part of Traditional Chinese medicine that has the potential to manage many chronic diseases. Based on an integrative health care approach, the accreditation standard guideline initiative for TQ instructors and training institutions was developed in collaboration with health professionals, integrative medicine academics, Tai Chi and Qigong master instructors and consumers including public safety officers from several countries, such as Australia, Canada, China, Germany, Italy, Korea, Sweden and USA. In this paper, the rationale for organizing the Medical Tai Chi and Qigong Association (MTQA) is discussed and the accreditation standard guideline for TQ instructors and training institutions developed by the committee members of MTQA is presented. The MTQA acknowledges that the proposed guidelines are broad, so that the diversity of TQ instructors and training institutions can be integrated with recognition that these guidelines can be developed with further refinement. Additionally, these guidelines face challenges in understanding the complexity of TQ associated with different principles, philosophies and schools of thought. Nonetheless, these guidelines represent a necessary first step as primary resource to serve and guide health care professionals and consumers, as well as the TQ community.

Oh, H-S, Constancias, F, Ramasamy, C, Tang, PYP, Yee, MO, Fane, AG, McDougald, D & Rice, SA 2018, 'Biofouling control in reverse osmosis by nitric oxide treatment and its impact on the bacterial community', Journal of Membrane Science, vol. 550, pp. 313-321.
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© 2018 The Authors Recent discoveries regarding the regulation of the biofilm life cycle by bacterial signaling systems have identified novel strategies for manipulation of biofilm development to control the biofouling of membrane-based water purification systems. Nitric oxide (NO) signaling has been shown to induce dispersal of a wide range of single- and multi-species biofilms. However, the impact of NO-mediated biofilm dispersal on the taxa composition of natural communities as well as the potential selection for non-responding community members have rarely been addressed. Here, we investigated the effect of diethylenetriamine (DETA) NONOate, an NO donor with a long half-life, on biofilm dispersal of a bacterial community responsible for membrane biofouling to address this question. The biofilm of a complex community from a fouled industrial reverse osmosis (RO) membrane was dispersed over 50% by 500 μM of DETA NONOate treatment in a continuous flow system. Once-daily treatment with DETA NONOate in a laboratory-scale RO system demonstrated its anti-biofouling effect by delaying the transmembrane pressure increase during constant-flux filtration. Characterization of the bacterial communities of dispersed cells and remaining biofilm cells using a 16S Illumina MiSeq metabarcoding approach demonstrated that biofilm dispersal by DETA NONOate had no selection bias in the community.

Oh, JE, Walsh, S & Zaslawski, CJ 2018, 'A 10 year comparison update: A survey of socio-demogrpahics and practice characteritics of members of the Australian Acupuncture and Chinese Medicine Association', Australian Journal of Acupuncture and Chinese Medicine, vol. 12, no. 1, pp. 19-25.
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Background: A previous study in 2006 reported on the demographic and practice characteristics of 386 AACMAmembers’ responses. In the intervening decade since the 2006 data collection many changes have occurred, includingthe introduction of the National Registration and Accreditation Scheme for the Chinese medicine (CM) profession.It was therefore decided to undertake a new survey in order to update and compare the demographic and practicecharacteristics of AACMA members, to determine whether there had been a significant change.Method: An online version of the survey that replicated the 2006 paper instrument was utilised to collect updateddata regarding AACMA practitioner attributes and practice characteristics. The 2016 responses (n = 148) wascompared against the earlier 2006 survey responses (n = 386) and the Chinese Medicine Board of Australia’s (CMBA)registrant data for the corresponding period.Results: A natural ageing of practitioners was observed, but similar gender distribution (higher female ratio to malepractitioners) and practice locality clustering (majority of respondents being located in Queensland, New SouthWales or Victoria) was noted. The majority of respondents answered that their training in CM was undertaken withinAustralia, most likely through a university or a private college and holding a Bachelor’s degree. A trend to practice ina full-time capacity was noted across the 10 year time period, as well as a preference to combine treatment modalitieswhen practising. Acupuncture and Chinese herbal medicine were the most frequently used modalities. It was alsoobserved that the 2016 respondents preferred to work solo, whereas the 2006 respondents preferred group practice.For those who were working in a group practice, they were most likely to be working with other CM practitioners,followed by other CAM practitioners. The average patient consultations completed remained steady at 15-24 patientsper week for the majority of ...

Ollivier, QR, Hammill, E, Booth, DJ, Madin, EMP, Hinchliffe, C, Harborne, AR, Lovelock, CE, Macreadie, PI & Atwood, TB 2018, 'Benthic meiofaunal community response to the cascading effects of herbivory within an algal halo system of the Great Barrier Reef', PLOS ONE, vol. 13, no. 3, pp. e0193932-e0193932.
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© 2018 Ollivier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Benthic fauna play a crucial role in organic matter decomposition and nutrient cycling at the sediment-water boundary in aquatic ecosystems. In terrestrial systems, grazing herbivores have been shown to influence below-ground communities through alterations to plant distribution and composition, however whether similar cascading effects occur in aquatic systems is unknown. Here, we assess the relationship between benthic invertebrates and above-ground fish grazing across the ‘grazing halos’ of Heron Island lagoon, Australia. Grazing halos, which occur around patch reefs globally, are caused by removal of seagrass or benthic macroalgae by herbivorous fish that results in distinct bands of unvegetated sediments surrounding patch reefs. We found that benthic algal canopy height significantly increased with distance from patch reef, and that algal canopy height was positively correlated with the abundances of only one invertebrate taxon (Nematoda). Both sediment carbon to nitrogen ratios (C:N) and mean sediment particle size (?m) demonstrated a positive correlation with Nematoda and Arthropoda (predominantly copepod) abundances, respectively. These positive correlations indicate that environmental conditions are a major contributor to benthic invertebrate community distribution, acting on benthic communities in conjunction with the cascading effects of above-ground algal grazing. These results suggest that benthic communities, and the ecosystem functions they perform in this system, may be less responsive to changes in above-ground herbivorous processes than those previously studied in terrestrial systems. Understanding how above-ground organisms, and processes, affect their benthic invertebrate counter...

O'Rourke, MB, Djordjevic, SP & Padula, MP 2018, 'The quest for improved reproducibility in MALDI mass spectrometry', Mass Spectrometry Reviews, vol. 37, no. 2, pp. 217-228.
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Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat “hit and miss” with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217–228, 2018.

O'Rourke, MB, Padula, MP, Smith, C, Youssef, P, Cordwell, S, Witting, P, Sutherland, G & Crossett, B 2018, 'Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows', Journal of Visualized Experiments, vol. 2018, no. 131.
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© 2018, Journal of Visualized Experiments. All rights reserved. The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host of biomolecules from drugs and lipids to N-glycans. Although various sample preparation techniques exist, detecting peptides from formaldehyde preserved tissues remains one of the most difficult challenges for this type of mass spectrometric analysis. For this reason, we have created and optimized a robust methodology that preserves the spatial information contained within the sample, while eliciting the greatest number of ionizable peptides. We have also aimed to achieve this in a cost effective and simple way, thereby eliminating potential bias or preparation error, which can occur when using automated instrumentation. The end result is a reproducible and inexpensive protocol.

Osman, EO, Smith, DJ, Ziegler, M, Kürten, B, Conrad, C, El‐Haddad, KM, Voolstra, CR & Suggett, DJ 2018, 'Thermal refugia against coral bleaching throughout the northern Red Sea', Global Change Biology, vol. 24, no. 2, pp. e474-e484.
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AbstractTropical reefs have been impacted by thermal anomalies caused by global warming that induced coral bleaching and mortality events globally. However, there have only been very few recordings of bleaching within the Red Sea despite covering a latitudinal range of 15° and consequently it has been considered a region that is less sensitive to thermal anomalies. We therefore examined historical patterns of sea surface temperature (SST) and associated anomalies (1982–2012) and compared warming trends with a unique compilation of corresponding coral bleaching records from throughout the region. These data indicated that the northern Red Sea has not experienced mass bleaching despite intensive Degree Heating Weeks (DHW) of >15°C‐weeks. Severe bleaching was restricted to the central and southern Red Sea where DHWs have been more frequent, but far less intense (DHWs <4°C‐weeks). A similar pattern was observed during the 2015–2016 El Niño event during which time corals in the northern Red Sea did not bleach despite high thermal stress (i.e. DHWs >8°C‐weeks), and bleaching was restricted to the central and southern Red Sea despite the lower thermal stress (DHWs < 8°C‐weeks). Heat stress assays carried out in the northern (Hurghada) and central (Thuwal) Red Sea on four key reef‐building species confirmed different regional thermal susceptibility, and that central Red Sea corals are more sensitive to thermal anomalies as compared to those from the north. Together, our data demonstrate that corals in the northern Red Sea have a much higher heat tolerance than their prevailing temperature regime would suggest. In contrast, corals from the central Red Sea are close to their ...

Pagnucco, R & Phillips, ML 2018, 'Comparative effectiveness of natural by-products and synthetic sorbents in oil spill booms', Journal of Environmental Management, vol. 225, pp. 10-16.
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© 2018 Sorbent booms are considered a ‘first line of defence’ technology used for containing and minimizing the impacts of crude oil spills. Booms containing human hair waste as sorbent were compared to other natural sorbents, including cotton by-product, recycled cellulose, as well as booms containing synthetic polypropylene, in order to evaluate their effectiveness in adsorbing petroleum crude oil pollution, remaining buoyant, and adsorbing seawater. A series of oceanic mesocosm experiments were used to simulate oil spill pollution events and to test sorbent effectiveness. Hair by-product was found to be significantly better at adsorbing crude oil on average (i.e. 0.84 g of crude oil per 1 g of sorbent) than all other materials, although it had wider variation in adsorbency likely associated with the non-homogeneous nature of mixed human hair. Hair sorbent was also observed to be less naturally buoyant than other materials, potentially due to low surface tension or increased porosity.

Pamphlett, R, Bishop, DP, Kum Jew, S & Doble, PA 2018, 'Age-related accumulation of toxic metals in the human locus ceruleus', PLOS ONE, vol. 13, no. 9, pp. e0203627-e0203627.
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© 2018 Pamphlett et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Damage to the locus ceruleus has been implicated in the pathogenesis of a number of neurological conditions. Locus ceruleus neurons accumulate toxic metals such as mercury selectively, however, the presence of toxic metals in locus ceruleus neurons of people of different ages, and with a variety of disorders, is not known. To demonstrate at what age toxic metals are first detectable in the locus ceruleus, and to evaluate whether their presence is more common in certain clinicopathological conditions, we looked for these metals in 228 locus ceruleus samples. Samples were taken at coronial autopsies from individuals with a wide range of ages, pre-existing conditions and causes of death. Paraffin sections of pons containing the locus ceruleus were stained with silver nitrate autometallography, which indicates inorganic mercury, silver and bismuth within cells (termed autometallography-detected toxic metals, or AMG™). No locus ceruleus AMG neurons were seen in 38 individuals aged under 20 years. 47% of the 190 adults (ie, aged 20 years and over) had AMG locus ceruleus neurons. The proportion of adults with locus ceruleus AMG neurons increased during aging, except for a decreased proportion in the 90-plus years age group. No differences were found in the proportions of locus ceruleus AMG neurons between groups with different neurological, psychiatric, or other clinicopathological conditions, or among various causes of death. Elemental analysis with laser ablation-inductively coupled plasma-mass spectrometry was used to cross-validate the metals detected by AMG, by looking for silver, gold, bismuth, cadmium, chromium, iron, mercury, nickel, and lead in the locus ceruleus of ten individuals. This confirme...

Pan, GJ, Rayner, BS, Zhang, Y, van Reyk, DM & Hawkins, CL 2018, 'A pivotal role for NF-κB in the macrophage inflammatory response to the myeloperoxidase oxidant hypothiocyanous acid', Archives of Biochemistry and Biophysics, vol. 642, pp. 23-30.
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Atherosclerosis is characterised by the infiltration of macrophages at sites of inflammation within the vessel wall and the release of myeloperoxidase (MPO), which forms hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN). HOCl is a damaging oxidant implicated in the development of atherosclerosis. Preferential formation of HOSCN occurs under conditions where thiocyanate ions are elevated, as is the case in smokers. HOSCN reacts selectively with thiols, which can result in more enzyme inactivation and damage than HOCl at susceptible sites, which may contribute to atherosclerosis in smokers. In this study, we show that exposure of macrophages to HOSCN results in a time- and dose-dependent increase in the mRNA expression and release of pro-inflammatory cytokines and chemokines, including monocyte chemotactic protein 1, tumour necrosis factor alpha, and interleukins 6, 8 and 1β. At high oxidant concentrations (>200 μM), a significant loss of cellular thiols and increased cell death is observed. HOSCN-induced cytokine/chemokine expression and cell death were decreased on pharmacological inhibition of nuclear factor kappa B. These data highlight a pathway by which HOSCN could promote inflammation and the development of atherosclerosis, in the presence of supra-physiological levels of the precursor thiocyanate, which are achievable by cigarette smoking.

Pankratova, N, Cuartero, M, Jowett, LA, Howe, ENW, Gale, PA, Bakker, E & Crespo, GA 2018, 'Fluorinated tripodal receptors for potentiometric chloride detection in biological fluids', Biosensors and Bioelectronics, vol. 99, pp. 70-76.
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Panth, N, Paudel, KR, Gong, D-S & Oak, M-H 2018, 'Vascular Protection by Ethanol Extract of Morus alba Root Bark: Endothelium‐Dependent Relaxation of Rat Aorta and Decrease of Smooth Muscle Cell Migration and Proliferation', Evidence-Based Complementary and Alternative Medicine, vol. 2018, no. 1, pp. 1-8.
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Morus alba (white mulberry) is native to the northern part of Korea and popularly used as a traditional medicine due to its numerous health benefits against human’s disease. However, the possibility that M. alba may also affect the cardiovascular system remains unexplored. This study sought to investigate the vascular protective effects of the root bark extract of M. alba (MAE). Vascular reactivity was performed in organ baths using isolated rat thoracic aorta, while platelet derived growth factor (PDGF) induced proliferation and migration of vascular smooth muscle cells (VSMCs) were studied by 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium (MTS) and wound healing assay, respectively. MAE evoked a concentration dependent vasorelaxation following endothelium‐dependent pathway. However, vessel relaxations in response to MAE were markedly reduced after endothelium removal; treatment of endothelial nitric oxide synthase inhibitor, guanylyl cyclase inhibitor, and nonspecific potassium channel inhibitor, however, was not altered by cyclooxygenase inhibitor. Furthermore, MAE also significantly blunted contractile response to vasoconstrictor agent, phenylephrine. Taken together, the current evidence revealed that MAE is a potent endothelium‐dependent vasodilator and this effect was involved in, at least in part, nitric oxide cyclic‐guanosine monophosphate (NO‐cGMP) pathway in combination with potassium (K+) channel activation. Moreover, MAE inhibited proliferation and migration of VSMCs induced by PDGF. Therefore, MAE could be a promising candidate of natural medicine for preventing and controlling cardiovascular diseases linked with endothelial dysfunction.

Parker, LM, O'Connor, WA, Byrne, M, Dove, M, Coleman, RA, Pörtner, H-O, Scanes, E, Virtue, P, Gibbs, M & Ross, PM 2018, 'Ocean acidification but not warming alters sex determination in the Sydney rock oyster, Saccostrea glomerata', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1872, pp. 20172869-20172869.
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Whether sex determination of marine organisms can be altered by ocean acidification and warming during this century remains a significant, unanswered question. Here, we show that exposure of the protandric hermaphrodite oyster, Saccostrea glomerata to ocean acidification, but not warming, alters sex determination resulting in changes in sex ratios. After just one reproductive cycle there were 16% more females than males. The rate of gametogenesis, gonad area, fecundity, shell length, extracellular pH and survival decreased in response to ocean acidification. Warming as a sole stressor slightly increased the rate of gametogenesis, gonad area and fecundity, but this increase was masked by the impact of ocean acidification at a level predicted for this century. Alterations to sex determination, sex ratios and reproductive capacity will have flow on effects to reduce larval supply and population size of oysters and potentially other marine organisms.

Parvez Mahmud, MA, Huda, N, Farjana, SH, Asadnia, M & Lang, C 2018, 'Recent Advances in Nanogenerator‐Driven Self‐Powered Implantable Biomedical Devices', Advanced Energy Materials, vol. 8, no. 2, pp. 1701210-1701210.
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AbstractImplantable medical devices (IMDs) have experienced a rapid progress in recent years to the advancement of state‐of‐the‐art medical practices. However, the majority of this equipment requires external power sources like batteries to operate, which may restrict their application for in vivo situations. Furthermore, these external batteries of the IMDs need to be changed at times by surgical processes once expired, causing bodily and psychological annoyance to patients and rising healthcare financial burdens. Currently, harvesting biomechanical energy in vivo is considered as one of the most crucial energy‐based technologies to ensure sustainable operation of implanted medical devices. This review aims to highlight recent improvements in implantable triboelectric nanogenerators (iTENG) and implantable piezoelectric nanogenerators (iPENG) to drive self‐powered, wireless healthcare systems. Furthermore, their potential applications in cardiac monitoring, pacemaker energizing, nerve‐cell stimulating, orthodontic treatment and real‐time biomedical monitoring by scavenging the biomechanical power within the human body, such as heart beating, blood flowing, breathing, muscle stretching and continuous vibration of the lung are summarized and presented. Finally, a few crucial problems which significantly affect the output performance of iTENGs and iPENGs under in vivo environments are addressed.

Parvez Mahmud, MA, Huda, N, Hisan Farjana, S & Lang, C 2018, 'Environmental profile evaluations of piezoelectric polymers using life cycle assessment', IOP Conference Series: Earth and Environmental Science, vol. 154, pp. 012017-012017.
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Pasalic, L, Wing‐Lun, E, Lau, JK, Campbell, H, Pennings, GJ, Lau, E, Connor, D, Liang, HP, Muller, D, Kritharides, L, Hogg, PJ & Chen, VM 2018, 'Novel assay demonstrates that coronary artery disease patients have heightened procoagulant platelet response', Journal of Thrombosis and Haemostasis, vol. 16, no. 6, pp. 1198-1210.
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Patel, NR, Padalia, H, Devadas, R, Huete, A, Senthil Kumar, A & Krishna Murthy, YVN 2018, 'Estimating Net Primary Productivity of Croplands in Indo-Gangetic Plains Using GOME-2 Sun-Induced Fluorescence and MODIS NDVI', Current Science, vol. 114, no. 06, pp. 1333-1333.
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© 2018 Current Science Association, Bengaluru. Recently evolved satellite-based sun-induced fluorescence (SIF) spectroscopy is considered as a direct measure of photosynthetic activity of vegetation. We have used monthly averages of satellite-based SIF retrievals for three agricultural year cycles, i.e. May to April for each of the three years, viz. 2007-08, 2008-09 and 2009-10 to assess comparative performance of SIF and normalized difference vegetation index (NDVI) for predicting net primary productivity (NPP) over the Indo-Gangetic Plains, India. Results show that SIF values for C4 crop-dominated districts were higher than C3 crop-dominated districts during summer and low during winter for all three years. SIF explained more or less above 70% of variance in NPP. The variance explained by integrated NDVI ranged from 60% to 67%. Thus the present study has shown the potential of SIF data for improved modelling of agricultural productivity at a regional scale.

Pathinayake, PS, Hsu, AC-Y, Waters, DW, Hansbro, PM, Wood, LG & Wark, PAB 2018, 'Understanding the Unfolded Protein Response in the Pathogenesis of Asthma', Frontiers in Immunology, vol. 9, no. FEB.
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© 2018 Pathinayake, Hsu, Waters, Hansbro, Wood and Wark. Asthma is a heterogeneous, chronic inflammatory disease of the airways. It is a complex disease with different clinical phenotypes and results in a substantial socioeconomic burden globally. Poor understanding of pathogenic mechanisms of the disease hinders the investigation into novel therapeutics. Emerging evidence of the unfolded protein response (UPR) in the endoplasmic reticulum (ER) has demonstrated previously unknown functions of this response in asthma development. A worsening of asthmatic condition can be brought on by stimuli such as oxidative stress, pathogenic infections, and allergen exposure. All of which can induce ER stress and activate UPR leading to activation of different inflammatory responses and dysregulate the innate immune functions in the airways. The UPR as a central regulator of asthma pathogenesis may explain several unknown mechanism of the disease onset, which leads us in new directions for future asthma treatments. In this review, we summarize and discuss the causes and impact of ER-UPR in driving the pathogenesis of asthma and highlight its importance in clinical implications.

Paul, PK, Kumari, N, Panigrahi, N, Mishra, A & Singh, R 2018, 'Implementation of cell-to-cell routing scheme in a large scale conceptual hydrological model', Environmental Modelling & Software, vol. 101, pp. 23-33.
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Paull, NJ, Irga, PJ & Torpy, FR 2018, 'Active green wall plant health tolerance to diesel smoke exposure', Environmental Pollution, vol. 240, pp. 448-456.
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© 2018 Elsevier Ltd Poor air quality is an emerging world-wide problem, with most urban air pollutants arising from vehicular emissions. As such, localized high pollution environments, such as traffic tunnels pose a significant health risk. Phytoremediation, including the use of active (ventilated) green walls or botanical biofilters, is gaining recognition as a potentially effective method for air pollution control. Research to date has tested the capacity of these systems to remove low levels of pollutants from indoor environments. If botanical biofilters are to be used in highly polluted environments, the plants used in these systems must be resilient, however, this idea has received minimal research. Thus, testing was conducted to assess the hardiness of the vegetated component of a botanical biofilter to simulated street level air pollutant exposure. A range of morphological, physiological, and biochemical tests were conducted on 8 common green wall plant species prior to and post 5-week exposure to highly concentrated diesel fuel combustion effluent; as a pilot study to investigate viability in in situ conditions. The results indicated that species within the fig family were the most tolerant species of those assessed. It is likely that species within the fig family can withstand enhanced air pollutant conditions, potentially a result of its leaf morphology and physiology. Other species tested were all moderately tolerant to the pollution treatment. We conclude that most common green wall plant species have the capacity to withstand high pollutant environments, however, extended experimentation is needed to rule out potential long term effects along with potential decreases in filter efficiency from accumulative effects on the substrate. MS capsule summary: The results obtained from the multi-trait plant health assessment provide proof-of-concept that active botanical biozfilters are able to withstand short term, high level pollutant exposure.

Pech, M, Weckmann, M, König, IR, Franke, A, Heinsen, F-A, Oliver, B, Ricklefs, I, Fuchs, O, Rabe, K, Hansen, G, v. Mutius, E & Kopp, MV 2018, 'Rhinovirus infections change DNA methylation and mRNA expression in children with asthma', PLOS ONE, vol. 13, no. 11, pp. e0205275-e0205275.
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© 2018 Pech et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Human rhinovirus infection (HRVI) plays an important role in asthma exacerbations and is thought to be involved in asthma development during early childhood. We hypothesized that HRVI causes differential DNA methylation and subsequently differential mRNA expression in epithelial cells of children with asthma. Primary nasal epithelial cells from children with (n = 10) and without (n = 10) asthma were cultivated up to passage two and infected with Rhinovirus-16 (RV-16). HRVI-induced genome-wide differences of DNA methylation in asthmatics (vs. controls) and resulting mRNA expression were analyzed by the Human-Methylation450 BeadChip Kit (Illumina) and RNA sequencing. These results were further verified by pyrosequencing and quantitative PCR, respectively. 471 CpGs belonging to 268 genes were identified to have HRVI-induced asthma-specifically modified DNA methylation and mRNA expression. A minimum-change criteria was applied to restrict assessment of genes with changes in DNA methylation and mRNA expression of at least 3% and least 0.1 reads/kb per million mapped reads, respectively. Using this approach we identified 16 CpGs, including HLA-B-associated transcript 3 (BAT3) and Neuraminidase 1 (NEU1), involved in host immune response against HRVI. HRVI in nasal epithelial cells leads to specific modifications of DNA methylation with altered mRNA expression in children with asthma. The HRVI-induced alterations in DNA methylation occurred in genes involved in the host immune response against viral infections and asthma pathogenesis. The findings of our pilot study may partially explain how HRVI contribute to the persistence and progression of asthma, and aid to identify possible new therapeutic targets. The p...

Peng, D, Wu, C, Zhang, X, Yu, L, Huete, AR, Wang, F, Luo, S, Liu, X & Zhang, H 2018, 'Scaling up spring phenology derived from remote sensing images', Agricultural and Forest Meteorology, vol. 256-257, pp. 207-219.
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Land surface phenology, especially spring phenology, has been reported as a powerful indicator of ecosystem responses to climate change. It also exerts strong control on the carbon, water and energy balances and, hence, climatic feedbacks. Researchers have produced numerous spring phenology products from various coarse-resolution remote sensing data at regional or global scales. Scaling up observations of spring phenology from plot-level (or finer resolution) to coarser resolution is important for the validation, synthesis, and evaluation of those products. The best method for scaling up is unclear although coarse resolution data can be obtained by averaging across fine-scale pixels, or selecting the start of spring phenology (SOS) date associated with the earliest 30% (or another percentile) of fine-scale pixels within a coarse-scale pixel. In this study, we tested different methods that were average and percentile approaches to aggregate SOS as measured at 250 m (SOS (250 m)) resolution to 8 km (SOS (8 km)) resolution pixels, and then to ecosystems and national scales for the continental United States. The results indicated that the average absolute difference (AAD) between SOS (250 m) and SOS (8 km) from the average approach was close to that achieved by the percentile approach. Relatively large AAD values occurred in the western and southern regions of the continental United States. The distribution of AAD was positively related to landscape heterogeneity. The percentile approach generally yielded smaller AADs than the average approach did, but these two approaches performed similarly. Across landscapes and ecosystems, the optimal percentile usually ranged from 30–45th instead of a single value. Our findings indicated that the percentile approach may be best for finer scale areas, but that the average approach is an adequate alternative for scaling up SOS in most circumstances. In addition, the detailed error distributions of scaling up spring pheno...

Periyalil, HA, Wood, LG, Wright, TA, Karihaloo, C, Starkey, MR, Miu, AS, Baines, KJ, Hansbro, PM & Gibson, PG 2018, 'Obese asthmatics are characterized by altered adipose tissue macrophage activation', Clinical & Experimental Allergy, vol. 48, no. 6, pp. 641-649.
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SummaryBackgroundAdipose tissue‐derived inflammation is linked to obesity‐related comorbidities. This study aimed to quantify and immuno‐phenotype adipose tissue macrophages (ATMs) from obese asthmatics and obese non‐asthmatics and to examine associations between adipose tissue, systemic and airway inflammation.MethodsVisceral (VAT) adipose tissue and subcutaneous (SAT) adipose tissue were collected from obese adults undergoing bariatric surgery and processed to obtain the stromovascular fraction. Pro‐inflammatory (M1) and anti‐inflammatory (M2) macrophages were quantified by flow cytometry. Cytospins of induced sputum were stained for differential cell counts. Plasma C‐reactive protein (CRP) and CD163 were measured by ELISA.ResultsVAT contained a higher number of ATMs compared to SAT. A higher percentage of M1 ATMs was observed in VAT of obese asthmatics compared to obese non‐asthmatics. The M1:M2 ratio in VAT was negatively associated with FEV1%. Sputum macrophage count was correlated positively with M1

Petrou, K & Nielsen, DA 2018, 'Uptake of dimethylsulphoniopropionate (DMSP) by the diatom Thalassiosira weissflogii: a model to investigate the cellular function of DMSP', Biogeochemistry, vol. 141, no. 2, pp. 265-271.
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One of the most abundant organic sulphur molecules in the ocean, dimethylsulphoniopropionate (DMSP) has been implicated in numerous biochemical functions and ecological interactions, from osmotic and oxidative stress regulation within the cell, to the chemical attraction of bacteria, mammals and birds in the environment. Notwithstanding these varied and important discoveries, the primary role of DMSP in the cell remains elusive. In this study, we take a new approach to investigating the role of DMSP in cell physiology. Rather than utilising a known DMSP-producer, we instead exploit the propensity for the non-DMSP producing diatom Thalassiosira weissflogii to take up DMSP from its environment. We characterise the uptake and retention of the molecule under growth conditions and salinity stress with the aim to elucidate its utility as a model system for investigating the cellular function of DMSP. Thalassiosira weissflogii showed concentration-dependent uptake of DMSP and complete retention within the cell for at least 6 h. Saturation of intracellular DMSP occurred at > 87 mM, equivalent to some of the most prolific DMSP-producing species. Salinity shifts resulted in a reduction in DMSP uptake rate, but only at extremely low (17) or very high (45) salinities. These data demonstrate the potential for using T. weissflogii in physiological studies, providing a true (DMSP-free) control, as well as a DMSP-enriched version of the same strain. In this way, orthogonal experiments may be conducted with the aim to uncover the physiological purpose of DMSP in phytoplankton and potentially add key pieces to the enigmatic DMSP puzzle.

Petrou, K, Nielsen, DA & Heraud, P 2018, 'Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion', Frontiers in Marine Science, vol. 5, no. MAR.
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© 2018 Petrou, Nielsen and Heraud. The success of corals in nutrient poor environments is largely attributed to the symbiosis between the cnidarian host and its intracellular alga. Warm water anomalies have been shown to destabilize this symbiosis, yet detailed analysis of the effect of temperature and expulsion on cell-specific carbon and nutrient allocation in the symbiont is limited. Here, we exposed colonies of the hard coral Acropora millepora to heat stress and using synchrotron-based infrared microspectroscopy measured the biomolecular profiles of individual in hospite and expelled symbiont cells at an acute state of bleaching. Our results showed symbiont metabolic profiles to be remarkably distinct with heat stress and expulsion, where the two effectors elicited opposing metabolic adjustments independent of treatment or cell type. Elevated temperature resulted in biomolecular changes reflecting cellular stress, with relative increases in free amino acids and phosphorylation of molecules and a concomitant decline in protein content, suggesting protein modification and degradation. This contrasted with the metabolic profiles of expelled symbionts, which showed relative decreases in free amino acids and phosphorylated molecules, but increases in proteins and lipids, suggesting expulsion lessens the overall effect of heat stress on the metabolic signature of the algal symbionts. Interestingly, the combined effects of expulsion and thermal stress were additive, reducing the overall shifts in all biomolecules, with the notable exception of the significant accumulation of lipids and saturated fatty acids. This first use of a single-cell metabolomics approach on the coral symbiosis provides novel insight into coral bleaching and emphasizes the importance of a single-cell approach to demark the cell-to-cell variability in the physiology of coral cellular populations.

Pettit, T, Irga, PJ & Torpy, FR 2018, 'Functional green wall development for increasing air pollutant phytoremediation: Substrate development with coconut coir and activated carbon', Journal of Hazardous Materials, vol. 360, pp. 594-603.
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© 2018 Functional green walls are gaining attention due to their air cleaning abilities, however the air cleaning capacity of these systems may be improved through substrate modification. This experiment investigated the capacity of several green wall media to filter a range of air pollutants. Media, consisting of differently sized coconut husk-based substrates, and with different ratios of activated carbon were evaluated through the use of scaled down model ‘cassettes’. Tests were conducted assessing each substrate's ability to filter particulate matter, benzene, ethyl acetate and ambient total VOCs. While the particle size of coconut husk did not influence removal efficiency, the addition of activated carbon to coconut husk media improved the removal efficiency for all gaseous pollutants. Activated carbon as a medium component, however, inhibited the removal efficiency of particulate matter. Once the substrate concentration of activated carbon approached ∼50%, its gas remediation capacity became asymptotic, suggesting that a 50:50 composite medium provided the best VOC removal. In full-scale botanical biofilter modules, activated carbon-based substrates increased benzene removal, yet decreased particulate matter removal despite the addition of plants. The findings suggest that medium design should be target pollutant dependent, while further work is needed to establish plant viability in activated carbon-based media.

Pettit, T, Irga, PJ & Torpy, FR 2018, 'Towards practical indoor air phytoremediation: A review', Chemosphere, vol. 208, pp. 960-974.
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© 2018 Elsevier Ltd Indoor air quality has become a growing concern due to the increasing proportion of time people spend indoors, combined with reduced building ventilation rates resulting from an increasing awareness of building energy use. It has been well established that potted-plants can help to phytoremediate a diverse range of indoor air pollutants. In particular, a substantial body of literature has demonstrated the ability of the potted-plant system to remove volatile organic compounds (VOCs) from indoor air. These findings have largely originated from laboratory scale chamber experiments, with several studies drawing different conclusions regarding the primary VOC removal mechanism, and removal efficiencies. Advancements in indoor air phytoremediation technology, notably active botanical biofilters, can more effectively reduce the concentrations of multiple indoor air pollutants through the action of active airflow through a plant growing medium, along with vertically aligned plants which achieve a high leaf area density per unit of floor space. Despite variable system designs, systems available have clear potential to assist or replace existing mechanical ventilation systems for indoor air pollutant removal. Further research is needed to develop, test and confirm their effectiveness and safety before they can be functionally integrated in the broader built environment. The current article reviews the current state of active air phytoremediation technology, discusses the available botanical biofiltration systems, and identifies areas in need of development.

Pham, TH & Wand, MP 2018, 'Generalised additive mixed models analysis via gammSlice', Australian & New Zealand Journal of Statistics, vol. 60, no. 3, pp. 279-300.
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SummaryWe demonstrate the use of ourRpackage,gammSlice, for Bayesian fitting and inference in generalised additive mixed model analysis. This class of models includes generalised linear mixed models and generalised additive models as special cases. Accurate Bayesian inference is achievable via sufficiently large Markov chain Monte Carlo (MCMC) samples. Slice sampling is a key component of the MCMC scheme. Comparisons with existing generalised additive mixed model software shows thatgammSliceoffers improved inferential accuracy, albeit at the cost of longer computational time.

Phillips, S, Vodstrcil, LA, Huston, WM, Lawerence, A, Timms, P, Chen, MY, Worthington, K, McIver, R, Bradshaw, CS, Garland, SM, Tabrizi, SN & Hocking, JS 2018, 'Detection of Chlamydia trachomatis mRNA using digital PCR as a more accurate marker of viable organism', European Journal of Clinical Microbiology & Infectious Diseases, vol. 37, no. 11, pp. 2117-2122.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Spontaneous resolution of urogenital Chlamydia trachomatis (CT) without treatment has previously been described, but a limitation of these reports is that DNA or RNA-based amplification tests used do not differentiate between viable infection and non-viable DNA. We modified a previously published CT mRNA detection (omp2) method to differentiate between viable infection and non-viable DNA in a sample of CT DNA PCR positive women. We modified a CT mRNA detection (omp2) method from reverse transcriptase qPCR (RTqPCR) to digital PCR (dPCR) and evaluated it in samples from CT DNA positive women. Firstly, CT infected McCoy B cells treated with azithromycin in vitro identified detectable mRNA levels disappeared <2 days, while DNA persisted up to 6 days. We used 55 self-collected vaginal swabs from a cohort of women diagnosed as DNA positive for chlamydia obtained pre- and 7 days of post-azithromycin treatment. Concordance with DNA results was higher for dPCR than RTqPCR (74.5% versus 65.5%). At visit 1, there was a strong linear relationship between DNA and mRNA (r = 0.9, p < 0.000); 24 samples had both mRNA and DNA detected (82.8%) and 5 had only DNA detected with a potential false positive proportion of 17.2% (95%CI: 5.8, 35.8). At visit 2, there was poor correlation between DNA and mRNA (r = 0.14, p = 0.55); eight specimens had only DNA detected (42.1%; 95%CI: 20.25, 66.50) and one had mRNA detected. DNA detection methods alone may detect non-viable DNA. Consideration should be given to further develop mRNA assays as ancillary tests to improve detection of viable chlamydia.

Philp, M & Fu, S 2018, 'A review of chemical ‘spot’ tests: A presumptive illicit drug identification technique', Drug Testing and Analysis, vol. 10, no. 1, pp. 95-108.
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AbstractChemical ‘spot’ tests are a presumptive illicit drug identification technique commonly used by law enforcement, border security personnel, and forensic laboratories. The simplicity, low cost, and rapid results afforded by these tests make them particularly attractive for presumptive identification globally. In this paper, we review the development of these long‐established methods and discuss color test recommendations and guidelines. A search of the scientific literature revealed the chemical reactions occurring in many color tests are either not actively investigated or reported as unknown. Today, color tests face many challenges, from the appearance of new psychoactive substances to concerns regarding selectivity, sensitivity, and safety. Advances in technology have seen color test reagents used in digital image color analysis, solid sensors, and microfluidic devices for illicit drug detection. This summarizes current research and suggests the future of presumptive color testing.

Philp, M, Shimmon, R, Tahtouh, M & Fu, S 2018, 'Color Spot Test As a Presumptive Tool for the Rapid Detection of Synthetic Cathinones', Journal of Visualized Experiments, vol. 2018, no. 132.
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© 2018 Journal of Visualized Experiments. Synthetic cathinones are a large class of new psychoactive substances (NPS) that are increasingly prevalent in drug seizures made by law enforcement and other border protection agencies globally. Color testing is a presumptive identification technique indicating the presence or absence of a particular drug class using rapid and uncomplicated chemical methods. Owing to their relatively recent emergence, a color test for the specific identification of synthetic cathinones is not currently available. In this study, we introduce a protocol for the presumptive identification of synthetic cathinones, employing three aqueous reagent solutions: copper(II) nitrate, 2,9-dimethyl-1,10-phenanthroline (neocuproine) and sodium acetate. Small pin-head sized amounts (approximately 0.1-0.2 mg) of the suspected drugs are added to the wells of a porcelain spot plate, and each reagent is then added dropwise sequentially before heating on a hotplate. A color change from very light blue to yellow-orange after 10 min indicates the likely presence of synthetic cathinones. The highly stable and specific test reagent has the potential for use in the presumptive screening of unknown samples for synthetic cathinones in a forensic laboratory. However, the nuisance of an added heating step for the color change result limits the test to laboratory application and decreases the likelihood of an easy translation to field testing.

Pijning, AE, Chiu, J, Yeo, RX, Wong, JWH & Hogg, PJ 2018, 'Identification of allosteric disulfides from labile bonds in X-ray structures', Royal Society Open Science, vol. 5, no. 2, pp. 171058-171058.
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Protein disulfide bonds link pairs of cysteine sulfur atoms and are either structural or functional motifs. The allosteric disulfides control the function of the protein in which they reside when cleaved or formed. Here, we identify potential allosteric disulfides in all Protein Data Bank X-ray structures from bonds that are present in some molecules of a protein crystal but absent in others, or present in some structures of a protein but absent in others. We reasoned that the labile nature of these disulfides signifies a propensity for cleavage and so possible allosteric regulation of the protein in which the bond resides. A total of 511 labile disulfide bonds were identified. The labile disulfides are more stressed than the average bond, being characterized by high average torsional strain and stretching of the sulfur–sulfur bond and neighbouring bond angles. This pre-stress likely underpins their susceptibility to cleavage. The coagulation, complement and oxygen-sensing hypoxia inducible factor-1 pathways, which are known or have been suggested to be regulated by allosteric disulfides, are enriched in proteins containing labile disulfides. The identification of labile disulfide bonds will facilitate the study of this post-translational modification.

Pingle, H, Wang, P-Y, Cavaliere, R, Whitchurch, CB, Thissen, H & Kingshott, P 2018, 'Minimal attachment of Pseudomonas aeruginosa to DNA modified surfaces', Biointerphases, vol. 13, no. 6, pp. 06E405-06E405.
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Extracellular deoxyribonucleic acid (eDNA) exists in biological environments such as those around medical implants since prokaryotic or eukaryotic cells can undergo processes such as autolysis, necrosis, and apoptosis. For bacteria, eDNA has been shown to be involved in biofilm formation and gene transfer and acts as a nutrient source. In terms of biofilm formation, eDNA in solution has been shown to be very important in increasing attachment; however, very little is known about the role played by surface immobilized eDNA in initiating bacterial attachment and whether the nature of a DNA layer (physically adsorbed or covalently attached, and molecular weight) influences biofilm formation. In this study, the authors shed light on the role that surface attached DNA plays in the early biofilm formation by using Si wafers (Si) and allylamine plasma polymer (AAMpp) coated Si wafers to adsorb and covalently immobilize salmon sperm DNA of three different molecular weights. Pseudomonas aeruginosa was chosen to study the bacterial interactions with these DNA functionalized surfaces. Characterization of surface chemistry and imaging of attached bacteria were performed via x-ray photoelectron spectroscopy (XPS), scanning electron microscopy, and epi-fluorescence microscopy. XPS results confirmed the successful grafting of DNA on the AAMpp and Si surfaces, and surprisingly the results showed that the surface attached DNA actually reduced initial bacterial attachment, which was contrary to the initial hypothesis. This adds speculation about the specific role played by DNA in the dynamics of how it influences biofilm formation, with the possibility that it could actually be used to make bacterial resistant surfaces.

Pitt, ME, Elliott, AG, Cao, MD, Ganesamoorthy, D, Karaiskos, I, Giamarellou, H, Abboud, CS, Blaskovich, MAT, Cooper, MA & Coin, LJM 2018, 'Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae', Microbial Genomics, vol. 4, no. 3.
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Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high mortality and are disseminating globally. Identifying the genetic basis underpinning resistance allows for rapid diagnosis and treatment. XDR isolates sourced from Greece and Brazil, including 19 polymyxin-resistant and five polymyxin-susceptible strains, were subjected to whole genome sequencing. Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or within mgrB. The most common mutation identified was an insertion at nucleotide position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13 in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations (C28STOP, Q30STOP) or a missense mutation (D29E) affecting mgrB. Complementation assays revealed all mgrB perturbations contributed to resistance. Missense mutations in phoQ (T281M, G385C) were also found to facilitate resistance. Several variants in phoPQ co-segregating with the ISKpn26-like insertion were identified as potential partial suppressor mutations. Three ST258 samples were found to contain subpopulations with different resistance-conferring mutations, including the ISKpn26-like insertion colonizing with a novel mutation in pmrB (P158R), both confirmed via complementation assays. These findings highlight the broad spectrum of chromosomal modifications which can facilitate and regulate resistance against polymyxins in K. pneumoniae.

Poddar, N, Sen, R & Martin, GJO 2018, 'Glycerol and nitrate utilisation by marine microalgae Nannochloropsis salina and Chlorella sp. and associated bacteria during mixotrophic and heterotrophic growth', Algal Research, vol. 33, pp. 298-309.
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Portbury, SD, Hare, DJ, Bishop, DP, Finkelstein, DI, Doble, PA & Adlard, PA 2018, 'Trehalose elevates brain zinc levels following controlled cortical impact in a mouse model of traumatic brain injury', Metallomics, vol. 10, no. 6, pp. 846-853.
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Zinc (Zn) deficiency is a clinical consequence of brain injury that can result in neuropathological outcomes that are exacerbated with age.

Prasansuklab, A, Theerasri, A, Payne, M, Ung, AT & Tencomnao, T 2018, 'Acid-base fractions separated from Streblus asper leaf ethanolic extract exhibited antibacterial, antioxidant, anti-acetylcholinesterase, and neuroprotective activities', BMC Complementary and Alternative Medicine, vol. 18, no. 1, pp. 223-223.
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Streblus asper is a well-known plant native to Southeast Asia. Different parts of the plant have been traditionally used for various medicinal purposes. However, there is very little scientific evidence reporting its therapeutic benefits for potential treatment of Alzheimer's disease (AD). The study aimed to evaluate antibacterial, antioxidant, acetylcholinesterase (AChE) inhibition, and neuroprotective properties of S. asper leaf extracts with the primary objective of enhancing therapeutic applications and facilitating activity-guided isolation of the active chemical constituents.The leaves of S. asper were extracted in ethanol and subsequently fractionated into neutral, acid and base fractions. The phytochemical constituents of each fraction were analyzed using GC-MS. The antibacterial activity was evaluated using a broth microdilution method. The antioxidant activity was determined using DPPH and ABTS radical scavenging assays. The neuroprotective activity against glutamate-induced toxicity was tested on hippocampal neuronal HT22 cell line by evaluating the cell viability using MTT assay. The AChE inhibitory activity was screened by thin-layer chromatography (TLC) bioautographic method.The partition of the S. asper ethanolic leaf extract yielded the highest mass of phytochemical constitutions in the neutral fraction and the lowest in the basic fraction. Amongst the three fractions, the acidic fraction showed the strongest antibacterial activity against gram-positive bacteria. The antioxidant activities of three fractions were found in the order of acidic > basic > neutral, whereas the decreasing order of neuroprotective activity was neutral > basic > acidic. TLC bioautography revealed one component in the neutral fraction exhibited anti-AChE activity. While in the acid fraction, two components showed inhibitory activity against AChE. GC-MS analysis of three fractions showed the presence of major phytochemical constituents including terpenoids, steroids, phenol...

Prosser, C, Meyer, W, Ellis, J & Lee, R 2018, 'Evolutionary ARMS Race: Antimalarial Resistance Molecular Surveillance', Trends in Parasitology, vol. 34, no. 4, pp. 322-334.
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Molecular surveillance of antimalarial drug resistance markers has become an important part of resistance detection and containment. In the current climate of multidrug resistance, including resistance to the global front-line drug artemisinin, there is a consensus to upscale molecular surveillance. The most salient limitation to current surveillance efforts is that skill and infrastructure requirements preclude many regions. This includes sub-Saharan Africa, where Plasmodium falciparum is responsible for most of the global malaria disease burden. New molecular and data technologies have emerged with an emphasis on accessibility. These may allow surveillance to be conducted in broad settings where it is most needed, including at the primary healthcare level in endemic countries, and extending to the village health worker.

Prosser, C, Meyer, W, Ellis, J & Lee, R 2018, 'Resistance screening and trend analysis of imported falciparum malaria in NSW, Australia (2010 to 2016)', PLOS ONE, vol. 13, no. 5, pp. e0197369-e0197369.
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BACKGROUND:The World Health Organization currently recommends artemisinin (along with a partner drug) as the global frontline treatment for Plasmodium falciparum malaria. Artemisinin resistant P. falciparum are now found throughout the greater Mekong subregion of South East Asia. Several polymorphisms in the parasite's kelch gene have been demonstrated to confer artemisinin resistance. While genotypes within the greater Mekong subregion are thoroughly examined in the literature, P. falciparum populations within several areas that do not (yet) have endemic resistance are underrepresented. RESULTS:This investigation characterised the Pfkelch13 propeller domains from 153 blood samples of 140 imported cases of P. falciparum malaria in New South Wales from 2010 to 2016. A low level of propeller domain diversity was observed, including the C580Y coding mutation most strongly associated with artemisinin resistance in South East Asia. The resistance genotype was found in a sample originating in Papua New Guinea, where this mutation, or artemisinin treatment failure, have not been previously reported. Sequencing a panel of geographically informative polymorphisms within the organellar genomes identified the C580Y parasite as having Oceanic origins. Patient data analysis revealed that New South Wales, Australia, P. falciparum malaria cases often originated from regions with limited drug resistance screening. CONCLUSIONS:The C580Y finding from outside of the greater Mekong subregion supports the consensus to upscale molecular surveillance of artemisinin resistance outside of South East Asia. The genetic screening results identify a risk of importing resistant falciparum malaria to Australia, supporting an ongoing surveillance protocol to pre-empt treatment failure and contribute to global data gathering.

Pu, N, Zhao, G, Yin, H, Li, J-A, Nuerxiati, A, Wang, D, Xu, X, Kuang, T, Jin, D, Lou, W & Wu, W 2018, 'CD25 and TGF-β blockade based on predictive integrated immune ratio inhibits tumor growth in pancreatic cancer', Journal of Translational Medicine, vol. 16, no. 1.
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Pushpamalar, J, Langford, SJ, Ahmad, MB, Lim, YY & Hashim, K 2018, 'Eco-friendly smart hydrogels for soil conditioning and sustain release fertilizer', International Journal of Environmental Science and Technology, vol. 15, no. 10, pp. 2059-2074.
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Quinlan, RA & Hogg, PJ 2018, 'γ-Crystallin redox–detox in the lens', Journal of Biological Chemistry, vol. 293, no. 46, pp. 18010-18011.
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Quinnell, R, May, E, Davila, Y & Peat, M 2018, 'Profiling our students' learning orchestrations to evaluate the biology curriculum', International Journal of Innovation in Science and Mathematics Education, vol. 26, no. 3, pp. 21-39.
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We have identified the major shifts in individual student study orchestrations over the first semester of a university biology course. We offer evidence that our curriculum, designed and taught by generalist biologists, has engaged generalist degree students. Professional degree students have not engaged with this course to the same level and many were demonstrably dissonant. At the end of semester, dissonant students, from both generalist and professional degrees, demonstrated little engagement with the curriculum, which is consistent with previous reports of the high degree of disengagement of first year students. The challenge to improve the engagement of students in professional degrees and to address the tendency towards dissonance and disengagement by our first year students is discussed and improvements in engagement are likely to be aided by systems that allow students to assess for themselves their approaches to study and conceptions of discipline development over the course of their degree.

Quiroz, M, Villani, M, Kohn, R, Tran, M-N & Dang, K-D 2018, 'Subsampling MCMC - An introduction for the survey statistician', Sankhya A, vol. 80, pp. 33-69.
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The rapid development of computing power and efficient Markov Chain MonteCarlo (MCMC) simulation algorithms have revolutionized Bayesian statistics,making it a highly practical inference method in applied work. However, MCMCalgorithms tend to be computationally demanding, and are particularly slow forlarge datasets. Data subsampling has recently been suggested as a way to makeMCMC methods scalable on massively large data, utilizing efficient samplingschemes and estimators from the survey sampling literature. These developmentstend to be unknown by many survey statisticians who traditionally work withnon-Bayesian methods, and rarely use MCMC. Our article explains the idea ofdata subsampling in MCMC by reviewing one strand of work, Subsampling MCMC, aso called pseudo-marginal MCMC approach to speeding up MCMC through datasubsampling. The review is written for a survey statistician without previousknowledge of MCMC methods since our aim is to motivate survey sampling expertsto contribute to the growing Subsampling MCMC literature.

Rädecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Corrigendum: Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses', Frontiers in Physiology, vol. 9.
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[This corrects the article on p. 214 in vol. 9, PMID: 29615919.].

Rädecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses', Frontiers in Physiology, vol. 9, no. MAR.
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© 2018 Rädecker, Raina, Pernice, Perna, Guagliardo, Kilburn, Aranda and Voolstra. The symbiosis between cnidarian hosts and microalgae of the genus Symbiodinium provides the foundation of coral reefs in oligotrophic waters. Understanding the nutrient-exchange between these partners is key to identifying the fundamental mechanisms behind this symbiosis, yet has proven difficult given the endosymbiotic nature of this relationship. In this study, we investigated the respective contribution of host and symbiont to carbon and nitrogen assimilation in the coral model anemone Aiptaisa. For this, we combined traditional measurements with nanoscale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling to investigate patterns of nutrient uptake and translocation both at the organismal scale and at the cellular scale. Our results show that the rate of carbon and nitrogen assimilation in Aiptasia depends on the identity of the host and the symbiont. NanoSIMS analysis confirmed that both host and symbiont incorporated carbon and nitrogen into their cells, implying a rapid uptake and cycling of nutrients in this symbiotic relationship. Gross carbon fixation was highest in Aiptasia associated with their native Symbiodinium communities. However, differences in fixation rates were only reflected in the δ13C enrichment of the cnidarian host, whereas the algal symbiont showed stable enrichment levels regardless of host identity. Thereby, our results point toward a 'selfish' character of the cnidarian-Symbiodinium association in which both partners directly compete for available resources. Consequently, this symbiosis may be inherently instable and highly susceptible to environmental change. While questions remain regarding the underlying cellular controls of nutrient exchange and the nature of metabolites involved, the approach outlined in this study constitutes a powerful toolset to address these questions.

Rafeek, AD, Choi, G & Evans, LA 2018, 'Morphological, spectroscopic and crystallographic studies of calcium phosphate bioceramic powders', Journal of the Australian Ceramic Society, vol. 54, no. 1, pp. 161-168.
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Rahimi, E & Reimers, JR 2018, 'Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation', Physical Chemistry Chemical Physics, vol. 20, no. 26, pp. 17881-17888.
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A new way of using molecules to enact switches in quantum cellular automata (QCA) is proposed, utilizing monostable molecules that neither provide latching nor consume power; properties are compared to those for conventional bistable switches that both latch and consume power.

Rahman, MA, Scott, JA, Gentle, A, Phillips, MR & Ton-That, C 2018, 'A facile method for bright, colour-tunable light-emitting diodes based on Ga-doped ZnO nanorods', Nanotechnology, vol. 29, no. 42, pp. 425707-425707.
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© 2018 IOP Publishing Ltd. Bottom-up fabrication of nanowire-based devices is highly attractive for oxide photonic devices because of high light extraction efficiency; however, unsatisfactory electrical injection into ZnO and poor carrier transport properties of nanowires severely limit their practical applications. Here, we demonstrate that ZnO nanorods doped with Ga donors by in situ dopant incorporation during vapour-solid growth exhibit superior optoelectronic properties that exceed those currently synthesised by chemical vapour deposition, and accordingly can be electrically integrated into Si-based photonic devices. Significantly, the doping method was found to improve the nanorod quality by decreasing the concentration of point defects. Light-emitting diodes (LEDs) fabricated from the Ga-doped ZnO nanorod/p-Si heterojunction display bright and colour-tunable electroluminescence (EL). These nanorod LEDs possess a dramatically enhanced performance and an order of magnitude higher EL compared with equivalent devices fabricated with undoped nanorods. These results point to an effective route for large-scale fabrication of conductive, single-crystalline ZnO nanorods for photonic and optoelectronic applications.

Raina, J-B 2018, 'The Life Aquatic at the Microscale', mSystems, vol. 3, no. 2.
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There are more than one million microbial cells in every drop of seawater, and their collective metabolisms not only recycle nutrients that can then be used by larger organisms but also catalyze key chemical transformations that maintain Earth’s habitability. Understanding how these microbes interact with each other and with multicellular hosts is critical to reliably quantify any functional aspect of their metabolisms and to predicting their outcomes on larger scales.

Raina, J-B, Eme, L, Pollock, FJ, Spang, A, Archibald, JM & Williams, TA 2018, 'Symbiosis in the microbial world: from ecology to genome evolution', Biology Open, vol. 7, no. 2.
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ABSTRACT The concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.

Ranieri, MRM, Whitchurch, CB & Burrows, LL 2018, 'Mechanisms of biofilm stimulation by subinhibitory concentrations of antimicrobials', Current Opinion in Microbiology, vol. 45, pp. 164-169.
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© 2018 Elsevier Ltd Biofilms are a typical mode of growth for most microorganisms and provide them with a variety of survival benefits. Biofilms can pose medical and industrial challenges due to their increased tolerance of antimicrobials and disinfectants. Exposure of bacteria to subinhibitory concentrations of those compounds can further exacerbate the problem, as they provoke physiological changes that lead to increased biofilm production and potential therapeutic failure. The protected niche of a biofilm provides conditions that promote selection for persisters and resistant mutants. In this review we discuss our current understanding of the mechanisms underlying biofilm stimulation in response to subinhibitory antimicrobials, and how we might exploit this ‘anti-antibiotic’ phenotype to treat biofilm-related infections and discover new compounds.

Rath, EM, Cheng, YY, Pinese, M, Sarun, KH, Hudson, AL, Weir, C, Wang, YD, Håkansson, AP, Howell, VM, Liu, GJ, Reid, G, Knott, RB, Duff, AP & Church, WB 2018, 'BAMLET kills chemotherapy-resistant mesothelioma cells, holding oleic acid in an activated cytotoxic state', PLOS ONE, vol. 13, no. 8, pp. e0203003-e0203003.
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© 2018 Rath et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Malignant pleural mesothelioma is an aggressive cancer with poor prognosis. Here we have investigated in vitro efficacy of BAMLET and BLAGLET complexes (anti-cancer complexes consisting of oleic acid and bovine α-lactalbumin or β-lactoglobulin respectively) in killing mesothelioma cells, determined BAMLET and BLAGLET structures, and investigated possible biological mechanisms. We performed cell viability assays on 16 mesothelioma cell lines. BAMLET and BLAGLET having increasing oleic acid content inhibited human and rat mesothelioma cell line proliferation at decreasing doses. Most of the non-cancer primary human fibroblasts were more resistant to BAMLET than were human mesothelioma cells. BAMLET showed similar cytotoxicity to cisplatin-resistant, pemetrexed-resistant, vinorelbine-resistant, and parental rat mesothelioma cells, indicating the BAMLET anti-cancer mechanism may be different to drugs currently used to treat mesothelioma. Cisplatin, pemetrexed, gemcitabine, vinorelbine, and BAMLET, did not demonstrate a therapeutic window for mesothelioma compared with immortalised non-cancer mesothelial cells. We demonstrated by quantitative PCR that ATP synthase is downregulated in mesothelioma cells in response to regular dosing with BAMLET. We sought structural insight for BAMLET and BLAGLET activity by performing small angle X-ray scattering, circular dichroism, and scanning electron microscopy. Our results indicate the structural mechanism by which BAMLET and BLAGLET achieve increased cytotoxicity by holding increasing amounts of oleic acid in an active cytotoxic state encapsulated in increasingly unfolded protein. Our structural studies revealed similarity in the molecular structure of the protein com...

Raymond, BBA, Jenkins, C, Turnbull, L, Whitchurch, CB & Djordjevic, SP 2018, 'Extracellular DNA release from the genome-reduced pathogen Mycoplasma hyopneumoniae is essential for biofilm formation on abiotic surfaces', Scientific Reports, vol. 8, no. 1, pp. 10373-10373.
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AbstractMycoplasma hyopneumoniaeis an economically devastating, globally disseminated pathogen that can maintain a chronic infectious state within its host, swine. Here, we depict the events underpinningM.hyopneumoniaebiofilm formation on an abiotic surface and demonstrate for the first time, biofilms forming on porcine epithelial cell monolayers and in the lungs of pigs, experimentally infected withM.hyopneumoniae. Nuclease treatment prevents biofilms forming on glass but not on porcine epithelial cells indicating that extracellular DNA (eDNA), which localises at the base of biofilms, is critical in the formation of these structures on abiotic surfaces. Subpopulations ofM.hyopneumoniaecells, denoted by their ability to take up the dye TOTO-1 and release eDNA, were identified. A visually distinct sub-population of pleomorphic cells, that we refer to here as large cell variants (LCVs), rapidly transition from phase dark to translucent “ghost” cells. The translucent cells accumulate the membrane-impermeable dye TOTO-1, forming readily discernible membrane breaches immediately prior to lysis and the possible release of eDNA and other intracellular content (public goods) into the extracellular environment. Our novel observations expand knowledge of the lifestyles adopted by this wall-less, genome-reduced pathogen and provide further insights to its survival within farm environments and swine.

Raymond, BBA, Madhkoor, R, Schleicher, I, Uphoff, CC, Turnbull, L, Whitchurch, CB, Rohde, M, Padula, MP & Djordjevic, SP 2018, 'Extracellular Actin Is a Receptor for Mycoplasma hyopneumoniae', Frontiers in Cellular and Infection Microbiology, vol. 8, no. FEB.
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© 2018 Raymond, Madhkoor, Schleicher, Uphoff, Turnbull, Whitchurch, Rohde, Padula and Djordjevic. Mycoplasma hyopneumoniae, an agriculturally important porcine pathogen, disrupts the mucociliary escalator causing ciliostasis, loss of cilial function, and epithelial cell death within the porcine lung. Losses to swine production due to growth rate retardation and reduced feed conversion efficiency are severe, and antibiotics are used heavily to control mycoplasmal pneumonia. Notably, little is known about the repertoire of host receptors that M. hyopneumoniae targets to facilitate colonization. Here we show, for the first time, that actin exists extracellularly on porcine epithelial monolayers (PK-15) using surface biotinylation and 3D-Structured Illumination Microscopy (3D-SIM), and that M. hyopneumoniae binds to the extracellular β-actin exposed on the surface of these cells. Consistent with this hypothesis we show: (i) monoclonal antibodies that target β-actin significantly block the ability of M. hyopneumoniae to adhere and colonize PK-15 cells; (ii) microtiter plate binding assays show that M. hyopneumoniae cells bind to monomeric G-actin in a dose dependent manner; (iii) more than 100 M. hyopneumoniae proteins were recovered from affinity-chromatography experiments using immobilized actin as bait; and (iv) biotinylated monomeric actin binds directly to M. hyopneumoniae proteins in ligand blotting studies. Specifically, we show that the P97 cilium adhesin possesses at least two distinct actin-binding regions, and binds monomeric actin with nanomolar affinity. Taken together, these observations suggest that actin may be an important receptor for M. hyopneumoniae within the swine lung and will aid in the future development of intervention strategies against this devastating pathogen. Furthermore, our observations have wider implications for extracellular actin as an important bacterial receptor.

Raymond, BBA, Turnbull, L, Jenkins, C, Madhkoor, R, Schleicher, I, Uphoff, CC, Whitchurch, CB, Rohde, M & Djordjevic, SP 2018, 'Mycoplasma hyopneumoniae resides intracellularly within porcine epithelial cells', Scientific Reports, vol. 8, no. 1.
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AbstractEnzootic pneumonia incurs major economic losses to pork production globally. The primary pathogen and causative agent,Mycoplasma hyopneumoniae, colonises ciliated epithelium and disrupts mucociliary function predisposing the upper respiratory tract to secondary pathogens. Alleviation of disease is reliant on antibiotics, vaccination, and sound animal husbandry, but none are effective at eliminatingM. hyopneumoniaefrom large production systems. Sustainable pork production systems strive to lower reliance on antibiotics but lack of a detailed understanding of the pathobiology ofM. hyopneumoniaehas curtailed efforts to develop effective mitigation strategies.M. hyopneumoniaeis considered an extracellular pathogen. Here we show thatM. hyopneumoniaeassociates with integrin β1 on the surface of epithelial cells via interactions with surface-bound fibronectin and initiates signalling events that stimulate pathogen uptake into clathrin-coated vesicles (CCVs) and caveosomes. These early events allowM. hyopneumoniaeto exploit an intracellular lifestyle by commandeering the endosomal pathway. Specifically, we show: (i) using a modified gentamicin protection assay that approximately 8% ofM. hyopneumoniaecells reside intracellularly; (ii) integrin β1 expression specifically co-localises with the deposition of fibronectin precisely whereM. hyopneumoniaecells assemble extracellularly; (iii) anti-integrin β1 antibodies block entry ofM. hyopneumoniaeinto porcine cells; and (iv)M. hyopneumoniaesurvives phagolysosomal fusion, and resides within recycling endosomes that are trafficked to the cell membrane. Our data creates a paradigm shift by challenging the long-held...

Razavy, S, Gadau, M, Zhang, SP, Wang, FC, Bangrazi, S, Berle, C, Li, T, Li, WH & Zaslawski, C 2018, 'Anxiety related to De Qi psychophysical responses as measured by MASS: A sub-study embedded in a multisite randomised clinical trial', Complementary Therapies in Medicine, vol. 39, pp. 24-35.
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© 2018 Acupuncture has been broadly applied in the management of many diseases and conditions; however, its mechanism of action has been partially elucidated. Additionally, assessment of psychophysical responses in the acupuncture therapy is not common regarding anxiety disorder studies. Taken together, the therapeutic effect of acupuncture appears when De Qi psychophysical response is experienced following stimulation of the afferent sensory nerves. The present study investigates the level of anxiety perceived at different occasions in acupuncture and mock laser group. Furthermore, it examines the relationship between perceived De Qi psychophysical response and the level of anxiety experienced during administration of each intervention. The study was embedded in a two-arm parallel design multi-center, randomized clinical trial, the Tennis Elbow Acupuncture-International Study-China, Hong Kong, Australia, Italy. Participants’ level of anxiety was measured using a validated instrument, the Massachusetts General Hospital Acupuncture Sensation Mood Scale. Ninety-six participants with Lateral Elbow Pain were randomly allocated into two groups; the acupuncture treatment group (n = 47) and the inactive mock laser control group (n = 49). Data were collected immediately following the interventions at the first and the ninth session within the clinical trial. Acupuncture with De Qi did not induce higher level of anxiety compared to prior administration of acupuncture. In fact, participants were more relaxed after receiving acupuncture than those who received mock laser. There was also a weak association between participants’ perception of anxiety during acupuncture and the MASS De Qi Index in session nine only (p < 0.01). Further investigation of the result revealed weak positive correlation between anxiety perceived during administration of acupuncture and the following De Qi characteristics; ‘soreness’ (p < 0.01), ‘Deep pressure’ (p < 0.05), ‘Heaviness’ (p < 0...

Rehn, S, Eslick, GD & Brakoulias, V 2018, 'A Meta-Analysis of the Effectiveness of Different Cortical Targets Used in Repetitive Transcranial Magnetic Stimulation (rTMS) for the Treatment of Obsessive-Compulsive Disorder (OCD)', Psychiatric Quarterly, vol. 89, no. 3, pp. 645-665.
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Randomised and sham-controlled trials (RCTs) of repetitive transcranial magnetic stimulation (rTMS) in the treatment of obsessive-compulsive disorder (OCD) have yielded conflicting results, which may be due to the variability in rTMS parameters used. We performed an updated systematic review and meta-analysis on the effectiveness of rTMS for the treatment of OCD and aimed to determine whether certain rTMS parameters, such as cortical target, may be associated with higher treatment effectiveness. After conducting a systematic literature review for RCTs on rTMS for OCD through to 1 December 2016 using MEDLINE, PubMed, Web of Science, PsycINFO, Google, and Google Scholar, we performed a random-effects meta-analysis with the outcome measure as pre-post changes in Yale-Brown Obsessive Compulsive Scale (Y-BOCS) scores. To determine whether rTMS parameters may have influenced treatment effectiveness, studies were further analysed according to cortical target, stimulation frequency, and length of follow-up. Data were obtained from 18 RCTs on rTMS in the treatment of OCD. Overall, rTMS yielded a modest effect in reducing Y-BOCS scores with Hedge's g of 0.79 (95% CI = 0.43-1.15, p < 0.001). Stimulation of the supplementary motor area yielded the greatest reductions in Y-BOCS scores relative to other cortical targets. Subgroup analyses suggested that low frequency rTMS was more effective than high frequency rTMS. The effectiveness of rTMS was also greater at 12 weeks follow-up than at four weeks follow-up. Our meta-analysis implies that low frequency rTMS applied over the supplementary motor area may offer the greatest effectiveness in the treatment of OCD. The therapeutic effects of rTMS also appear to persist post-treatment and may offer beneficial long-term effectiveness. With our findings, it is suggested that future large-scale studies focus on the supplementary motor area and include follow-up periods of 12 weeks or more.

Rehn, S, Onuma, T, Rooney, KB & Boakes, RA 2018, 'Sodium saccharin can be more acceptable to rats than pure saccharin', Behavioural Processes, vol. 157, pp. 188-191.
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The artificial sweetener saccharin is available in several forms, including pure saccharin (S) and saccharin sodium salt hydrate (SSSH). Acceptance and preference relative to 2% sucrose for these two forms was assessed using both older female and young male rats. At the higher of two concentrations, ∼0.4%, SSSH was more acceptable and more greatly preferred over 2% sucrose than was a similar concentration of S, whereas little difference between the two forms was detected at the lower concentration, ∼0.1%. These results indicate the importance for researchers of care in choosing and reporting the form of saccharin they use.

Reid, AT, Veerati, PC, Gosens, R, Bartlett, NW, Wark, PA, Grainge, CL, Stick, SM, Kicic, A, Moheimani, F, Hansbro, PM & Knight, DA 2018, 'Persistent induction of goblet cell differentiation in the airways: Therapeutic approaches', Pharmacology & Therapeutics, vol. 185, pp. 155-169.
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© 2017 Dysregulated induction of goblet cell differentiation results in excessive production and retention of mucus and is a common feature of several chronic airways diseases. To date, therapeutic strategies to reduce mucus accumulation have focused primarily on altering the properties of the mucus itself, or have aimed to limit the production of mucus-stimulating cytokines. Here we review the current knowledge of key molecular pathways that are dysregulated during persistent goblet cell differentiation and highlights both pre-existing and novel therapeutic strategies to combat this pathology.

Reimers, JR 2018, 'How Equilibrium Gets Mimicked During Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers', Langmuir, vol. 34, no. 1, pp. 18-22.
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© 2017 American Chemical Society. The recent review of Hipps and Mazur is extended to consider the origins and significance of their conclusion that 'surface structures vary with relative component concentration in a way that may mimic equilibria but is not'. How this situation can arise during self-assembly is discussed, as well as a range of qualitative and quantitative observations and high-level free-energy calculations that document the effect for meso-tetraalkylporphyrins self-assembled monolayer (SAM) polymorphs. This leads to a discussion of modern challenges facing quantification of the effects caused by kinetic control, as well as to the usefulness of equilibrium mimicking in the design and synthesis of SAMs.

Reimers, JR, Sajid, A, Kobayashi, R & Ford, MJ 2018, 'Understanding and calibrating Density-Functional-Theory calculations describing the energy and spectroscopy of defect sites in hexagonal boron nitride', J. Chem. Theory Comput.2018, vol. 14, no. 3, pp. 1602-1613.
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Defect states in 2D materials present many possible uses but bothexperimental and computational characterization of their spectroscopicproperties is difficult. We provide and compare results from 13 DFT and abinitio computational methods for up to 25 excited states of a paradigm system,the VNCB defect in hexagonal boron nitride (h-BN). Studied include include: (i)potentially catastrophic effects for computational methods arising from themulti-reference nature of the closed-shell and open-shell states of the defect,which intrinsically involves broken chemical bonds, (ii) differing results fromDFT and time-dependent DFT (TDDFT) calculations, (iii) comparison of clustermodels to periodic-slab models of the defect, (iv) the starkly differingeffects of nuclear relaxation on the various electronic states as broken bondstry to heal that control the widths of photoabsorption and photoemissionspectra, (v) the effect of zero-point energy and entropy on free-energydifferences, (vi) defect-localized and conduction/valence band transitionnatures, and (vii) strategies needed to ensure that the lowest-energy state ofa defect can be computationally identified.

Reimers, JR, Tawfik, SA & Ford, MJ 2018, 'Van der Waals forces control ferroelectric-antiferroelectric ordering in ABP2X6 laminar materials', Chemical Science, vol. 9, no. 39, pp. 7620-7627.
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We show how van der Waals (vdW) forces outcompete covalent and ionic forcesto control ferroelectric ordering in CuInP2S6 nanoflakes as well as in CuInP2S6and CuBiP2Se6 crystals. While the self-assembly of these 2D layered materialsis clearly controlled by vdW effects, this result indicates that the internallayer structure is also similarly controlled. Using up to 14 first-principlescomputational methods, we predict that the bilayers of both materials should beantiferroelectric. However, antiferroelectric nanoflakes and bulk materials areshown to embody two fundamentally different types of inter-layer interactions,with vdW forces strongly favouring one and strongly disfavouring the othercompared to ferroelectric ordering. Strong specific vdW interactions involvingthe Cu atoms control this effect. Thickness-dependent significant cancellationof these two large opposing vdW contributions results in a small net effectthat interacts with weak ionic contributions to control ferroelectric ordering.

Ren, B, La, QT, O'Brien, BA, Nassif, NT, Tan, Y, Gerace, D, Martiniello‐Wilks, R, Torpy, F, Dane, AP, Alexander, IE & Simpson, AM 2018, 'Partial pancreatic transdifferentiation of primary human hepatocytes in the livers of a humanised mouse model', The Journal of Gene Medicine, vol. 20, no. 5, pp. e3017-e3017.
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AbstractBackgroundGene therapy is one treatment that may ultimately cure type 1 diabetes. We have previously shown that the introduction of furin‐cleavable human insulin (INS‐FUR) to the livers in several animal models of diabetes resulted in the reversal of diabetes and partial pancreatic transdifferentiation of liver cells. The present study investigated whether streptozotocin‐diabetes could be reversed in FRG mice in which chimeric mouse‐human livers can readily be established and, in addition, whether pancreatic transdifferentiation occurred in the engrafted human hepatocytes.MethodsEngraftment of human hepatocytes was confirmed by measuring human albumin levels. Following delivery of the empty vector or the INS‐FUR vector to diabetic FRG mice, mice were monitored for weight and blood glucose levels. Intraperitoneal glucose tolerance tests (IPGTTs) were performed. Expression levels of pancreatic hormones and transcription factors were determined by a reverse transcriptase‐polymerase chain reaction (RT‐PCR) and immunohistochemistry.ResultsDiabetes was reversed for a period of 60 days (experimental endpoint) after transduction with INS‐FUR. IPGTTs of the insulin‐transduced animals were not significantly different from nondiabetic animals. Immunofluorescence microscopy revealed the expression of human albumin and insulin in transduced liver samples. Quantitative RT‐PCR showed expression of human and mouse endocrine hormones and β‐cell transcription factors, indicating partial pancreatic transdifferentiation of mouse and human hepatocytes. Nonfasting human C‐peptide levels were significantly higher than mouse levels, suggesting that transdifferentiated human hepatocytes made a significant contribution to the reversal of diabetes.

Ren, W, Wen, S, Tawfik, SA, Su, QP, Lin, G, Ju, LA, Ford, MJ, Ghodke, H, van Oijen, AM & Jin, D 2018, 'Anisotropic functionalization of upconversion nanoparticles', Chemical Science, vol. 9, no. 18, pp. 4352-4358.
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Ligand competition directs heterogeneous bio-chemistry surface and self-assembly for upconversion nanoparticles.

Ren, W, Zhou, Y, Wen, S, He, H, Lin, G, Liu, D & Jin, D 2018, 'DNA-mediated anisotropic silica coating of upconversion nanoparticles', Chemical Communications, vol. 54, no. 52, pp. 7183-7186.
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We report a facile approach of using DNA molecules as switches to selectively activate silica coating onto specific facets of upconversion nanoparticles.

Renchon, AA, Griebel, A, Metzen, D, Williams, CA, Medlyn, B, Duursma, RA, Barton, CVM, Maier, C, Boer, MM, Isaac, P, Tissue, D, Resco de Dios, V & Pendall, E 2018, 'Upside-down fluxes Down Under: CO₂ net sink in winter and net source in summer in a temperate evergreen broadleaf forest', Biogeosciences, vol. 15, no. 12, pp. 3703-3716.
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Abstract. Predicting the seasonal dynamics of ecosystem carbon fluxes is challenging inbroadleaved evergreen forests because of their moderate climates and subtlechanges in canopy phenology. We assessed the climatic and biotic drivers ofthe seasonality of net ecosystem–atmosphere CO2 exchange (NEE) ofa eucalyptus-dominated forest near Sydney, Australia, using the eddycovariance method. The climate is characterised by a mean annualprecipitation of 800 mm and a mean annual temperature of 18 ∘C, hotsummers and mild winters, with highly variable precipitation. In the 4-yearstudy, the ecosystem was a sink each year (−225 g C m−2 yr−1on average, with a standard deviation of 108 g C m−2 yr−1);inter-annual variations were not related to meteorological conditions. Dailynet C uptake was always detected during the cooler, drier winter months (Junethrough August), while net C loss occurred during the warmer, wetter summermonths (December through February). Gross primary productivity (GPP)seasonality was low, despite longer days with higher light intensity insummer, because vapour pressure deficit (D) and air temperature(Ta) restricted surface conductance during summer while wintertemperatures were still high enough to support photosynthesis. Maximum GPPduring ideal environmental conditions was significantly correlated withremotely sensed enhanced vegetation index (EVI; r2 = 0.46) and withcanopy leaf area index (LAI; r2 = 0.29), which increased rapidlyafter mid-summer rainfall events. Ecosystem respiration (ER) was highestduring summer in wet soils and lowest during winter months. ER had largerseasonal amplitude compared to GPP, and therefore drove the seasonalvariation of NEE. Because summer carbon uptake may become increasinglylimited by atmospheric demand and high temperature, and because ecosystemrespiration could be enhanced by rising temperatures, our results suggest the potential for large-scale seasonalshifts in NEE in scle...

Reyna Zeballos, JL & Meier, P 2018, 'A Practical Model for Implementing Digital Media Assessments in Tertiary Science Education', American Journal of Educational Research, vol. 6, no. 1, pp. 27-31.
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Learner-Generated Digital Media (LGDM) has been incorporated as a learning tool to assess students in Higher Education over the last decade. There are models developed for video making in the classroom that considers technical know-how, pedagogies or a combination of both. However, there is the absence of a student-centred, practical framework to inform academics and students on the implementation of digital presentations as an assessment tool in the curricula. This conceptual paper proposes a new framework to assist with the design, implementation and evaluation of LGDM as assessment tools. The framework considers the following elements: (1) pedagogy; (2) student training; (3) hosting of videos; (4) marking schemes; (5) group contribution; (6) feedback; (7) reflection, and; (8) evaluation. The purpose of this paper is to outline the basic elements of the framework and provide practical implementation strategies that academics from any discipline could apply to their classrooms.

Reyna, J & Meier, P 2018, 'Learner-Generated Digital Media (LGDM) as an Assessment Tool in Tertiary Science Education: A Review of Literature', IAFOR Journal of Education, vol. 6, no. 3, pp. 93-109.
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© 2018, The International Academic Forum (IAFOR). All rights reserved. Learner-Generated Digital Media (LGDM) in tertiary science education focuses on research skills, inquiry, active learning, teamwork, and collaboration. LGDM across disciplines is under-theorised, under-researched, and only in its early development. This paper evaluates the research in the field of LGDM in tertiary science education. The literature review had four stages – identification, screening, filtering, and selection of relevant scholarly research. Results showed that research in the field of LGDM assignments had been done without a systematic approach to designing, implementing, and evaluating the assessment task. Most studies neglected student digital media training and are characterised by a lack of compelling marking rubrics or strategies to ensure efficient groupwork. Studies also lack rigorous methodologies for data capture to evaluate the intervention and they use small sample size cohorts and different digital media types that require different sets of production skills. With the empirical data available, validation of the benefits of LGDM assignments in science education is not possible, and studies have limited scalability. These gaps in the literature create a need to develop theoretical models for the design, implementation, and evaluation of LGDM in the classroom. This paper discusses future research needs in this field and the implications for assessment design.

Reyna, J & Meier, P 2018, 'Using the Learner-Generated Digital Media (LGDM) Framework in Tertiary Science Education: A Pilot Study', Education Sciences, vol. 8, no. 3, pp. 106-106.
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Learner-Generated Digital Media (LGDM) has become prevalent in higher education. Frameworks have been developed for video-making in the classroom that consider technical requirements, pedagogies, and the combination of both. However, missing is a practical model to guide academics and students on the implementation of LGDM assignments. This research aims to test a model to design, implement, and evaluate LGDM as an assessment tool. The model was built based on research gaps and it considers the following elements: (1) pedagogy, (2) student training, (3) hosting of videos, (4) marking schemes, (5) group contribution, (6) feedback, (7) reflection, and (8) evaluation. For this purpose, five science subjects (N = 270) were used to test the model as a guide to implementing LGDM assignments. Data was gathered using a validated 33-step questionnaire instrument. Additionally, group contributions were received using the SPARKPlus peer review application, and marks attained were gathered. Methodological triangulation of the datasets suggested that students have a positive attitude toward LGDM for science learning. Students enjoyed the group work and creativity, and they identified digital media support as a critical component of their learning experience. Preliminary data support using the LGDM framework to design digital media assignments for science education.

Reyna, J, Hanham, J & Meier, P 2018, 'The Internet explosion, digital media principles and implications to communicate effectively in the digital space', E-Learning and Digital Media, vol. 15, no. 1, pp. 36-52.
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Being literate has traditionally meant being able to read and write using the media of the day. In the 21st century, being literate requires additional skills such as competence with digital media creation. Until recently, those who could afford and use equipment and applications to produce digital media content were typically developers and technicians. With the development of prosumer electronics, in conjunction with the use of mobile devices and tablets, a shift has occurred in the accessibility of these tools, becoming more affordable for the general population. Video sharing services, social software and Web 2.0 applications have made it possible to host a digital media ecosystem on the Internet, and this has led to the proliferation of User-Generated Content. These technological advances have changed how we communicate, socialise and learn. Effective communication using digital media is underpinned by a set of design principles which most students are not likely to be aware. This paper built on two previous papers on the Digital Media Literacy Framework and the Taxonomy of Digital Media types for teaching and learning. It argues the importance of digital media principles to develop effective communication in the digital space. Students now require knowledge of these principles, in conjunction with conceptual and functional skills, for effective communication in the digital space.

Reyna, J, Hanham, J & Meier, PC 2018, 'A framework for digital media literacies for teaching and learning in higher education', E-Learning and Digital Media, vol. 15, no. 4, pp. 176-190.
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Across a broad range of subjects in higher education institutions, students are required to complete assessment tasks that involve the production of digital artefacts. Examples include podcasts, digital stories, animations, video and blended media. To produce effective digital artefacts, one must be digitally literate. This requires a certain set of technical, audio-visual, behavioural, critical and social skills. In this article, the authors propose a framework that can be used to develop digital media literacies and train students in digital media creation. The framework considers three interdependent domains: conceptual, functional and audio-visual. A series of examples will be provided to illustrate the importance and interdependent nature of these domains. Implications of the framework on student training are discussed.

Richier, S, Achterberg, EP, Humphreys, MP, Poulton, AJ, Suggett, DJ, Tyrrell, T & Moore, CM 2018, 'Geographical CO₂ sensitivity of phytoplankton correlates with ocean buffer capacity', Global Change Biology, vol. 24, no. 9, pp. 4438-4452.
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AbstractAccumulation of anthropogenic CO2 is significantly altering ocean chemistry. A range of biological impacts resulting from this oceanic CO2 accumulation are emerging, however, the mechanisms responsible for observed differential susceptibility between organisms and across environmental settings remain obscure. A primary consequence of increased oceanic CO2 uptake is a decrease in the carbonate system buffer capacity, which characterizes the system's chemical resilience to changes in CO2, generating the potential for enhanced variability in pCO2 and the concentration of carbonate [], bicarbonate [], and protons [H+] in the future ocean. We conducted a meta‐analysis of 17 shipboard manipulation experiments performed across three distinct geographical regions that encompassed a wide range of environmental conditions from European temperate seas to Arctic and Southern oceans. These data demonstrated a correlation between the magnitude of natural phytoplankton community biological responses to short‐term CO2 changes and variability in the local buffer capacity across ocean basin scales. Specific...

Richman, MB & Leslie, LM 2018, 'The 2015-2017 Cape Town Drought: Attribution and Prediction Using Machine Learning', Procedia Computer Science, vol. 140, pp. 248-257.
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Cape Town was declared a disaster area after the worst drought in almost a century, following its driest three consecutive wet seasons (April 1-October 31), in 2015 -2017. Cape Town’s drought was extreme, with “zero day” water storage months away, causing severe water rationing to Cape Town’s ~3.8 million population. The crisis extended into surrounding farmlands, as agriculture is vital for the region’s economy. Possible drought causes are numerous and, aside from the decreasing wet season precipitation, the effects are exacerbated by the increasing population with associated water demand, greater agricultural acreage and land surface changes. As rainfall decreases, water management becomes critical, requiring predictions for future rainfall. Possible climate drivers associated with available Cape Town precipitation and temperature include: The Southern Annular Mode, Atlantic Meridional Mode, Indian Ocean Dipole, an Integrated Southern Hemisphere temperature index and several El Niño indices. Several variable selection techniques suggest signals in both the Atlantic and Indian Oceans contribute to Cape Town droughts. Machine learning techniques are applied to these drivers for the first time and provide encouraging predictive skill levels. Results suggest that machine learning holds promise for adapting to drought by managing water resources in Cape Town and, more generally for global locations depending solely on rainfall under a warming climate.

Ritchie, RJ, Larkum, AWD & Ribas, I 2018, 'Could photosynthesis function on Proxima Centauri b?', International Journal of Astrobiology, vol. 17, no. 2, pp. 147-176.
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AbstractCould oxygenic and/or anoxygenic photosynthesis exist on planet Proxima Centauri b? Proxima Centauri (spectral type – M5.5 V, 3050 K) is a red dwarf, whereas the Sun is type G2 V (5780 K). The light regimes on Earth and Proxima Centauri b are compared with estimates of the planet's suitability for Chlorophylla(Chla) and Chld-based oxygenic photosynthesis and for bacteriochlorophyll (BChl)-based anoxygenic photosynthesis. Proxima Centauri b has low irradiance in the oxygenic photosynthesis range (400–749 nm: 64–132 µmol quanta m−2s−1). Much larger amounts of light would be available for BChl-based anoxygenic photosynthesis (350–1100 nm: 724–1538 µmol quanta m−2s−1). We estimated primary production under these light regimes. We used the oxygenic algaeSynechocystisPCC6803,Prochlorothrix hollandica,Acaryochloris marina,Chlorella vulgaris,Rhodomonassp. andPhaeodactylum tricornutumand the anoxygenic photosynthetic bacteriaRhodopseudomonas palustris(BChla),Afifella marina(BChla),Thermochromatium tepidum(BChla),Chlorobaculum tepidum(BChla + c) andBlastochloris viridis(BChlb) as representative photosynthetic organisms. Proxima Centauri b has only ≈3% of the PAR (400–700 nm) of Earth irradiance, but we found that potential gross photosynthesis (Pg) on Proxima Centauri b could be surprisingl...

Rodgers, KJ, Main, BJ & Samardzic, K 2018, 'Cyanobacterial Neurotoxins: Their Occurrence and Mechanisms of Toxicity', Neurotoxicity Research, vol. 33, no. 1, pp. 168-177.
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Cyanobacteria are some of the oldest organisms on earth, and have evolved to produce a battery of toxic metabolites, including hepatotoxins, dermatoxins, and neurotoxins. In this review, we focus on the occurrence and mechanisms of toxicity of a number of neurotoxins synthesised by these ancient photosynthetic prokaryotes. We discuss the evidence linking β-methylamino-L-alanine (BMAA), a non-protein amino acid, to an unusual neurological disease complex reported on the island of Guam in the 1950s, and how 60 years later, the role that BMAA plays in human disease is still unclear. There is now evidence that BMAA is also produced by some eukaryotes, and can bioaccumulate in food chains; this combined with higher frequency of cyanobacterial blooms globally, increases the potential for human exposure. Three BMAA isomers that often co-occur with BMAA have been identified, and the current knowledge on the toxicity of these molecules is presented. The acute alkaloid toxins; anatoxin-a, homoanatoxin-a and the saxitoxins, and the organophosphate neurotoxin anatoxin-a(S) are also discussed. In many cases, human exposure to a cocktail of cyanobacterial neurotoxins is likely; however, the implications of combined exposure to these toxins have not been fully explored. Increased understanding of the combined effects of cyanobacterial neurotoxins is required to fully understand how these molecules impact on human health.

Roediger, B, Lee, Q, Tikoo, S, Cobbin, JCA, Henderson, JM, Jormakka, M, O’Rourke, MB, Padula, MP, Pinello, N, Henry, M, Wynne, M, Santagostino, SF, Brayton, CF, Rasmussen, L, Lisowski, L, Tay, SS, Harris, DC, Bertram, JF, Dowling, JP, Bertolino, P, Lai, JH, Wu, W, Bachovchin, WW, Wong, JJ-L, Gorrell, MD, Shaban, B, Holmes, EC, Jolly, CJ, Monette, S & Weninger, W 2018, 'An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis', Cell, vol. 175, no. 2, pp. 530-543.e24.
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© 2018 Elsevier Inc. The occurrence of a spontaneous nephropathy with intranuclear inclusions in laboratory mice has puzzled pathologists for over 4 decades, because its etiology remains elusive. The condition is more severe in immunodeficient animals, suggesting an infectious cause. Using metagenomics, we identify the causative agent as an atypical virus, termed “mouse kidney parvovirus” (MKPV), belonging to a divergent genus of Parvoviridae. MKPV was identified in animal facilities in Australia and North America, is transmitted via a fecal-oral or urinary-oral route, and is controlled by the adaptive immune system. Detailed analysis of the clinical course and histopathological features demonstrated a stepwise progression of pathology ranging from sporadic tubular inclusions to tubular degeneration and interstitial fibrosis and culminating in renal failure. In summary, we identify a widely distributed pathogen in laboratory mice and establish MKPV-induced nephropathy as a new tool for elucidating mechanisms of tubulointerstitial fibrosis that shares molecular features with chronic kidney disease in humans. A kidney parvovirus found in multiple laboratory mouse colonies causes spontaneous nephropathy and represents a new tool for studying chronic kidney disease.

Rohlfs, A-M, Williams, S, Rees, GN, Lim, RP, Werry, L & Mitrovic, SM 2018, 'Experimental dam releases stimulate respiration in an epilithic biofilm community', Hydrobiologia, vol. 820, no. 1, pp. 175-187.
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© 2018, Springer International Publishing AG, part of Springer Nature. This study explored biofilm metabolism as a functional indicator of ecological responses to dissolved organic carbon and inorganic nutrients from managed dam releases. We hypothesised that the dam releases would stimulate epilithic biofilm community respiration (CR), and trigger a larger increase in biofilm CR relative to gross primary production (GPP). We predicted that biofilm respiration would be related to water column dissolved carbon and nutrient concentrations. Tiles colonised with epilithic biofilm were exposed to dam release waters in a stream-side mesocosm system that separated out the physical effects of flow velocity. Biofilm CR increased during two of three releases, and increases in CR were larger relative to GPP during all three releases. Biofilm CR was not linearly related to dissolved resources or abiotic environmental variables. These results show that managed dam releases can influence biofilm metabolism via a mechanism independent from the direct physical effects of increased flow velocity. This study provides new insights into the complex pathways through which managed dam releases may influence ecological processes. The stimulation of benthic CR through physical and chemical variations in dam water is a potential mechanism through which dam releases may influence biogeochemical processing and energy flow through the riverine food web.

Roux, C, Ribaux, O & CRISPINO, F 2018, 'Forensic science 2020 – the end of the crossroads?', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-12.
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© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group. Forensic science has been at the crossroads for over a decade. While this situation is a fertile ground for discussion, security problem solving and the sound administration of justice cannot be put on hold until solutions pleasing everyone emerge. In all practical reality, forensic science will continue to be applied because it is simply the most reliable way to reconstruct the past through the exploitation of relics of criminal activities and by logical treatment of the collected information. In this paper, it is argued that instead of exclusively focusing on error management and processes, we should also question the very ontological nature of forensic science. Not only should the dominant conception of forensic sciences as a patchwork of disciplines assisting the criminal justice system be challenged, but forensic science’s own fundamental principles should also be better enunciated and promoted so they can be more broadly accepted and understood. Such changes invite operations, education and research to become more collective and interdisciplinary. This is necessary to fully exploit the investigative, epidemiological, court and social functions of forensic science. We ought to ask the question: will forensic science reach the end of the crossroads soon?.

Rumman, R, Atkin, OK, Bloomfield, KJ & Eamus, D 2018, 'Variation in bulk‐leaf ¹³C discrimination, leaf traits and water‐use efficiency–trait relationships along a continental‐scale climate gradient in Australia', Global Change Biology, vol. 24, no. 3, pp. 1186-1200.
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AbstractLarge spatial and temporal gradients in rainfall and temperature occur across Australia. This heterogeneity drives ecological differentiation in vegetation structure and ecophysiology. We examined multiple leaf‐scale traits, including foliar 13C isotope discrimination (Δ13C), rates of photosynthesis and foliar N concentration and their relationships with multiple climate variables. Fifty‐five species across 27 families were examined across eight sites spanning contrasting biomes. Key questions addressed include: (i) Does Δ13C and intrinsic water‐use efficiency (WUEi) vary with climate at a continental scale? (ii) What are the seasonal and spatial patterns in Δ13C/WUEi across biomes and species? (iii) To what extent does Δ13C reflect variation in leaf structural, functional and nutrient traits across climate gradients? and (iv) Does the relative importance of assimilation and stomatal conductance in driving variation in Δ13C differ across seasons? We found that MAP, temperature seasonality, isothermality and annual temperature range exerted independent effects on foliar Δ13C/WUEi. Temperature‐related variables exerted larger effects than rainfall‐related variables. The relative importance of photosynthesis and stomatal conductance (gs) in determining Δ13C differed across seasons: Δ13C was more strongly regulated by gs during the dry‐season and by photosynthetic capacity during the wet‐season. Δ13C was most strongly correlated, inversely, with leaf mass area ratio among all leaf attributes considered. Leaf Nmass was significantly and positively correlated with MAP during dry‐ and wet‐s...

Rumman, R, Cleverly, J, Nolan, RH, Tarin, T & Eamus, D 2018, 'Speculations on the application of foliar ¹³C discrimination to reveal groundwater dependency of vegetation and provide estimates of root depth and rates of groundwater use', Hydrology and Earth System Sciences, vol. 22, no. 9, pp. 4875-4889.
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Abstract. Groundwater-dependent vegetation is globally distributed, having importantecological, social, and economic value.Along with the groundwater resources upon which it depends, this vegetationis under increasing threat through excessive rates of groundwater extraction. In this study we examined one shallow-rooted and two deep-rooted tree speciesat multiple sites along a naturally occurring gradient indepth-to-groundwater. We measured (i) stable isotope ratios of leaves(δ13C), xylem, and groundwater (δ2H andδ18O); and (ii) leaf-vein density. We established that foliardiscrimination of 13C (Δ13C) is a reliable indicatorof groundwater use by vegetation and can also be used to estimate rootingdepth. Through comparison with a continental-scale assessment of foliarΔ13C, we also estimated the upper limits to annual rates ofgroundwater use. We conclude that maximum rooting depth for both deep-rootedspecies ranged between 9.4 and 11.2 m and that annual rates of groundwateruse ranged from ca. 1400 to 1700 mm for Eucalyptus camaldulensisand from 600 to 900 mm for Corymbia opaca. Several predictionsabout hydraulic and leaf traits arising from the conclusion that these twospecies made extensive use of groundwater were supported by additionalindependent studies of these species in central Australia.

Russo, AG, Eden, J-S, Enosi Tuipulotu, D, Shi, M, Selechnik, D, Shine, R, Rollins, LA, Holmes, EC & White, PA 2018, 'Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches', Journal of Virology, vol. 92, no. 17.
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Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.

Rust, L, Nizio, KD, Wand, MP & Forbes, SL 2018, 'Investigating the detection limits of scent-detection dogs to residual blood odour on clothing', Forensic Chemistry, vol. 9, pp. 62-75.
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© 2018 Elsevier B.V. Blood-detection dogs are trained to locate blood evidence and search for potential crime scenes in cases where a cadaver may not be present. The locations of crime scenes are often ambiguous and evidence may not always be obvious during initial processing. In cases of foul play, a criminal may attempt to clean biological evidence from a crime scene; however, trace evidence that appears invisible to the naked eye may still be detectable. For example, it has been reported anecdotally that blood-detection dogs are capable of detecting blood on clothing that has been washed up to five times, or on surfaces which have been scrubbed clean. This study aimed to investigate the baseline detection limits of blood-detection dogs and cadaver-detection dogs to latent blood evidence on washed clothing and to compare the dogs’ responses to current presumptive chemical and analytical techniques. Blood was deposited onto cotton swatches and washed up to five times with a standard household washing machine. Following washing, the cotton swatches were allowed to dry and presented to blood-detection and cadaver-detection dogs during law enforcement training. Replicates of these samples were tested with luminol spray and analysed using headspace solid phase microextraction – comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). Results indicated that the olfactory system of blood-detection and cadaver-detection dogs is a viable complementary technique to presumptive chemical tests and more sensitive than current scientific instrumentation, with some of the dogs able to detect blood after five washes but HS-SPME-GC×GC-TOFMS only able to detect blood after two washes or less. This limit of detection could likely be lowered for the dogs with further and more consistent training. Luminol was similarly able to detect blood washed up to five times, which indicates that the scenting abilities of these dogs can provide...

Rutting, S, Papanicolaou, M, Xenaki, D, Wood, LG, Mullin, AM, Hansbro, PM & Oliver, BG 2018, 'Dietary ω-6 polyunsaturated fatty acid arachidonic acid increases inflammation, but inhibits ECM protein expression in COPD', Respiratory Research, vol. 19, no. 1, pp. 211-211.
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© 2018 The Author(s). Background: The obesity paradox in COPD describes protective effects of obesity on lung pathology and inflammation. However, the underlying relationships between obesity, diet and disease outcomes in COPD are not fully understood. In this study we measured the response to dietary fatty acids upon markers of inflammation and remodelling in human lung cells from people with and without COPD. Methods: Pulmonary fibroblasts were challenged with ω-3 polyunsaturated fatty acids (PUFAs), ω-6 PUFAs, saturated fatty acids (SFAs) or the obesity-associated cytokine TNFα. After 48-72 h release of the pro-inflammatory cytokines interleukin (IL)-6 and CXCL8 was measured using ELISA and mRNA expression and deposition of the extracellular matrix (ECM) proteins fibronectin, type I collagen, tenascin and perlecan were measured using qPCR or ECM ELISA, respectively. Results: Challenge with the ω-6 PUFA arachidonic acid (AA), but not ω-3 PUFAs or SFAs, resulted in increased IL-6 and CXCL8 release from fibroblasts, however IL-6 and CXCL8 release was reduced in COPD (n = 19) compared to non-COPD (n = 36). AA-induced cytokine release was partially mediated by downstream mediators of cyclooxygenase (COX)-2 in both COPD and non-COPD. In comparison, TNFα-induced IL-6 and CXCL8 release was similar in COPD and non-COPD, indicating a specific interaction of AA in COPD. In patients with or without COPD, regression analysis revealed no relationship between BMI and cytokine release. In addition, AA, but not SFAs or ω-3 PUFAs reduced the basal deposition of fibronectin, type I collagen, tenascin and perlecan into the ECM in COPD fibroblasts. In non-COPD fibroblasts, AA-challenge decreased basal deposition of type I collagen and perlecan, but not fibronectin and tenascin. Conclusions: This study shows that AA has disease-specific effects on inflammation and ECM protein deposition. The impaired response to AA in COPD might in part explain why obesity appears to have...

Rutting, S, Xenaki, D, Lau, E, Horvat, J, Wood, LG, Hansbro, PM & Oliver, BG 2018, 'Dietary omega-6, but not omega-3, polyunsaturated or saturated fatty acids increase inflammation in primary lung mesenchymal cells', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 314, no. 6, pp. L922-L935.
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Obesity is an important risk factor for developing severe asthma. Dietary fatty acids, which are increased in sera of obese individuals and after high-fat meals, activate the innate immune system and induce inflammation. This study investigated whether dietary fatty acids directly cause inflammation and/or synergize with obesity-induced cytokines in primary human pulmonary fibroblasts in vitro. Fibroblasts were challenged with BSA-conjugated fatty acids [ω-6 polyunsaturated fatty acids (PUFAs) and ω-3 PUFAs or saturated fatty acids (SFAs)], with or without TNF-α, and release of the proinflammatory cytokines, IL-6 and CXCL8, was measured. We found that the ω-6 PUFA arachidonic acid (AA), but not ω-3 PUFAs or SFAs, upregulates IL-6 and CXCL8 release. Combined AA and TNF-α challenge resulted in substantially greater cytokine release than either alone, demonstrating synergy. Synergistic upregulation of IL-6, but not CXCL8, was mainly mediated via cyclooxygenase (COX). Inhibition of p38 MAPK reduced CXCL8 release, induced by AA and TNF-α alone, but not in combination. Synergistic CXCL8 release, following AA and TNF-α challenge, was not medicated via a single signaling pathway (MEK1, JNK, phosphoinositide 3-kinase, and NF-κB) nor by hyperactivation of NF-κB or p38. To investigate if these findings occur in other airway cells, effects of AA in primary human airway smooth muscle (ASM) cells and human bronchial epithelial cells were also investigated. We found proinflammatory effects in ASM cells but not epithelial cells. This study suggests that diets rich in ω-6 PUFAs might promote airway inflammation via multiple pathways, including COX-dependent and -independent pathways, and in an obese person, may lead to more severe airway inflammation.

Ruvindy, R, Bolch, CJ, MacKenzie, L, Smith, KF & Murray, SA 2018, 'qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium', Frontiers in Microbiology, vol. 9.
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Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia.

Rychener, L, In-Albon, S, Djordjevic, SP, Chowdhury, PR, Nicholson, P, Ziech, RE, de Vargas, AC, Frey, J & Falquet, L 2018, 'Corrigendum: Clostridium chauvoei, an Evolutionary Dead-End Pathogen', Frontiers in Microbiology, vol. 9.
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[This corrects the article on p. 1054 in vol. 8, PMID: 28649238.].

Saad, S, Al‐Odat, I, Chan, YL, McGrath, KC, Pollock, CA, Oliver, BG & Chen, H 2018, 'Maternal L‐carnitine supplementation improves glucose and lipid profiles in female offspring of dams exposed to cigarette smoke', Clinical and Experimental Pharmacology and Physiology, vol. 45, no. 7, pp. 694-703.
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SummarySex differences in disease susceptibility due to maternal programming have been reported. We previously observed that maternal smoking induced renal disease and neurological changes are restricted to males, while both male and female offspring develop metabolic disorders. We have also found that maternal L‐carnitine supplementation during gestation and lactation can significantly improve glucose intolerance and hyperlipidaemia in male offspring. This study aimed to determine whether such beneficial effects can also occur in female offspring. Balb/c female mice were exposed to cigarette smoke (SE) 6 weeks prior to gestation, during gestation and lactation. A subgroup of the SE dams was given L‐carnitine (1.5 mmol/L in drinking water) during gestation and lactation. Female offspring were studied at 20 days (weaning) and 13 weeks (adulthood). Maternal smoking increased liver weight (%) and blood glucose levels at 20 days, as well as glucose intolerance and plasma triglycerides levels at adulthood (P < .05). The hepatic lipid metabolic marker adipose triglyceride lipase was downregulated in the SE offspring at 20 days (P < .05). At 13 weeks, the hepatic pro‐inflammatory markers IL‐1β and TNF‐α mRNA expression were upregulated, while the anti‐inflammatory marker IL‐10 mRNA expression was downregulated in the SE o...

Sablok, G, Hayward, RJ, Davey, PA, Santos, RP, Schliep, M, Larkum, A, Pernice, M, Dolferus, R & Ralph, PJ 2018, 'SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants', Scientific Reports, vol. 8, no. 1.
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AbstractSeagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.

Sack, BK, Behet, M, Mikolajczak, S, Cardamone, H, Nguyen, T, Flannery, E, Vaughan, AM, Oliver, B, Vigdorovich, V, Carbonetti, S, Sather, N, Scholzen, A, Sauerwein, R & Kappe, SHI 2018, 'Antibodies targeting the intracellular liver stage malaria parasite after infection can be a potent means of reducing parasite liver burden', The Journal of Immunology, vol. 200, no. 1_Supplement, pp. 180.30-180.30.
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Abstract Malaria is one of the oldest and deadliest diseases known to humans, and in 2017 an estimated 216 million people were infected with 445,000 succumbing to disease. Antibodies which block the skin-to-liver stages of malaria infection continue to be pursued due to their potential to stop infection prior to the progression to the disease and transmission-causing blood stages. Phase III clinical trials with a vaccine targeting the major sporozoite surface protein (circumsporozoite protein) have provided suboptimal efficacy in the field which must be improved before large scale use for malaria prevention and eradication. New antibody targets will likely be needed in order to provide complete, sterilizing protection. Thus far, the search has largely been limited to targeting surface and secreted proteins of the sporozoite, merozoite or gametocyte stages. Here, we present data demonstrating that antibodies which instead target the intracellular liver stage parasite after hepatocyte infection can be a potent means of limiting parasite liver infection in vivo. This was done in a rodent malaria model by targeting two different proteins found on the parasitophorous vacuole membrane that forms the border between parasite and host cytoplasm—indicating antibodies are entering the hepatocyte to mediate their effect. This phenomenon was also demonstrated using the most common human malaria species Plasmodium falciparum in humanized liver chimeric mice where human antibodies targeting the parasite periphery were able to potently reduce liver burden and parasite liver growth between days 5–6. These data present a new class of antibody targets for malaria and strongly argue for the inclusion of intracellular antigens in novel vaccine formulations.

Sajid, A, Reimers, JR & Ford, MJ 2018, 'Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation', Physical Review B, vol. 97, no. 6, p. 064101.
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Key properties of nine possible defect sites in hexagonal boron nitride(h-BN) are predicted using density-functional theory and are corrected byapplying results from high-level ab initio calculations. Observed h-BNelectron-paramagnetic resonance signals at 22.4, 20.83, and 352.70 MHz areassigned to VN, CN, and VNO2B, respectively, while the observed photoemissionat 1.95 eV is assigned to VNCB. Detailed consideration of the available excitedstates, allowed spin-orbit couplings, zero-field splitting, and opticaltransitions are made for the two related defects VNCB and VBCN. VNCB isproposed for realizing long-lived quantum memory in h-BN. VBCN is predicted tohave a triplet ground state, implying that spin initialization by optical meansis feasible and suitable optical excitations are identified, making this defectof interest for possible quantum-qubit operations.

Sankaran, J, Karampatzakis, A, Rice, SA & Wohland, T 2018, 'Quantitative imaging and spectroscopic technologies for microbiology', FEMS Microbiology Letters, vol. 365, no. 9.
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© FEMS 2018. Light microscopy has enabled the observation of the structure and organisation of biofilms. Typically, the contrast in an image obtained from light microscopy is given by the time-averaged intensity that is effective in visualising the overall structure. Technological advancements in light microscopy have led to the creation of techniques that not only provide a static intensity image of the biofilm, but also enable one to quantify various dynamic physicochemical properties of biomolecules in microbial biofilms. Such light microscopy-based techniques can be grouped into two main classes, those that are based on luminescence and those that are based on scattering. Here, we review the fundamentals and applications of luminescence and scattering-based techniques, specifically, fluorescence lifetime imaging, Förster resonance energy transfer, fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single-particle tracking, transient state imaging, and Brillouin and Raman microscopy. These techniques provide information about the abundance, interactions and mobility of various molecules in the biofilms and also properties of the local microenvironment at optical resolution. Further, one could use any of these techniques to probe the real-time changes in these physical parameters upon the addition of external agents or at different stages during the growth of biofilms.

Santini, NS, Cleverly, J, Faux, R, McBean, K, Nolan, R & Eamus, D 2018, 'Root xylem characteristics and hydraulic strategies of species co-occurring in semi-arid Australia', IAWA Journal, vol. 39, no. 1, pp. 43-62.
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Xylem traits such as xylem vessel size can influence the efficiency and safety of water transport and thus plant growth and survival. Root xylem traits are much less frequently examined than those of branches despite such studies being critical to our understanding of plant hydraulics. In this study, we investigated primary lateral and sinker roots of six co-occurring species of semi-arid Australia. Two species are restricted to a floodplain, two were sampled only from the adjacent sand plain, and two species co-occur in both habitats. We assessed root wood density, xylem traits (i.e., vessel diameter, fibre and vessel wall thickness), outer pit aperture diameter and calculated theoretical hydraulic conductivity and vessel implosion resistance. We hypothesized that (1) roots have larger xylem vessel diameters and lower wood density than branches of the same species and that (2) there is an inverse correlation between theoretical sapwood hydraulic conductivity and vessel implosion resistance for roots. Variation in root wood density was explained by variations in xylem vessel lumen area across the different species (r2 = 0.73, p = 0.03), as hypothesized. We rejected our second hypothesis, finding instead that the relationship between theoretical hydraulic conductivity and vessel implosion resistance was not maintained in roots of all of our studied species, in contrast to our previous study of branches from the same species. Xylem traits were found to depend upon habitat and eco-hydrological niche, with the groupings including (i) arid-adapted shrubs and trees with shallow lateral roots (Acacia aneura and Psydrax latifolia), (ii) trees restricted to the floodplain habitat, both evergreen (Eucalyptus camaldulensis) and deciduous (Erythrina vespertilio) and (iii) evergreen trees co-occurring in ...

Satija, S, Kamboj, S, Kaur, J, Mahajan, S, Neeta, Sharma, N, Khurana, N, Vyas, M & Mehta, M 2018, 'Morphological and anatomical studies of stem of Ageratum conyzoides', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 127-130.
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Context: Ageratum conyzoides Linn. (Asteraceae) is an important medicinal plant used in African traditional medicine for healing mental and infectious disorders. Objective: The objective of this work was to contribute to the pharmacobotanical standardization of A. conyzoides. Materials and Methods: Cross sections of the stem were obtained, by hand, for microscopic characterization of the stem. Powder microscopical characteristics were studied by microscope and scanning electron microscopy. Macroscopic characters and physiochemical standards of drug were also studied through standard methods mentioned in the WHO. Results and Discussion: Morphology of A. conyzoides showed that the outer surface of the stem was light green and inner surface was cream white in color, having slight bitter taste, and aromatic odor. Acicular calcium oxalate, sclerenchyma, thin long fibers, and hexagonal cork cells were observed in powder microscopy. Scanning electron microscopy showed the arrangement of vascular tissue in transverse section of the stem. Conclusion: These anatomical features are useful for the diagnosis of the species and provide support to their quality control.

Satija, S, Kamboj, S, Kaur, J, Ripdaman, Vyas, M & Mehta, M 2018, 'Pharmacognostic and pharmacological screening of Ageratum conyzoides stem extract for its antianxiety potential', International Journal of Green Pharmacy, vol. 12, no. 2, pp. S414-S418.
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Objective: The current study assessed the antianxiety potential of standardized stem extracts of Ageratum conyzoides. Materials and Methods: Methanol extract of A. conyzoides stem was prepared using Soxhlet apparatus. Phytochemical investigation was done using standard procedures. Fractionation of methanol extract was done using liquid-liquid extraction. Methanol extract and its fractions (ethyl acetate and butanol) were evaluated for antianxiety potential using elevated plus maze model. Results and Discussion: The methanol extract gave the yield of 12% w/w and its ethyl acetate and butanol fractions gave 5.03% w/w and 2.0% w/w, respectively. The methanol extract of A. conyzoides showed a significant increase in mean of a number of entries by mice in open arms and average time spent when compared to control group. Results revealed that ethyl acetate fraction was responsible for its anxiolytic effect. Conclusion: The present study validates the traditional claim of A. conyzoides as anxiolytic drug as methanol extract of stem produced a significant antianxiety effect.

Satija, S, Mahajan, S, Vyas, M & Mehta, M 2018, 'Pharmacognostic study of dioscorea villosa leaves', International Journal of Green Pharmacy, vol. 12, no. 2, pp. S428-S432.
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Context: Yam (Dioscorea spp.) is an important edible tuber plant used for medicinal purposes to promote health and longevity in Chinese tradition. Steroidal saponins were reported to be the major physiologically active constituents in yams. Therefore, this study was designed to investigate its pharmacognostic characters for its standardization. Materials and Methods: Macroscopic, microscopic, and physiochemical evaluation of Dioscorea villosa was performed using standardized procedures as mentioned in the WHO guidelines. Thin-layer chromatography (TLC) was done to check the purity and identification of the drug. Results and Discussion: Morphology of D. villosa showed that the upper surface of leaves was green in color, having bitter taste and some characteristic odor. The presence of calcium oxalate crystal, thin long fibers, xylem vessels, and epidermal cells was observed in powder microscopy. Phytochemical analysis of crude extracts indicated the presence of alkaloids, glycosides, saponins, and flavonoids. The presence of saponins was also confirmed by foaming index. TLC was done for all the extracts which showed a number of spots indicating the presence of number of chemical constituents. Conclusion: All the above pharmacognostic parameters could be useful for the authentication and preparation of monograph for D. villosa.

Satija, S, Prince, Gupta, R, Mahajan, S, Sharma, N, Khurana, N, Kalsi, V, Duggal, N, Singh, A & Mehta, M 2018, 'Chromatographic fingerprinting, antioxidant, and anti-inflammatory potential of Dioscorea villosa (Wild Yam) leaves', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 102-106.
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Context: Free radicals have been implicated in a wide range diversity of diseases and ailments, and therefore, the compounds having the ability to scavenge these free radicals are under extensive investigation, of which Dioscorea species have been actively involved. Objective: The current study assessed the anti-inflammatory and antioxidant potential of standardized leaf extracts of Dioscorea villosa. Material and Methods: Anti-inflammatory activity was carried out using carrageenan-induced paw edema assay, and antioxidant activity was evaluated using 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. Chromatographic fingerprinting of the crude methanolic extract was carried out using high-performance liquid chromatography (HPLC) whereby diosgenin was used as a standard marker compound. Results: Among all the crude successive extracts, methanolic extract showed significant anti-inflammatory activity in comparison with the standard whereby the extract showed maximum inhibition of paw edema after 3 h of carrageenan injection. The aqueous extract showed noticeable antioxidant activity with the half maximal inhibitory concentration of 21.36 μg/ml. Discussion: The preliminary phytochemical screening showed the presence of flavonoids and tannins that may be responsible for the observed effect. In addition, the presence of steroids marks toward the observed anti-inflammatory activity. In addition, the extract showed noticeable levels of diosgenin, which were marked and quantified using HPLC. Conclusion: The results strongly support the ethnobotanical use of the plant.

Saunders, BM, Rudnicka, C, Filipovska, A, Davies, S, Ward, N, Hricova, J, Schlaich, MP & Matthews, VB 2018, 'Shining LIGHT on the metabolic role of the cytokine TNFSF14 and the implications on hepatic IL‐6 production', Immunology & Cell Biology, vol. 96, no. 1, pp. 41-53.
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AbstractThe cytokine Tumor Necrosis Factor Superfamily member 14, TNFSF14 (or LIGHT), is a controversial player in numerous diseases. We investigated the role of endogenously expressed TNFSF14 in diet‐induced obesity in vivo. Firstly, we studied the effects of Tnfsf14 ablation on the development of obesity, glucose intolerance, insulin resistance, steatosis, tissue inflammation, and mitochondrial respiration in the liver. Secondly, we examined the role of TNFSF14 expression in hematopoietic cells on obesity and insulin sensitivity. Male Tnfsf14 knockout (KO) and wild type mice were fed chow or high fat diet (HFD) for 12 weeks and were assessed for weight gain, glucose intolerance, insulin resistance, hepatosteatosis, mitochondrial dysfunction, and cytokine expression. Wild‐type mice were also reconstituted with bone marrow cells from Tnfsf14 knockout mice and were fed chow or HFD for 12 weeks. These mice were examined for weight gain and insulin resistance. HFD fed mice had elevated circulating levels of serum TNFSF14. Liver and white adipose tissue are potential sources of this elevated TNFSF14. Tnfsf14 deficient mice displayed increased obesity, glucose intolerance, insulin resistance, hepatosteatosis, and mitochondrial dysfunction compare...

Saunders, C, Brown, JJ, Carter, DJ & Lapkin, S 2018, 'Chronic disease management support in Australian workplaces—low base, rising need', Health Promotion Journal of Australia, vol. 29, no. 3, pp. 257-264.
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AbstractIssue addressedThis study investigates the current nature, levels and perceived need for workplace support among mature age Australian workers with chronic illness.MethodsA cross‐sectional population survey was conducted via a double opt‐in panel sample of Australian workers aged 45 years and older with one or more of six major chronic diseases (diabetes and/or chronic heart, kidney, lung, mental health and/or musculoskeletal conditions).ResultsThree hundred and fourteen respondents reported being in the workforce and having at least one of the chronic conditions under investigation, of which almost one third reported having more than one of the conditions. The findings reveal a number of considerable gaps in Australian workplace support for employees 45 years and older with chronic illness, including workplace flexibility, supportive policies and co‐worker support.ConclusionsThis research adds to a scarce existing literature base on workplace support for workers with chronic illness in Australia. Future research is needed to identify opportunities for effective public policy and implementation of workplace interventions to better support this cohort.So what?If timely progress is not made in this area, the projected increase in the aged population and scheduled public policy changes impacting retirement age will multiply potential adverse effects on the health of employees with chronic illness and Australia's labour market productivity.

Scanes, E, Kutti, T, Fang, JKH, Johnston, EL, Ross, PM & Bannister, RJ 2018, 'Mine Waste and Acute Warming Induce Energetic Stress in the Deep-Sea Sponge Geodia atlantica and Coral Primnoa resedeaformis; Results From a Mesocosm Study', Frontiers in Marine Science, vol. 5, no. APR.
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There is the potential for climate change to interact with pollution in all of the Earth's oceans. In the fjords of Norway, mine tailings are released into fjords generating suspended sediment plumes that impact deep-sea ecosystems. These same deep-sea ecosystems are expected to undergo periodic warming as climate change increases the frequency of down-welling events in fjords. It remains unknown how a polluted deep-sea ecosystem would respond to down-welling because multiple stressors will often interact in unpredictable ways. Here, we exposed two deep-sea foundation species; the gorgonian coral Primnoa resedaeformis and the demosponge Geodia atlantica to suspended sediment (10 mg L-1) and acute warming (+5°C) in a factorial mesocosm experiment for 40 days. Physiology (respiration, nutrient flux) and cellular responses (lysosomal cell stability) were measured for both the coral and sponge. Exposure to elevated suspended sediment reduced metabolism, supressed silicate uptake and induced cellular instability of the sponge G. atlantica. However, combining sediment with warming caused G. atlantica to respire and excrete nitrogen at a greater rate. For the coral P. resedaeformis, suspended sediments reduced O:N ratios after 40 days, however, warming had a greater effect on P. resedaeformis physiology compared to sediment. Warming increased respiration, nitrogen excretion, and cellular instability which resulted in lower O:N ratios. We argue that suspended sediment and warming can act alone and also interact to cause significant harm to deep-sea biota, however responses are likely to be species-specific. Warming and pollution could interact in the deep-sea to cause mortality to the coral P. resedaeformis and to a lesser extent, the sponge G. atlantica. As foundation species, reducing the abundance of deep sea corals and sponges would likely impact the ecosystems they support.

Scanes, E, Parker, LM, O’Connor, WA, Gibbs, MC & Ross, PM 2018, 'Copper and ocean acidification interact to lower maternal investment, but have little effect on adult physiology of the Sydney rock oyster Saccostrea glomerata', Aquatic Toxicology, vol. 203, pp. 51-60.
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It remains unknown how molluscs will respond to oceans which are increasingly predicted to be warmer, more acidic, and heavily polluted. Ocean acidification and trace metals will likely interact to increase the energy demands of marine organisms, especially oysters. This study tested the interactive effect of exposure to elevated pCO2 and copper on the energetic demands of the Sydney rock oyster (Saccostrea glomerata) during reproductive conditioning and determined whether there were any positive or negative effects on their offspring. Oysters were exposed to elevated pCO2 (1000 μatm) and elevated copper (Cu 50 μg L-1 [0.787 μM]) in an orthogonal design for eight weeks during reproductive conditioning. After eight weeks, energetic demands on oysters were measured including standard metabolic rate (SMR), nitrogen excretion, molar oxygen to nitrogen (O:N) ratio, and pHe of adult oysters as well as the size and total lipid content of their eggs. To determine egg viability, the gametes were collected and fertilised from adult oysters, the percentage of embryos that had reached the trochophore stage after 24 h was recorded. Elevated pCO2 caused a lower extracellular pH and there was a greater O:N ratio in adult oysters exposed to copper. While the two stressors did not interact to cause significant effects on adult physiology, they did interact to reduce the size and lipid content of eggs indicating that energy demand on adult oysters was greater when both elevated pCO2 and copper were combined. Despite the lower energy, there were no negative effects on early embryonic development. In conclusion, elevated pCO2 can interact with metals and cause greater energetic demands on oysters; in response oysters may lower maternal investment to offspring.

Schelch, K, Kirschner, MB, Williams, M, Cheng, YY, van Zandwijk, N, Grusch, M & Reid, G 2018, 'A link between the fibroblast growth factor axis and the miR‐16 family reveals potential new treatment combinations in mesothelioma', Molecular Oncology, vol. 12, no. 1, pp. 58-73.
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Malignant pleural mesothelioma (MPM) is an aggressive malignancy with very limited therapeutic options. Fibroblast growth factor (FGF) signals play important roles in mesothelioma cell growth. Several FGFs and FGF receptors (FGFRs) are predicted targets of the miR‐15/16 family, which is downregulated in MPM. The aim of this study was to explore the link between the miR‐15/16 family and the FGF axis in MPM. Expression analyses via RT‐qPCR showed downregulation of the FGF axis after transfection with miR‐15/16 mimics. Direct interaction was confirmed by luciferase reporter assays. Restoration of miR‐15/16 led to dose‐dependent growth inhibition in MPM cell lines, which significantly correlated with their sensitivity to FGFR inhibition. Treatment with recombinant FGF2 prevented growth inhibition and further reduced the levels of FGF/R‐targeting microRNAs, indicating a vicious cycle between miR‐15/16 down‐ and FGF/<...

Schmidt, MK, Helt, LG, Poulton, CG & Steel, MJ 2018, 'Elastic Purcell Effect', Physical Review Letters, vol. 121, no. 6, pp. 064301-064301.
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© 2018 American Physical Society. In this work, we introduce an elastic analog of the Purcell effect and show theoretically that spherical nanoparticles can serve as tunable and robust antennas for modifying the emission from localized elastic sources. This effect can be qualitatively described by introducing elastic counterparts of the familiar electromagnetic parameters: local density of elastic states, elastic Purcell factor, and effective volume of elastic modes. To illustrate our framework, we consider the example of a submicron gold sphere as a generic elastic GHz antenna and find that shear and mixed modes of low orders in such systems offer considerable elastic Purcell factors. This formalism opens pathways towards extended control over dissipation of vibrations in various optomechanical systems and contributes to closing the gap between classical and quantum-mechanical treatments of phonons localized in elastic nanoresonators.

Schofield, ZV, Croker, D, Robertson, AAB, Massey, NL, Donovan, C, Tee, E, Edwards, D, Woodruff, TM, Halai, R, Hansbro, PM & Cooper, MA 2018, 'Characterisation of small molecule ligands 4CMTB and 2CTAP as modulators of human FFA2 receptor signalling', Scientific Reports, vol. 8, no. 1.
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AbstractShort chain fatty acids (SCFAs) are protective against inflammatory diseases. Free fatty acid receptor 2 (FFA2), is a target of SCFAs however, their selectivity for FFA2 over other FFA receptors is limited. This study aimed to functionally characterise 2-(4-chlorophenyl)-3-methyl-N-(thiazole-2-yl)butanamide (4CMTB) and 4-((4-(2-chlorophenyl)thiazole-2-yl)amino)-4oxo-3-phenylbutanoic acid (2CTAP), and their enantiomers, in modulating FFA2 activity. The racemic mixture (R/S) and its constituents (R-)and (S-) 4CMTB or 2CTAP were used to stimulate human (h)FFA2 in the absence or presence of acetate. Calcium ions (Ca2+), phosphorylated extracellular signal-regulated kinase 1 and 2 (pERK1/2) and cyclic adenosine monophosphate (cAMP) were measured.R/S-4CMTB is a functionally selective ago-allosteric ligand that enhances Ca2+response to acetate. BothR/S-4CMTB andS-4CMTB are more potent activators of pERK1/2 and inhibitors of forskolin-induced cAMP than acetate.S-4CMTB increased neutrophil infiltration in intestinal ischemia reperfusion injury (IRI). 2CTAP inhibited constitutive Ca2+levels, antagonised acetate-induced pERK1/2 and prevented damage following IRI. This study characterises enantiomers of functionally selective ligands for FFA2 in cells stably expressing hFFA2. It highlights the novel roles of selective FFA2 enantiomers 4CMTB and 2CTAP on Ca2+, pERK1/2 and cAMP and their roles as allosteric modulators which, may assist in efforts to design novel therapeutic agents for FFA2-driven inflammatory diseases.

Schrameyer, V, York, PH, Chartrand, K, Ralph, PJ, Kühl, M, Brodersen, KE & Rasheed, MA 2018, 'Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef)', Marine Environmental Research, vol. 136, pp. 38-47.
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© 2018 Elsevier Ltd Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.

Schumann-Gillett, A, Mark, AE, Deplazes, E & O’Mara, ML 2018, 'A potential new, stable state of the E-cadherin strand-swapped dimer in solution', European Biophysics Journal, vol. 47, no. 1, pp. 59-67.
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E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.

Scott, JA, Angeloski, A, Aharonovich, I, Lobo, CJ, McDonagh, A & Toth, M 2018, 'In situstudy of the precursor conversion reactions during solventless synthesis of Co₉S₈, Ni₃S₂, Co and Ni nanowires', Nanoscale, vol. 10, no. 33, pp. 15669-15676.
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Synthesis of Co₉S₈, Ni₃S₂, Co and Ni nanowires by solventless thermolysis of a mixture of metal(ii) acetate and cysteine in vacuum is reported.

Scott, PD, Coleman, HM, Khan, S, Lim, R, McDonald, JA, Mondon, J, Neale, PA, Prochazka, E, Tremblay, LA, Warne, MSJ & Leusch, FDL 2018, 'Histopathology, vitellogenin and chemical body burden in mosquitofish (Gambusia holbrooki) sampled from six river sites receiving a gradient of stressors', Science of The Total Environment, vol. 616-617, pp. 1638-1648.
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© 2017 Elsevier B.V. There are over 40,000 chemical compounds registered for use in Australia, and only a handful are monitored in the aquatic receiving environments. Their effects on fish species in Australia are largely unknown. Mosquitofish (Gambusia holbrooki) were sampled from six river sites in Southeast Queensland identified as at risk from a range of pollutants. The sites selected were downstream of a wastewater treatment plant discharge, a landfill, two agricultural areas, and two sites in undeveloped reaches within or downstream of protected lands (national parks). Vitellogenin analysis, histopathology of liver, kidney and gonads, morphology of the gonopodium, and chemical body burden were measured to characterize fish health. Concentrations of trace organic contaminants (TrOCs) in water were analyzed by in vitro bioassays and chemical analysis. Estrogenic, anti-estrogenic, anti-androgenic, progestagenic and anti-progestagenic activities and TrOCs were detected in multiple water samples. Several active pharmaceutical ingredients (APIs), industrial compounds, pesticides and other endocrine active compounds were detected in fish carcasses at all sites, ranging from < 4–4700 ng/g wet weight, including the two undeveloped sites. While vitellogenin protein was slightly increased in fish from two of the six sites, the presence of micropollutants did not cause overt sexual endocrine disruption in mosquitofish (i.e., no abnormal gonads or gonopodia). A correlation between lipid accumulation in the liver with total body burden warrants further investigation to determine if exposure to low concentrations of TrOCs can affect fish health and increase stress on organs such as the liver and kidneys via other mechanisms, including disruption of non-sexual endocrine axes involved in lipid regulation and metabolism.

Scudder, N, McNevin, D, Kelty, SF, Walsh, SJ & Robertson, J 2018, 'Forensic DNA phenotyping: Developing a model privacy impact assessment', Forensic Science International: Genetics, vol. 34, pp. 222-230.
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Forensic scientists around the world are adopting new technology platforms capable of efficiently analysing a larger proportion of the human genome. Undertaking this analysis could provide significant operational benefits, particularly in giving investigators more information about the donor of genetic material, a particularly useful investigative lead. Such information could include predicting externally visible characteristics such as eye and hair colour, as well as biogeographical ancestry. This article looks at the adoption of this new technology from a privacy perspective, using this to inform and critique the application of a Privacy Impact Assessment to this emerging technology. Noting the benefits and limitations, the article develops a number of themes that would influence a model Privacy Impact Assessment as a contextual framework for forensic laboratories and law enforcement agencies considering implementing forensic DNA phenotyping for operational use.

Scudder, N, McNevin, D, Kelty, SF, Walsh, SJ & Robertson, J 2018, 'Massively parallel sequencing and the emergence of forensic genomics: Defining the policy and legal issues for law enforcement', Science & Justice, vol. 58, no. 2, pp. 153-158.
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© 2017 The Chartered Society of Forensic Sciences Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as ‘big data’ privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities.

Seckiner, D, Mallett, X, Roux, C, Meuwly, D & Maynard, P 2018, 'Forensic image analysis – CCTV distortion and artefacts', Forensic Science International, vol. 285, pp. 77-85.
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© 2018 Elsevier B.V. As a result of the worldwide deployment of surveillance cameras, authorities have gained a powerful tool that captures footage of activities of people in public areas. Surveillance cameras allow continuous monitoring of the area and allow footage to be obtained for later use, if a criminal or other act of interest occurs. Following this, a forensic practitioner, or expert witness can be required to analyse the footage of the Person of Interest. The examination ultimately aims at evaluating the strength of evidence at source and activity levels. In this paper, both source and activity levels are inferred from the trace, obtained in the form of CCTV footage. The source level alludes to features observed within the anatomy and gait of an individual, whilst the activity level relates to activity undertaken by the individual within the footage. The strength of evidence depends on the value of the information recorded, where the activity level is robust, yet source level requires further development. It is therefore suggested that the camera and the associated distortions should be assessed first and foremost and, where possible, quantified, to determine the level of each type of distortion present within the footage. A review of the ‘forensic image analysis’ review is presented here. It will outline the image distortion types and detail the limitations of differing surveillance camera systems. The aim is to highlight various types of distortion present particularly from surveillance footage, as well as address gaps in current literature in relation to assessment of CCTV distortions in tandem with gait analysis. Future work will consider the anatomical assessment from surveillance footage.

Segečová, A, Červený, J & Roitsch, T 2018, 'Advancement of the cultivation and upscaling of photoautotrophic suspension cultures using Chenopodium rubrum as a case study', Plant Cell, Tissue and Organ Culture (PCTOC), vol. 135, no. 1, pp. 37-51.
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Seymour, JR & Raina, J-B 2018, 'Swimming in the sea: chemotaxis by marine bacteria', Microbiology Australia, vol. 39, no. 1, pp. 12-12.
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Like many organisms, bacteria regularly inhabit environments characterised by spatiotemporal heterogeneity in the availability of resources required for growth and energy generation, meaning they must either tune their metabolism to prevailing conditions or have the capacity to migrate to favourable microenvironments1. To achieve the latter, bacteria measure their resource landscape and suitably direct their locomotion using a behaviour called chemotaxis, which is the ability to guide movement up or down chemical gradients. The capacity to perform chemotaxis is widespread across the bacterial domain, although most of our understanding of this phenotype is derived from enteric bacteria2,3. In the ocean, marine bacteria are often motile4, and in fact capable of much higher swimming speeds5 and chemotactic precision6 than these enteric models for chemotaxis2. Here we discuss the underlying motives and purposes for bacterial chemotaxis in the ocean, by noting that marine bacteria experience a surprisingly heterogeneous chemical seascape7,8, whereby chemotaxis can provide substantial fitness advantages and even influence large-scale processes including marine ecosystem productivity, biogeochemical cycling and disease.

Seymour, JR, Barbasch, TA & Buston, PM 2018, 'Lunar cycles of reproduction in the clown anemonefish Amphiprion percula: individual-level strategies and population-level patterns', Marine Ecology Progress Series, vol. 594, pp. 193-201.
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Shad, KF, Luqman, N, Simpson, AM & Lal, S 2018, 'Peripheral Biomarker for Vascular Disorders', Biomarker Insights, vol. 13, pp. 117727191881246-117727191881246.
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Atherosclerosis is the underlying cause of most myocardial infarction (MI) and ischaemic stroke episodes. An early sign of atherosclerosis is hypertrophy of the arterial wall. It is known that increased intima media thickness (IMT) is a non-invasive marker of arterial wall alteration, which can easily be assessed in the carotid arteries by high-resolution B-mode ultrasound. Similarly, the other key element of MI and ischaemic strokes is the N-methyl-D-aspartate (NMDA) receptor which is an ionotropic glutamate receptor that mediates the vast majority of excitatory neurotransmission in the brain. NMDA activation requires the binding of both glutamate and a coagonist like D-serine to its glycine site. A special enzyme, serine racemase (SR), is required for the conversion of L-serine into D-serine, and alterations in SR activities lead to a variety of physiological and pathological conditions ranging from synaptic plasticity to ischemia, MI, and stroke. The amount of D-serine available for the activation of glutamatergic signalling is largely determined by SR and we have developed ways to estimate its levels in human blood samples and correlate it with the IMT. This research based short communication describes our pilot study, which clearly suggests that there is a direct relationship between the SR, D-serine, and IMT. In this article, we will discuss whether the activity of SR can determine the future consequences resulting from vascular pathologies such as MI and stroke.

Shah, JS, Gard, GB, Yang, J, Maidens, J, Valmadre, S, Soon, PS & Marsh, DJ 2018, 'Combining serum microRNA and CA-125 as prognostic indicators of preoperative surgical outcome in women with high-grade serous ovarian cancer', Gynecologic Oncology, vol. 148, no. 1, pp. 181-188.
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The most widely used approach for the clinical management of women with high-grade serous ovarian cancer (HGSOC) is surgery, followed by platinum and taxane based chemotherapy. The degree of macroscopic disease remaining at the conclusion of surgery is a key prognostic factor determining progression free and overall survival. We sought to develop a non-invasive test to assist surgeons to determine the likelihood of achieving complete surgical resection. This knowledge could be used to plan surgical approaches for optimal clinical management.We profiled 170 serum microRNAs (miRNAs) using the Serum/Plasma Focus miRNA PCR panel containing locked nucleic acid (LNA) primers (Exiqon) in women with HGSOC (N=56) and age-matched healthy volunteers (N=30). Additionally, we measured serum CA-125 levels in the same samples. The HGSOC cohort was further classified based on the degree of macroscopic disease at the conclusion of surgery. Stepwise logistic regression was used to identify predictive markers.We identified a combination of miR-375 and CA-125 as the strongest discriminator of healthy versus HGSOC serum, with an area under the curve (AUC) of 0.956. The inclusion of miR-210 increased the AUC to 0.984; however, miR-210 was affected by hemolysis. The combination of miR-34a-5p and CA-125 was the strongest predictor of completeness of surgical resection with an AUC of 0.818.A molecular test incorporating circulating miRNA to predict completeness of surgical resection for women with HGSOC has the potential to contribute to planning for optimal patient management, ultimately improving patient outcome.

Shang, Y, Bao, G, Zhou, J, Wong, K, Yang, C & Jin, D 2018, 'Lanthanide-Doped Upconversion Luminescent Materials for Point of Care Diagnosis', Zhongguo Xitu Xuebao/Journal of the Chinese Rare Earth Society, vol. 36, no. 2, pp. 129-146.
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Point of care (POC) diagnosis has attracted much research interest due to its rapid, specific and sensitive detection of biomarkers and pathogens. This decentralized diagnostic approach undoubtedly has huge advantage over laboratory testing at large hospitals or community laboratories regarding cost-effectiveness, healthcare delivery, especially with the emerging and spreading of smart technologies. Among all the materials for POC, lanthanides have become a rising star because of their excellent photophysical properties such as long life time, characteristic luminescence. Here, we focus on the wide-spread platforms of POC diagnostic devices and the applications of lanthanide upconverting materials in this field. With the market and social trend analysis, we will give our future perspective about the applications of lanthanide materials in POC.

Shanmukaraj, D, Kretschmer, K, Sahu, T, Bao, W, Rojo, T, Wang, G & Armand, M 2018, 'Highly Efficient, Cost Effective, and Safe Sodiation Agent for High‐Performance Sodium‐Ion Batteries', ChemSusChem, vol. 11, no. 18, pp. 3286-3291.
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AbstractThe development of sodium‐ion batteries has been hindered so far by the large irreversible capacity of hard carbon anodes and other anode materials in the initial few cycles, as sodium ions coming from cathode materials is consumed in the formation of the solid–electrolyte interface (SEI) and irreversibly trapped in anodes. Herein, the successful synthesis of an environmentally benign and cost‐effective sodium salt (Na2C4O4) is reported that could be applied as additive in cathodes to solve the irreversible‐capacity issues of anodes in sodium‐ion batteries. When added to Na3(VO)2(PO4)2F cathode, the cathode delivered a highly stable capacity of 135 mAh g−1 and stable cycling performance. The water‐stable Na3(VO)2(PO4)2F cathode in combination with a water‐soluble sacrificial salt eliminates the need for using any toxic solvents for laminate preparation, thus paving way for greener electrode fabrication techniques. A 100 % increase in capacity of sodium cells (full‐cell configuration) has been observed when using the new sodium salt at a C‐rate of 2C. Regardless of the electrode fabrication technique, this new salt finds use in both aqueous and non‐aqueous cathode‐fabrication techniques for sodium‐ion batteries.

She, L, Xue, Y, Yang, X, Guang, J, Li, Y, Che, Y, Fan, C & Xie, Y 2018, 'Dust Detection and Intensity Estimation Using Himawari-8/AHI Observation', Remote Sensing, vol. 10, no. 4, pp. 490-490.
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In this study, simple dust detection and intensity estimation methods using Himawari-8 Advanced Himawari Imager (AHI) data are developed. Based on the differences of thermal radiation characteristics between dust and other typical objects, brightness temperature difference (BTD) among four channels (BT11–BT12, BT8–BT11, and BT3–BT11) are used together for dust detection. When considering the thermal radiation variation of dust particles over different land cover types, a dynamic threshold scheme for dust detection is adopted. An enhanced dust intensity index (EDII) is developed based on the reflectance of visible/near-infrared bands, BT of thermal-infrared bands, and aerosol optical depth (AOD), and is applied to the detected dust area. The AOD is retrieved using multiple temporal AHI observations by assuming little surface change in a short time period (i.e., 1–2 days) and proved with high accuracy using the Aerosol Robotic Network (AERONET) and cross-compared with MODIS AOD products. The dust detection results agree qualitatively with the dust locations that were revealed by AHI true color images. The results were also compared quantitatively with dust identification results from the AERONET AOD and Ångström exponent, achieving a total dust detection accuracy of 84%. A good agreement is obtained between EDII and the visibility data from National Climatic Data Center ground measurements, with a correlation coefficient of 0.81, indicating the effectiveness of EDII in dust monitoring.

Shen, J, Huete, A, Tran, NN, Devadas, R, Ma, X, Eamus, D & Yu, Q 2018, 'Diverse sensitivity of winter crops over the growing season to climate and land surface temperature across the rainfed cropland-belt of eastern Australia', Agriculture, Ecosystems & Environment, vol. 254, pp. 99-110.
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© 2017 Elsevier B.V. The rainfed cropland belt in Australia is of great importance to the world grain market but has the highest climate variability of all such regions globally. However, the spatial-temporal impacts of climate variability on crops during different crop growth stages across broadacre farming systems are largely unknown. This study aims to quantify the contributions of climate and Land Surface Temperature (LST) variations to the variability of the Enhanced Vegetation Index (EVI) by using remote sensing methods. The datasets were analyzed at an 8-day time-scale across the rainfed cropland of eastern Australia. First, we found that EVI values were more variable during the crop reproductive growth stages than at any other crop life stage within a calendar year, but nevertheless had the highest correlation with crop grain yield (t ha−1). Second, climate factors and LST during the crop reproductive growth stages showed the largest variability and followed a typical east-west gradient of rainfall and a north-south temperature gradient across the study area during the crop growing season. Last, we identified two critical 8-day periods, beginning on day of the year (DoY) 257 and 289, as the key ‘windows’ of crop growth variation that arose from the variability in climate and LST. Our results show that the sum of the variability of the climate components within these two 8-day ‘windows’ explained >88% of the variability in the EVI, with LST being the dominant factor. This study offers a fresh understanding of the spatial-temporal climate-crop relationships in rainfed cropland and can serve as an early warning system for agricultural adaptation in broadacre rainfed cropping practices in Australia and worldwide.

Sheraton, MV, Yam, JKH, Tan, CH, Oh, HS, Mancini, E, Yang, L, Rice, SA & Sloot, PMA 2018, 'Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism', Antimicrobial Agents and Chemotherapy, vol. 62, no. 5.
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ABSTRACT Segregation of bacteria based on their metabolic activities in biofilms plays an important role in the development of antibiotic resistance. Mushroom-shaped biofilm structures, which are reported for many bacteria, exhibit topographically varying levels of multiple drug resistance from the cap of the mushroom to its stalk. Understanding the dynamics behind the formation of such structures can aid in design of drug delivery systems, antibiotics, or physical systems for removal of biofilms. We explored the development of metabolically heterogeneous Pseudomonas aeruginosa biofilms using numerical models and laboratory knockout experiments on wild-type and chemotaxis-deficient mutants. We show that chemotactic processes dominate the transformation of slender and hemispherical structures into mushroom structures with a signature cap. Cellular Potts model simulation and experimental data provide evidence that accelerated movement of bacteria along the periphery of the biofilm, due to nutrient cues, results in the formation of mushroom structures and bacterial segregation. Multidrug resistance of bacteria is one of the most threatening dangers to public health. Understanding the mechanisms of the development of mushroom-shaped biofilms helps to identify the multidrug-resistant regions. We decoded the dynamics of the structural evolution of bacterial biofilms and the physics behind the formation of biofilm structures as well as the biological triggers that produce them. Combining in vitro gene knockout experiments with in silico models showed that chemotactic motility is one of the main driving forces for the formation of stalks and caps. Our results provide physicists and biologists with a new perspectiv...

Shi, R, Han, C, Duan, H, Xu, L, Zhou, D, Li, H, Li, J, Kang, F, Li, B & Wang, G 2018, 'Redox‐Active Organic Sodium Anthraquinone‐2‐Sulfonate (AQS) Anchored on Reduced Graphene Oxide for High‐Performance Supercapacitors', Advanced Energy Materials, vol. 8, no. 31, pp. 1802088-1802088.
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AbstractRedox active organic quinones are potentially low cost, sustainable, and high‐energy pseudocapacitive materials due to their fast and reversible redox reactivity. However, their electrically insulating nature prevents any practical application. Herein, for the first time, sodium anthraquinone‐2‐sulfonate (AQS) is examined as an organic redox‐active compound and highly conductive graphene nanosheets are incorporated to enhance the electronic conductivity. The SO3− functional group of AQS offers excellent hydrophilicity, which promotes the molecular level binding of AQS with reduced graphene oxide (rGO) and leads to a 3D interconnected xerogel (AQS@rGO). The composite exhibits a high specific capacitance of 567.1 F g−1 at 1 A g−1 with a stable capacity retention of 89.1% over 10 000 cycles at 10 A g−1. More importantly, the optimized composite maintains a high capacitance of 315.1 F g−1 even at 30 A g−1 due to the high pseudocapacitance of AQS and the capacitive contribution of rGO. First‐principles calculations further elucidate that AQS offers strong adhesion to rGO sheets with the formation of a space‐charge layer, which is favorable for the pseudocapacitance of AQS. This work opens a new avenue for developing high‐performance supercapacitors though rational combination of redox organic molecules with highly conductive graphene.

Shi, X & Reimers, JR 2018, 'Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling', Scientific Reports, vol. 8, no. 1, pp. 2147-2147.
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AbstractAnalytical equations are derived depicting four possible scenarios resulting from pulsed signaling of a system subject to Hill-type dynamics. Pulsed Hill-type dynamics involves the binding of multiple signal molecules to a receptor and occurs e.g., when transcription factor p53 orchestrates cancer prevention, during calcium signaling, and during circadian rhythms. The scenarios involve: (i) enhancement of high-affinity binders compared to low-affinity ones, (ii) slowing reactions involving high-affinity binders, (iii) transfer of the clocking of low-affinity binders from the signal molecule to the products, and (iv) a unique clocking process that produces incremental increases in the activity of high-affinity binders with each signal pulse. In principle, these mostly non-linear effects could control cellular outcomes. An applications to p53 signaling is developed, with binding to most gene promoters identified as category (iii) responses. However, currently unexplained enhancement of high-affinity promoters such as CDKN1a (p21) by pulsed signaling could be an example of (i). In general, provision for all possible scenarios is required in the design of mathematical models incorporating pulsed Hill-type signaling as some aspect.

Shipunova, VO, Zelepukin, IV, Stremovskiy, OA, Nikitin, MP, Care, A, Sunna, A, Zvyagin, AV & Deyev, SM 2018, 'Versatile Platform for Nanoparticle Surface Bioengineering Based on SiO₂-Binding Peptide and Proteinaceous Barnase*Barstar Interface', ACS Applied Materials & Interfaces, vol. 10, no. 20, pp. 17437-17447.
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Singh, A, Mukhtar, HM, Satija, S & Mehta, M 2018, 'DEVELOPMENT OF QUALITATIVE PHARMACOGNOSTIC AND HIGH-PERFORMANCE THIN-LAYER CHROMATOGRAPHIC FINGERPRINTING OF MORPHOLOGICAL SIMILAR SPECIES OF GENUS FICUS', Asian Journal of Pharmaceutical and Clinical Research, vol. 11, no. 7, pp. 444-444.
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Objective: Ficus deltoidea (FD) and Ficus benjamina (FB), popularly known as “jack tree/mas cotek” and “pimpri/java fig,” respectively, in India and are used in folk medicine to treat the wound, ulcers, diabetes, microbial infections, and inflammatory disorders. Such therapeutic claims have also been justified in the literature by their rich chemical diversity. Both the plant species are morphologically similar and used unauthentically as the traditional medicinal product. Although these plants are sold in the local market by a traditional medicinal healer, we did not find any authenticated data on its quality.Methods: In the present study, quality standards of both the plant drugs have been developed and compared by performing morphological, microscopical, physicochemical, phytochemical, and high-performance thin-layer chromatographic (HPTLC) analysis. using CAMAG Linomat 5 instrument (Kindly delete the bold matter).Results: It was revealed that both the plant species have similar pharmacognostic features with some differences in type of stomata, presence of marked midrib, arrangement of the cell, cell structures, and meristele. HPTLC data revealed that the primary component in FD leaves (FDL) and FB leaves (FBL) extracts was found at Rf 0.67 and 0.37 with the respective peak area of 35.61% and 34.71%. The peaks at Rf 0.17 and 0.27 can be appeared as the chemical marker to highlight the quality of FDL, whereas peaks at Rf 0.87 and 0.95 can be considered to identify and chemically standardize the FBL.Conclusion: This study highlighted essential characters which contribute to the standardization, identification, and authentication of plant drugs.

Singh, A, Singh, V, Mehta, M, Mahajan, S & Satija, S 2018, 'Pharmacognostic standardization and high-performance thin-layer chromatography fingerprinting of ficus infectoria leaves', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 11-15.
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Introduction: Ficus infectoria popularly known as a white fig in India and is used in folk medicine to treat various physiological disorders. The pharmacological significance of this traditional Indian medicinal plant has also been justified in the literature by its rich chemical diversity. Due to its rich biochemical properties, plant material was used unauthentically as the traditional medicinal plant product in Indian market. Despite the fact that these plants are sold in the local market by a traditional medicinal healer, we did not find any authenticated data on its quality. Materials and Methods: In the present study, quality standards of plant leaves were developed by performing morphological, microscopical, physicochemical, phytochemical, and high-performance thin-layer chromatography (HPTLC) studies using CAMAG Linomat 5 instruments. Results: Microscopical studies of leaf and petiole of plant drug showed an arc of centrally located meristele surrounded by lignified parenchymatous tissue. Surface characteristic study of leaf lamina confirms the presence of a paracytic type of stomata. HPTLC data revealed that the primary component in the crude methanolic extract was found at Rf 0.02, 0.12, and 0.52 with the respective peak area of 22.63%, 12.22%, and 13.02%, respectively. Conclusion: This study highlighted essential characters which contribute to the standardization, identification, and authentication of plant drugs.

Singh, D, Bhardwaj, SV, Kumar, A, Kaushik, V, Mahajan, S & Satija, S 2018, 'Antimicrobial activity and molecular docking studies of a sesquiterpenoid alcohol from leaf solvent extracts of Juniperus communis L.', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 22-28.
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Aim: The present investigations were focused on isolation, characterization and antimicrobial evaluation and molecular docking of phytocompounds from Juniperus communis. Materials and Methods: α-Cadinol together with several other phytocompounds such as α-pinene, β-pinene, decanal, and α-terpineol were isolated from leaves of J. communis L using Soxhlet extraction with petroleum ether, ethanol, methanol, and aqueous solvents and identified through gas chromatography-mass spectrometry were then evaluated for the antimicrobial potential against Bacillus subtilis and Escherichia coli under in vitro conditions at different concentrations, namely 20, 40, 80, 100, 200, and 300 ppm. Furthermore, molecular docking analysis of α-Cadinol was performed against common antibiotic drug target proteins, namely penicillin-binding protein 2X (PBP), DNA gyrase Subunit B and topoisomerase IV using AutoDock4 (version 4.2) with the Lamarckian genetic algorithm. Results: Among these, maximum growth inhibition was observed at 300 ppm. Docking studies proclaim that α-Cadinol, a current phytochemical of J. communis L., has the most elevated wellness (fitness) score and more specificity toward the PBP than other protein targets and the bioactivity might be a result of these compounds exhibited in leaf extracts.

Singhvi, G, Girdhar, V, Patil, S, Gupta, G, Hansbro, PM & Dua, K 2018, 'Microbiome as therapeutics in vesicular delivery', Biomedicine & Pharmacotherapy, vol. 104, pp. 738-741.
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© 2018 Elsevier Masson SAS Microbiome refers to an ecological community of various symbiotic and pathogenic microorganisms, which plays a crucial role in human health and disease. The concept of novel drug delivery systems particularly the vesicular drug delivery systems is gaining massive attention. This emerging technology has started expanding its horizons in the area of microbiome delivery. This mini-review highlights the role of vesicular systems such as nanoparticles, liposomes etc. as a host/carrier for the microbiome in targeting various diseases. This review will be of interest for both the biological and formulation scientists to understand and explore the new vistas in the area of vesicular delivery system as carrier for microbiome delivery.

Smalla, K, Cook, K, Djordjevic, SP, Klümper, U & Gillings, M 2018, 'Environmental dimensions of antibiotic resistance: assessment of basic science gaps', FEMS Microbiology Ecology, vol. 94, no. 12, pp. 1-6.
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Antibiotic resistance is one of the major problems facing medical practice in the 21st century. Historical approaches to managing antibiotic resistance have often focused on individual patients, specific pathogens and particular resistance phenotypes. However, it is increasingly recognized that antibiotic resistance is a complex ecological and evolutionary problem. As such, understanding the dynamics of antibiotic resistance requires integration of data on the diverse mobile genetic elements often associated with antibiotic resistance genes, and their dissemination by various mechanisms of horizontal gene transfer between bacterial cells and environments. Most important is understanding the fate and effects of antibiotics at sub-inhibitory concentrations, and co-selection. This opinion paper identifies key knowledge gaps in our understanding of resistance phenomena, and outlines research needs that should be addressed to help us manage resistance into the future.

Söderström, B, Badrutdinov, A, Chan, H & Skoglund, U 2018, 'Cell shape-independent FtsZ dynamics in synthetically remodeled bacterial cells', Nature Communications, vol. 9, no. 1, p. 4323.
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AbstractFtsZ is the main regulator of bacterial cell division. It has been implicated in acting as a scaffolding protein for other division proteins, a force generator during constriction, and more recently, as an active regulator of septal cell wall production. FtsZ assembles into a heterogeneous structure coined the Z-ring due to its resemblance to a ring confined by the midcell geometry. Here, to establish a framework for examining geometrical influences on proper Z-ring assembly and dynamics, we sculpted Escherichia coli cells into unnatural shapes using division- and cell wall-specific inhibitors in a micro-fabrication scheme. This approach allowed us to examine FtsZ behavior in engineered Z-squares and Z-hearts. We use stimulated emission depletion (STED) nanoscopy to show that FtsZ clusters in sculpted cells maintain the same dimensions as their wild-type counterparts. Based on our results, we propose that the underlying membrane geometry is not a deciding factor for FtsZ cluster maintenance and dynamics in vivo.

Söderström, B, Chan, H, Shilling, PJ, Skoglund, U & Daley, DO 2018, 'Spatial separation of FtsZ and FtsN during cell division', Molecular Microbiology, vol. 107, no. 3, pp. 387-401.
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SummaryThe division of Escherichia coli is mediated by a collection of some 34 different proteins that are recruited to the division septum and are thought to assemble into a macromolecular complex known as ‘the divisome’. Herein, we have endeavored to better understand the structure of the divisome by imaging two of its core components; FtsZ and FtsN. Super resolution microscopy (SIM and gSTED) indicated that both proteins are localized in large assemblies, which are distributed around the division septum (i.e., forming a discontinuous ring). Although the rings had similar radii prior to constriction, the individual densities were often spatially separated circumferentially. As the cell envelope constricted, the discontinuous ring formed by FtsZ moved inside the discontinuous ring formed by FtsN. The radial and circumferential separation observed in our images indicates that the majority of FtsZ and FtsN molecules are organized in different macromolecular assemblies, rather than in a large super‐complex. This conclusion was supported by fluorescence recovery after photobleaching measurements, which indicated that the dynamic behavior of the two macromolecular assemblies was also fundamentally different. Taken together, the data indicates that constriction of the cell envelope is brought about by (at least) two spatially separated complexes.

Solntsev, AS, Kumar, P, Pertsch, T, Sukhorukov, AA & Setzpfandt, F 2018, 'LiNbO3 waveguides for integrated SPDC spectroscopy', APL Photonics, vol. 3, no. 2, pp. 021301-021301.
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Spontaneous parametric down-conversion (SPDC) spectroscopy using photon pairs is a promising avenue towards affordable mid-infrared (MIR) spectroscopy. Here, we experimentally investigate the feasibility of using periodically poled waveguides in lithium niobate for SPDC spectroscopy applications. We find the waveguides suitable to generate wavelength non-degenerate photon pairs with one photon in the MIR spectral range with high fluence. We use this to determine the cutoff wavelengths of the waveguide mode in the MIR by performing only measurements in the near-infrared spectral range.

Solowij, N, Broyd, SJ, Beale, C, Prick, J-A, Greenwood, L-M, van Hell, H, Suo, C, Galettis, P, Pai, N, Fu, S, Croft, RJ, Martin, JH & Yücel, M 2018, 'Therapeutic Effects of Prolonged Cannabidiol Treatment on Psychological Symptoms and Cognitive Function in Regular Cannabis Users: A Pragmatic Open-Label Clinical Trial', Cannabis and Cannabinoid Research, vol. 3, no. 1, pp. 21-34.
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Introduction: Chronic cannabis use has been associated with impaired cognition and elevated psychological symptoms, particularly psychotic-like experiences. While Δ9-tetrahydrocannabinol (THC) is thought to be primarily responsible for these deleterious effects, cannabidiol (CBD) is purported to have antipsychotic properties and to ameliorate cognitive, symptomatic, and brain harms in cannabis users. However, this has never been tested in a prolonged administration trial in otherwise healthy cannabis users. Here, we report the first study of prolonged CBD administration to a community sample of regular cannabis users in a pragmatic trial investigating potential restorative effects of CBD on psychological symptoms and cognition. Materials and Methods: Twenty frequent cannabis users (16 male, median age 25 years) underwent a 10-week open-label trial of 200 mg of daily oral CBD treatment, while continuing to use cannabis as usual. The majority of participants were daily cannabis users who had used cannabis for several years (median 5.5 years of regular use). Participants underwent psychological and cognitive assessments at baseline (BL) and post-treatment (PT) and were monitored weekly throughout the trial. Results: CBD was well tolerated with no reported side effects; however, participants retrospectively reported reduced euphoria when smoking cannabis. No impairments to cognition were found, nor were there deleterious effects on psychological function. Importantly, participants reported significantly fewer depressive and psychotic-like symptoms at PT relative to BL, and exhibited improvements in attentional switching, verbal learning, and memory. Increased plasma CBD concentrations were associated with improvements in attentional control and beneficial changes in psychological symptoms. Greater benefits were observed in dependent than in nondependent cannabis users. Conclusions: Prolonged CBD treatment appears to have promising therapeutic effects for im...

Song, J, Zhang, C, Guo, X, Zhang, J, Luo, L, Liu, H, Wang, F & Wang, G 2018, 'Entrapping polysulfides by using ultrathin hollow carbon sphere-functionalized separators in high-rate lithium-sulfur batteries', Journal of Materials Chemistry A, vol. 6, no. 34, pp. 16610-16616.
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Novel ultrathin hollow carbon spheres with a nonporous shell are employed as polysulfide reservoirs to improve the overall performance of Li-S batteries.

Song, L, Guanter, L, Guan, K, You, L, Huete, A, Ju, W & Zhang, Y 2018, 'Satellite sun‐induced chlorophyll fluorescence detects early response of winter wheat to heat stress in the Indian Indo‐Gangetic Plains', Global Change Biology, vol. 24, no. 9, pp. 4023-4037.
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AbstractExtremely high temperatures represent one of the most severe abiotic stresses limiting crop productivity. However, understanding crop responses to heat stress is still limited considering the increases in both the frequency and severity of heat wave events under climate change. This limited understanding is partly due to the lack of studies or tools for the timely and accurate monitoring of crop responses to extreme heat over broad spatial scales. In this work, we use novel spaceborne data of sun‐induced chlorophyll fluorescence (SIF), which is a new proxy for photosynthetic activity, along with traditional vegetation indices (Normalized Difference Vegetation Index NDVI and Enhanced Vegetation Index EVI) to investigate the impacts of heat stress on winter wheat in northwestern India, one of the world's major wheat production areas. In 2010, an abrupt rise in temperature that began in March adversely affected the productivity of wheat and caused yield losses of 6% compared to previous year. The yield predicted by satellite observations of SIF decreased by approximately 13.9%, compared to the 1.2% and 0.4% changes in NDVI and EVI, respectively. During early stage of this heat wave event in early March 2010, the SIF observations showed a significant reduction and earlier response, while NDVI and EVI showed no changes and could not capture the heat stress until late March. The spatial patterns of SIF anomalies closely tracked the temporal evolution of the heat stress over the study area. Furthermore, our results show that SIF can provide large‐scale, physiology‐related wheat stress response as indicated by the larger reduction in fluorescence yield (SIFyield) than fraction of photosynthetically active radiation during the grain‐filling phase, which may have eventually led to the reduction in wheat yield in 2010. This study implies that satellite observations of SIF have great potential to detect ...

Sornalingam, K, McDonagh, A, Zhou, JL, Johir, MAH & Ahmed, MB 2018, 'Photocatalysis of estrone in water and wastewater: Comparison between Au-TiO2 nanocomposite and TiO2, and degradation by-products', Science of The Total Environment, vol. 610-611, pp. 521-530.
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© 2017 Elsevier B.V. Gold-modified TiO2 (Au-TiO2) photocatalysts were utilised for the degradation of estrone (E1), a major endocrine disrupting chemical in water and wastewater. Au-TiO2 catalysts were synthesised by a deposition-precipitation method with gold loadings of 0–8% (wt%). The Au-TiO2 nanocomposite exhibited superior activity compared to P25 TiO2 under UVA (λ = 365 nm), cool white (λ > 420 nm) and green (λ = 523 nm) light emitting diodes (LEDs), for treating 1 mg l− 1 of E1. The 4 wt% Au loading was found to produce the best photocatalytic activity with a rate constant of 2.44 ± 0.36 h− 1, compared to 0.06 ± 0.01 h− 1 for P25 TiO2, under visible light. In total 4 by-products were identified, one from negative ionization mode (m/z = 269) and three from positive ionization mode (m/z = 287) during photocatalysis, which were also degraded with time by Au-TiO2. For different water matrices, the photodegradation rate of E1 decreased in the order: ultrapure water > synthetic wastewater ≈ wastewater effluent from membrane bio-reactor. Overall, 4 wt% Au-TiO2 demonstrated superior performance compared to P25 TiO2 in water and wastewater.

Spain, M, Wong, JK-H, Nagalingam, G, Batten, JM, Hortle, E, Oehlers, SH, Jiang, XF, Murage, HE, Orford, JT, Crisologo, P, Triccas, JA, Rutledge, PJ & Todd, MH 2018, 'Antitubercular Bis-Substituted Cyclam Derivatives: Structure–Activity Relationships and in Vivo Studies', Journal of Medicinal Chemistry, vol. 61, no. 8, pp. 3595-3608.
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Speed, T 2018, 'PETER GAVIN HALL', Statistica Sinica.
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Speer, MS 2018, 'Digitization of weekly Murrumbidgee River heights at Hay South Eastern Australia 1873–2017', Geoscience Data Journal, vol. 5, no. 1, pp. 9-13.
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Long‐term, high‐frequency river height measurements provide a direct method of relating changes in local water availability in a catchment to such phenomena as climate and changes in land use. Here, digitized weekly river height data from the Murrumbidgee River at Hay in south eastern Australia are presented for the first time covering the start of record from November 1873 to June 2017. There are two gauge board locations: (a) The town gauge at the southern edge of the township with data until March 1983, and (b) the Hay Private Irrigation District (PID) gauge on the north eastern outskirts of Hay about 2 km upstream from the Hay town gauge. There is a data overlap of about 13 years for the two locations. The underlying data quality is good taking into account missing values, outliers, continuity between the two gauge locations and measurement practice. The weekly data are available in both annual and seasonal files.Open PracticesThis article has earned an Open Data badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at http://doi.org/10.5281/zenodo.1184869. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.

Spooner, MJ & Gale, PA 2018, 'A tripodal tris-selenourea anion transporter matches the activity of its thio- analogue but shows distinct selectivity', Supramolecular Chemistry, vol. 30, no. 5-6, pp. 514-519.
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Srivastava, A, Sahoo, B, Raghuwanshi, NS & Chatterjee, C 2018, 'Modelling the dynamics of evapotranspiration using Variable Infiltration Capacity model and regionally calibrated Hargreaves approach', Irrigation Science, vol. 36, no. 4-5, pp. 289-300.
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Computation of reference evapotranspiration (ETO) at different spatiotemporal scales is constrained by limited in situ meteorological data availability which, in turn, led to alternate ET estimation methods using the commonly available meteorological data of maximum and minimum temperatures. In this study, the Hargreaves–Samani model and the water budget approach of the Variable Infiltration Capacity (VIC-3L) land surface model was evaluated for grid-scale actual ET estimation using the benchmark FAO-56 Penman–Monteith (PM) equation and crop coefficient relationships. These approaches were field-tested in the Kangsabati River basin in eastern India, a tropical monsoon-type climate region with dominant paddy land uses. The results revealed that the VIC model could estimate the grid-scale ET reasonably well; however, the corresponding estimates by the Hargreaves method were highly overestimated. To enhance the field applicability of the Hargreaves method for data-scarce regions, this method was coupled with a genetic algorithm-based bias correction approach that improved the Nash–Sutcliffe efficiency significantly. Hence, this study reveals that there is a need for regional-scale standardization of the Hargreaves ET estimates using the FAO-56 PM, lysimeter data or the VIC-3L model.

Stangenberg, S, Saad, S, Schilter, HC, Zaky, A, Gill, A, Pollock, CA & Wong, MG 2018, 'Lysyl oxidase-like 2 inhibition ameliorates glomerulosclerosis and albuminuria in diabetic nephropathy', Scientific Reports, vol. 8, no. 1.
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AbstractDiabetic nephropathy is characterised by the excessive amount of extracellular matrix in glomeruli and tubulointerstitial space. Lysyl oxidase-like 2 (LOXL2) is elevated in renal fibrosis and known to play key roles in ECM stabilisation by facilitating collagen cross-links, epithelial to mesenchymal transition and myofibroblast activation. Thus, targeting LOXL2 may prove to be a useful strategy to prevent diabetic nephropathy. We explored the renoprotective effect of a selective small molecule LOXL2 inhibitor (PXS-S2B) in a streptozotocin-induced diabetes model. Diabetic mice were treated with PXS-S2B for 24 weeks and outcomes compared with untreated diabetic mice and with telmisartan treated animals as comparator of current standard of care. Diabetic mice had albuminuria, higher glomerulosclerosis scores, upregulation of fibrosis markers and increased renal cortical LOXL2 expression. Treatment with PXS-S2B reduced albuminuria and ameliorated glomerulosclerosis. This was associated with reduced expression of glomerular fibronectin and tubulointerstitial collagen I. The renoprotective effects of both PXS-S2B and telmisartan were more marked in the glomerular compartment than in the tubulointerstitial space. The study reveals that LOXL2 inhibition was beneficial in preserving glomerular structure and function. Thus, LOXL2 may be a potential therapeutic target in diabetic nephropathy.

Stewart, J, Hegarty, A-M, Young, C & Fowler, AM 2018, 'Sex-specific differences in growth, mortality and migration support population resilience in the heavily exploited migratory marine teleost Mugil cephalus (Linnaeus 1758)', Marine and Freshwater Research, vol. 69, no. 3, pp. 385-385.
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Understanding mechanisms supporting the resilience of exploited fish populations is fundamental to sustainable management. Herein we identify sex-specific differences in life history traits that confer resilience in the heavily exploited population of Mugil cephalus along eastern Australia. M. cephalus in this region emigrate from estuaries and undergo an annual northerly spawning migration that is dominated by males. Males mature, on average, at younger ages than females and were most abundant in the spawning migration at age-4, whereas females were most abundant at age-5. Females grew significantly faster and larger than males, with both sexes being aged up to 14 years. These sex-specific differences relate directly to the population stability of M. cephalus under the reproductive strategy of a spawning migration. Males participate in the spawning migration at younger ages and in greater numbers than females to ensure a sufficient number of males for successful spawning. Females partition more energy to growth than males, maturing and participating in the spawning migration at older ages and larger sizes. The larger body size of females is related to increased fecundity, increased survivorship and more efficient swimming ability. These traits, combined with population strategies of both delayed and skipped spawning, convey substantial resilience.

Stifter, SA, Matthews, AY, Mangan, NE, Fung, KY, Drew, A, Tate, MD, Soares da Costa, TP, Hampsey, D, Mayall, J, Hansbro, PM, Garcia Minambres, A, Eid, SG, Mak, J, Scoble, J, Lovrecz, G, deWeerd, NA & Hertzog, PJ 2018, 'Defining the distinct, intrinsic properties of the novel type I interferon, IFNϵ', Journal of Biological Chemistry, vol. 293, no. 9, pp. 3168-3179.
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© 2018 by The American Society for Biochemistry and Molecular Biology, Inc. The type I interferons (IFNs) are a family of cytokines with diverse biological activities, including antiviral, antiproliferative, and immunoregulatory functions. The discovery of the hormonally regulated, constitutively expressed IFNϵ has suggested a function for IFNs in reproductive tract homeostasis and protection from infections, but its intrinsic activities are untested. We report here the expression, purification, and functional characterization of murine IFNϵ (mIFNϵ). Recombinant mIFNϵ (rmIFNϵ) exhibited an α-helical fold characteristic of type I IFNs and bound to IFNα/β receptor 1 (IFNAR1) and IFNAR2, but, unusually, it had a preference for IFNAR1. Nevertheless, rmIFNϵ induced typical type I IFN signaling activity, including STAT1 phosphorylation and activation of canonical type I IFN signaling reporters, demonstrating that it uses the JAK-STAT signaling pathway. We also found that rmIFNϵ induces the activation of T, B, and NK cells and exhibits antiviral, antiproliferative, and antibacterial activities typical of type I IFNs, albeit with 100-1000-fold reduced potency compared with rmIFNα1 and rmIFNβ. Surprisingly, although the type I IFNs generally do not display cross-species activities, rmIFNϵ exhibited high antiviral activity on human cells, suppressing HIV replication and inducing the expression of known HIV restriction factors in human lymphocytes. Our findings define the intrinsic properties of murine IFNϵ, indicating that it distinctly interacts with IFNAR and elicits pathogen-suppressing activity with a potency enabling host defense but with limited toxicity, appropriate for a protein expressed constitutively in a sensitive mucosal site, such as the reproductive tract.

Stiller, B, Merklein, M, Wolff, C, Vu, K, Ma, P, Poulton, CG, Madden, SJ & Eggleton, BJ 2018, 'On-chip multi-stage optical delay based on cascaded Brillouin light storage', Optics Letters, vol. 43, no. 18, pp. 4321-4321.
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© 2018 Optical Society of America. Storing and delaying optical signals plays a crucial role in data centers, phased array antennas, communication, and future computing architectures. Here, we show a delay scheme based on cascaded Brillouin light storage that achieves multi-stage delay at arbitrary positions within a photonic integrated circuit. Importantly these multiple resonant transfers between the optical and acoustic domain are controlled solely via external optical control pulses, allowing cascading of the delay without the need of aligning multiple structural resonances along the optical circuit.

Su, D, Zhou, D, Wang, C & Wang, G 2018, 'Lithium‐Sulfur Batteries: Toward High Performance Lithium–Sulfur Batteries Based on Li₂S Cathodes and Beyond: Status, Challenges, and Perspectives (Adv. Funct. Mater. 38/2018)', Advanced Functional Materials, vol. 28, no. 38, pp. 1870273-1870273.
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Su, D, Zhou, D, Wang, C & Wang, G 2018, 'Toward High Performance Lithium–Sulfur Batteries Based on Li₂S Cathodes and Beyond: Status, Challenges, and Perspectives', Advanced Functional Materials, vol. 28, no. 38, pp. 1800154-1800154.
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AbstractLithium sulfur (Li–S) batteries are attracting ever‐increasing interests as a new generation rechargeable battery system with high energy density and low cost. Li–S batteries will fulfill their theoretical potential if the problem of polysulfides shuttle effect can be solved. Therefore, tremendous efforts have been devoted to overcoming this problem from the aspects of physical confinement and chemisorption of polysulfides. Recently, it is discovered that replacing sulfur cathodes with lithium sulfide (Li2S) can not only largely avoid the volume expansion issue during cycling, but it can also work with anode materials other than lithium metal to eliminate serious safety concerns for traditional Li–S batteries. However, there are many challenges for developing practical Li metal‐free Li–S battery systems, because Li2S‐based cathode materials are moisture‐sensitive and prelithiation of the non‐Li metal anode materials is usually required for practical applications. This study reviews the recent advances of Li‐S batteries based on Li2S cathode with features of improved safety, high Coulombic efficiency, and high energy density. The electrode activation processes are also discussed, which is critical for achieving high performances. It is anticipated that the extensive efforts will lead to breakthroughs for the development of Li2S cathode ‐based Li‐S batteries.

Subedi, D, Vijay, AK, Kohli, GS, Rice, SA & Willcox, M 2018, 'Association between possession of ExoU and antibiotic resistance in Pseudomonas aeruginosa', PLOS ONE, vol. 13, no. 9, pp. e0204936-e0204936.
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Virulent strains of Pseudomonas aeruginosa are often associated with an acquired cytotoxic protein, exoenzyme U (ExoU) that rapidly destroys the cell membranes of host cells by its phospholipase activity. Strains possessing the exoU gene are predominant in eye infections and are more resistant to antibiotics. Thus, it is essential to understand treatment options for these strains. Here, we have investigated the resistance profiles and genes associated with resistance for fluoroquinolone and beta-lactams. A total of 22 strains of P. aeruginosa from anterior eye infections, microbial keratitis (MK), and the lungs of cystic fibrosis (CF) patients were used. Based on whole genome sequencing, the prevalence of the exoU gene was 61.5% in MK isolates whereas none of the CF isolates possessed this gene. Overall, higher antibiotic resistance was observed in the isolates possessing exoU. Of the exoU strains, all except one were resistant to fluoroquinolones, 100% were resistant to beta-lactams. 75% had mutations in quinolone resistance determining regions (T81I gyrA and/or S87L parC) which correlated with fluoroquinolone resistance. In addition, exoU strains had mutations at K76Q, A110T, and V126E in ampC, Q155I and V356I in ampR and E114A, G283E, and M288R in mexR genes that are associated with higher beta-lactamase and efflux pump activities. In contrast, such mutations were not observed in the strains lacking exoU. The expression of the ampC gene increased by up to nine-fold in all eight exoU strains and the ampR was upregulated in seven exoU strains compared to PAO1. The expression of mexR gene was 1.4 to 3.6 fold lower in 75% of exoU strains. This study highlights the association between virulence traits and antibiotic resistance in pathogenic P. aeruginosa.

Subedi, D, Vijay, AK, Kohli, GS, Rice, SA & Willcox, M 2018, 'Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites', Scientific Reports, vol. 8, no. 1, pp. 15668-15668.
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AbstractThe large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.

Subedi, D, Vijay, AK, Kohli, GS, Rice, SA & Willcox, M 2018, 'Nucleotide sequence analysis of NPS-1 β-lactamase and a novel integron (In1427)-carrying transposon in an MDR Pseudomonas aeruginosa keratitis strain', Journal of Antimicrobial Chemotherapy, vol. 73, no. 6, pp. 1724-1726.
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Subramanian, S, Ugoya, SO, Zhao, Z, McRobb, LS, Grau, GE, Combes, V, Inglis, DW, Gauden, AJ, Lee, VS, Moutrie, V, Santos, ED & Stoodley, MA 2018, 'Stable thrombus formation on irradiated microvascular endothelial cells under pulsatile flow: Pre-testing annexin V-thrombin conjugate for treatment of brain arteriovenous malformations', Thrombosis Research, vol. 167, pp. 104-112.
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© 2018 Elsevier Ltd Background: Our goal is to develop a vascular targeting treatment for brain arteriovenous malformations (AVMs). Externalized phosphatidylserine has been established as a potential biomarker on the endothelium of irradiated AVM blood vessels. We hypothesize that phosphatidylserine could be selectively targeted after AVM radiosurgery with a ligand-directed vascular targeting agent to achieve localized thrombosis and rapid occlusion of pathological AVM vessels. Objective: The study aim was to establish an in vitro parallel-plate flow chamber to test the efficacy of a pro-thrombotic conjugate targeting phosphatidylserine. Methods: Conjugate was prepared by Lys-Lys cross-linking of thrombin with the phosphatidylserine-targeting ligand, annexin V. Cerebral microvascular endothelial cells were irradiated (5, 15, and 25 Gy) and after 1 or 3 days assembled in a parallel-plate flow chamber containing whole human blood and conjugate (1.25 or 2.5 μg/mL). Confocal microscopy was used to assess thrombus formation after flow via binding and aggregation of fluorescently-labelled platelets and fibrinogen. Results and conclusions: The annexin V-thrombin conjugate induced rapid thrombosis (fibrin deposition) on irradiated endothelial cells under shear stress in the parallel-plate flow device. Unconjugated, non-targeting thrombin did not induce fibrin deposition. A synergistic interaction between radiation and conjugate dose was observed. Thrombosis was greatest at the highest combined doses of radiation (25 Gy) and conjugate (2.5 μg/mL). The parallel-plate flow system provides a rapid method to pre-test pro-thrombotic vascular targeting agents. These findings validate the translation of the annexin V-thrombin conjugate to pre-clinical studies.

Sukjamnong, S, Chan, YL, Zakarya, R, Nguyen, LT, Anwer, AG, Zaky, AA, Santiyanont, R, Oliver, BG, Goldys, E, Pollock, CA, Chen, H & Saad, S 2018, 'MitoQ supplementation prevent long-term impact of maternal smoking on renal development, oxidative stress and mitochondrial density in male mice offspring', Scientific Reports, vol. 8, no. 1.
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AbstractTo investigate the effect of maternal MitoQ treatment on renal disorders caused by maternal cigarette smoke exposure (SE). We have demonstrated that maternal SE during pregnancy increases the risk of developing chronic kidney disease (CKD) in adult offspring. Mitochondrial oxidative damage contributes to the adverse effects of maternal smoking on renal disorders. MitoQ is a mitochondria-targeted antioxidant that has been shown to protect against oxidative damage-related pathologies in many diseases. Female Balb/c mice (8 weeks) were divided into Sham (exposed to air), SE (exposed to cigarette smoke) and SEMQ (exposed to cigarette smoke with MitoQ supplemented from mating) groups. Kidneys from the mothers were collected when the pups weaned and those from the offspring were collected at 13 weeks. Maternal MitoQ supplementation during gestation and lactation significantly reversed the adverse impact of maternal SE on offspring’s body weight, kidney mass and renal pathology. MitoQ administration also significantly reversed the impact of SE on the renal cellular mitochondrial density and renal total reactive oxygen species in both the mothers and their offspring in adulthood. Our results suggested that MitoQ supplementation can mitigate the adverse impact of maternal SE on offspring’s renal pathology, renal oxidative stress and mitochondrial density in mice offspring.

Sun, B, Li, P, Zhang, J, Wang, D, Munroe, P, Wang, C, Notten, PHL & Wang, G 2018, 'Dendrite‐Free Sodium‐Metal Anodes for High‐Energy Sodium‐Metal Batteries', Advanced Materials, vol. 30, no. 29, pp. 1801334-1801334.
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AbstractSodium (Na) metal is one of the most promising electrode materials for next‐generation low‐cost rechargeable batteries. However, the challenges caused by dendrite growth on Na metal anodes restrict practical applications of rechargeable Na metal batteries. Herein, a nitrogen and sulfur co‐doped carbon nanotube (NSCNT) paper is used as the interlayer to control Na nucleation behavior and suppress the Na dendrite growth. The N‐ and S‐containing functional groups on the carbon nanotubes induce the NSCNTs to be highly “sodiophilic,” which can guide the initial Na nucleation and direct Na to distribute uniformly on the NSCNT paper. As a result, the Na‐metal‐based anode (Na/NSCNT anode) exhibits a dendrite‐free morphology during repeated Na plating and striping and excellent cycling stability. As a proof of concept, it is also demonstrated that the electrochemical performance of sodium–oxygen (Na–O2) batteries using the Na/NSCNT anodes show significantly improved cycling performances compared with Na–O2 batteries with bare Na metal anodes. This work opens a new avenue for the development of next‐generation high‐energy‐density sodium‐metal batteries.

Sun, B, Pompe, C, Dongmo, S, Zhang, J, Kretschmer, K, Schröder, D, Janek, J & Wang, G 2018, 'Challenges for Developing Rechargeable Room‐Temperature Sodium Oxygen Batteries', Advanced Materials Technologies, vol. 3, no. 9, pp. 1800110-1800110.
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AbstractThe development of high energy‐density and low‐cost energy storage devices requires new chemistry beyond the horizon of current state‐of‐the‐art lithium‐ion batteries. Recently, sodium/oxygen (Na/O2) batteries have attracted great attention as one possible battery type among the new generation of rechargeable batteries. They convince with superior energy density, a relatively simple cell reaction, and abundance of sodium. Research on Na/O2 batteries has progressed quickly in recent years. However, a fundamental understanding underpinning the complex chemical/electrochemical side reactions is still insufficient, and many challenges remain unsolved for real practical applications. Herein, recent achievements and remaining issues for the development of rechargeable Na/O2 batteries are summarized. The discussion focuses on cell reaction mechanisms as well as cathode materials, sodium anodes, and electrolytes as key components of this type of battery. Furthermore, perspectives for future research and technological advances of Na/O2 batteries are outlined.

Sun, B, Pompe, C, Dongmo, S, Zhang, J, Kretschmer, K, Schröder, D, Janek, J & Wang, G 2018, 'Next‐Generation Rechargeable Batteries: Challenges for Developing Rechargeable Room‐Temperature Sodium Oxygen Batteries (Adv. Mater. Technol. 9/2018)', Advanced Materials Technologies, vol. 3, no. 9, pp. 1870035-1870035.
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Sun, R, Carroll, RJ, Christiani, DC & Lin, X 2018, 'Testing for Gene–Environment Interaction under Exposure Misspecification', Biometrics, vol. 74, no. 2, pp. 653-662.
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Summary Complex interplay between genetic and environmental factors characterizes the etiology of many diseases. Modeling gene–environment (GxE) interactions is often challenged by the unknown functional form of the environment term in the true data-generating mechanism. We study the impact of misspecification of the environmental exposure effect on inference for the GxE interaction term in linear and logistic regression models. We first examine the asymptotic bias of the GxE interaction regression coefficient, allowing for confounders as well as arbitrary misspecification of the exposure and confounder effects. For linear regression, we show that under gene–environment independence and some confounder-dependent conditions, when the environment effect is misspecified, the regression coefficient of the GxE interaction can be unbiased. However, inference on the GxE interaction is still often incorrect. In logistic regression, we show that the regression coefficient is generally biased if the genetic factor is associated with the outcome directly or indirectly. Further, we show that the standard robust sandwich variance estimator for the GxE interaction does not perform well in practical GxE studies, and we provide an alternative testing procedure that has better finite sample properties.

Sun, S, Noorian, P & McDougald, D 2018, 'Dual Role of Mechanisms Involved in Resistance to Predation by Protozoa and Virulence to Humans', Frontiers in Microbiology, vol. 9, no. MAY.
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© 2018 Sun, Noorian and McDougald. Most opportunistic pathogens transit in the environment between hosts and the environment plays a significant role in the evolution of protective traits. The coincidental evolution hypothesis suggests that virulence factors arose as a response to other selective pressures rather for virulence per se. This idea is strongly supported by the elucidation of bacterial-protozoal interactions. In response to protozoan predation, bacteria have evolved various defensive mechanisms which may also function as virulence factors. In this review, we summarize the dual role of factors involved in both grazing resistance and human pathogenesis, and compare the traits using model intracellular and extracellular pathogens. Intracellular pathogens rely on active invasion, blocking of the phagosome and lysosome fusion and resistance to phagocytic digestion to successfully invade host cells. In contrast, extracellular pathogens utilize toxin secretion and biofilm formation to avoid internalization by phagocytes. The complexity and diversity of bacterial virulence factors whose evolution is driven by protozoan predation, highlights the importance of protozoa in evolution of opportunistic pathogens.

Sun, Y, Pham, AN, Hare, DJ & Waite, TD 2018, 'Kinetic Modeling of pH-Dependent Oxidation of Dopamine by Iron and Its Relevance to Parkinson's Disease', Frontiers in Neuroscience, vol. 12, no. NOV.
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© 2007 - 2018 Frontiers Media S.A. Parkinson's disease is the second most common neurodegenerative disease. While age is the most significant risk factor, the exact cause of this disease and the most effective approaches to mitigation remain unclear. It has long been proposed that dopamine may play a role in the pathology of Parkinson's disease in view of its ability to generate both protein-modifying quinones such as aminochrome and reactive oxygen species, especially in the presence of pathological iron accumulation in the primary site of neuron loss. Given the clinically measured acidosis of post-mortem Parkinson's disease brain tissue, the interaction between dopamine and iron was investigated over a pH range of 7.4 to 6.5 with emphasis on the accumulation of toxic quinones and generation of reactive oxygen species. Our results show that the presence of iron accelerates the formation of aminochrome with ferrous iron (Fe[II]) being more efficient in this regard than ferric iron (Fe[III]). Our results further suggest that a reduced aminochrome rearrangement rate coupled with an enhanced turnover rate of Fe[II] as a result of brain tissue acidosis could result in aminochrome accumulation within cells. Additionally, under these conditions, the enhanced redox cycling of iron in the presence of dopamine aggravates oxidative stress as a result of the production of damaging reactive species, including hydroxyl radicals.

Sun, Y, Zhang, W, Wang, B, Xu, X, Chou, J, Shimoni, O, Ung, AT & Jin, D 2018, 'A supramolecular self-assembly strategy for upconversion nanoparticle bioconjugation', Chemical Communications, vol. 54, no. 31, pp. 3851-3854.
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An efficient surface modification and bioconjugation strategy for upconversion nanoparticles is reported via supramolecular host–guest self-assembly.

Sunkara, KP, Gupta, G, Hansbro, PM, Dua, K & Bebawy, M 2018, 'Functional relevance of SATB1 in immune regulation and tumorigenesis', Biomedicine & Pharmacotherapy, vol. 104, pp. 87-93.
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© 2018 The Special AT-rich Sequence Binding Protein 1 (SATB1) is a chromatin organiser and transcription factor which regulates numerous cellular processes such as differentiation, proliferation and apoptosis through effects on gene expression. SATB1 undergoes various post-translational modifications, which determine its interaction with co-activators and co-repressors to induce regulation of gene transcription. SATB1 is an identified oncogene, its increased expression is associated with poor prognosis in many cancers. This paper provides a review on SATB1-mediated immune responses and on its target genes in the context of tumorigenesis and tumour progression. Specifically, we discuss the role of SATB1 in tumour immunity, Epithelial to Mesenchymal Transition (EMT), metastasis and multidrug resistance. Therapeutic targeting of aberrant SATB1 may be an important strategy in the treatment of cancer.

Tabassum, H, Zou, R, Mahmood, A, Liang, Z, Wang, Q, Zhang, H, Gao, S, Qu, C, Guo, W & Guo, S 2018, 'A Universal Strategy for Hollow Metal Oxide Nanoparticles Encapsulated into B/N Co‐Doped Graphitic Nanotubes as High‐Performance Lithium‐Ion Battery Anodes', Advanced Materials, vol. 30, no. 8, pp. 1705441-1705441.
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AbstractYolk–shell nanostructures have received great attention for boosting the performance of lithium‐ion batteries because of their obvious advantages in solving the problems associated with large volume change, low conductivity, and short diffusion path for Li+ ion transport. A universal strategy for making hollow transition metal oxide (TMO) nanoparticles (NPs) encapsulated into B, N co‐doped graphitic nanotubes (TMO@BNG (TMO = CoO, Ni2O3, Mn3O4) through combining pyrolysis with an oxidation method is reported herein. The as‐made TMO@BNG exhibits the TMO‐dependent lithium‐ion storage ability, in which CoO@BNG nanotubes exhibit highest lithium‐ion storage capacity of 1554 mA h g−1 at the current density of 96 mA g−1, good rate ability (410 mA h g−1 at 1.75 A g−1), and high stability (almost 96% storage capacity retention after 480 cycles). The present work highlights the importance of introducing hollow TMO NPs with thin wall into BNG with large surface area for boosting LIBs in the terms of storage capacity, rate capability, and cycling stability.

Tai, MC, Gentle, AR, Arnold, MD & Cortie, MB 2018, 'Spontaneous growth of polarizing refractory metal ‘nano-fins’', Nanotechnology, vol. 29, no. 10, pp. 105702-105702.
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© 2018 IOP Publishing Ltd. Traditional polymer polarizers degrade in harsh environments and at high temperatures, reducing the polarization effect. In contrast, polarizers produced with refractory metals have vastly improved thermal stability and resistance to harsh environments but are expensive to fabricate. Here we demonstrate prototype refractory metal wire grid polarizers produced by co-sputtering molybdenum and aluminum under specific conditions. Removal of the aluminum through selective dissolution enables the nanostructure array to transmit light. The polarization spans 500-1100 nm and the extinction ratio significantly increases to >100. Possessing broadband polarization and sufficient extinction ratios, the new polarizing film has potential applications in coatings for sunglasses, windows, pyrometers, scientific instruments, and LCD panels.

Takahashi, S, Osabe, K, Fukushima, N, Takuno, S, Miyaji, N, Shimizu, M, Takasaki-Yasuda, T, Suzuki, Y, Dennis, ES, Seki, M & Fujimoto, R 2018, 'Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.', DNA Research, vol. 25, no. 5, pp. 511-520.
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Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant's phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24 nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24 nt siRNAs and H3K9me2 are discussed.

Tamburic, B, Evenhuis, CR, Crosswell, JR & Ralph, PJ 2018, 'An empirical process model to predict microalgal carbon fixation rates in photobioreactors', Algal Research, vol. 31, pp. 334-346.
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© 2018 Elsevier B.V. An empirical process model was developed to infer the instantaneous net photosynthesis and carbon fixation rates from continuous pH and dissolved oxygen measurements during microalgal cultivation in photobioreactors. The model is based on the physical and chemical processes that govern the relationship between inorganic carbon supplied to a microalgal culture and the organic carbon fixed into microalgal biomass, with a particular focus on carbonate chemistry and mass transfer. Bayesian statistics were used to estimate the uncertainty in state variables, such as pH, net photosynthesis rate, and bicarbonate ion concentration, based on the constraints imposed by prior knowledge about these variables. The model was verified by batch-culturing the chlorophyte microalga Chlorella vulgaris in a photobioreactor under both bicarbonate-replete and bicarbonate-limiting conditions in order to test its predictive ability under different operational settings. The replicate photobioreactors were set up to simulate a scaled-down vertical cross-section of a typical raceway pond. This model could be used to test the activity and efficiency of carbon concentrating mechanisms in different microalgal species. It also provides a detailed understanding of how the rate of photosynthesis depends on dissolved inorganic carbon concentration, which could lead to better management of carbon supply in large-scale microalgal cultivation facilities.

Tang, X, Guo, X, Wu, W & Wang, G 2018, '2D Metal Carbides and Nitrides (MXenes) as High‐Performance Electrode Materials for Lithium‐Based Batteries', Advanced Energy Materials, vol. 8, no. 33, pp. 1801897-1801897.
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AbstractTremendous efforts are devoted to developing advanced electrode materials with superior electrochemical performance, high energy density, and high power density for energy storage and conversion. Two‐dimensional (2D) materials, owing to their unique properties, have shown great potential for energy storage. Following the discovery of graphene, a new family of 2D transition metal carbides/nitrides, MXenes, derived from MAX phase precursors, have attracted extensive attention in recent years. The superior physical and chemical properties of MXenes include high mechanical strength, excellent electrical conductivity, multiple possible surface terminations, hydrophilic features, superior specific surface area, and the ability to accommodate intercalants. When applied as electrodes in lithium‐based batteries, MXenes have demonstrated excellent performance. In this progress report, the authors summarize the recent advances of MXenes and MXene‐based composites in terms of synthesis strategies, morphology engineering, physical/chemical properties, and their applications in lithium‐ion batteries and lithium–sulfur batteries. Furthermore, challenges and perspectives for MXenes and MXene‐based composites for lithium‐based energy storage devices are also outlined.

Tang, X, Liu, H, Guo, X, Wang, S, Wu, W, Mondal, AK, Wang, C & Wang, G 2018, 'A novel lithium-ion hybrid capacitor based on an aerogel-like MXene wrapped Fe₂O₃nanosphere anode and a 3D nitrogen sulphur dual-doped porous carbon cathode', Materials Chemistry Frontiers, vol. 2, no. 10, pp. 1811-1821.
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A novel lithium-ion hybrid capacitor was assembled based on an aerogel-like Ti₃C₂T_x@Fe₂O₃anode and a 3-D dual-doped porous carbon cathode.

Tang, X, Liu, H, Su, D, Notten, PHL & Wang, G 2018, 'Hierarchical sodium-rich Prussian blue hollow nanospheres as high-performance cathode for sodium-ion batteries', Nano Research, vol. 11, no. 8, pp. 3979-3990.
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© 2018, Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature. Recently, Prussian blue and its analogues (PBAs) have attracted tremendous attention as cathode materials for sodium-ion batteries because of their good cycling performance, low cost, and environmental friendliness. However, they still suffer from kinetic problems associated with the solid-state diffusion of sodium ions during charge and discharge processes, which leads to low specific capacity and poor rate performances. In this work, novel sodium iron hexacyanoferrate nanospheres with a hierarchical hollow architecture have been fabricated as cathode material for sodium-ion batteries by a facile template method. Due to the unique hollow sphere morphology, sodium iron hexacyanoferrate nanospheres can provide large numbers of active sites and high diffusion dynamics for sodium ions, thus delivering a high specific capacity (142 mAh/g), a superior rate capability, and an excellent cycling stability. Furthermore, the sodium insertion/extraction mechanism has been studied by in situ X-ray diffraction, which provides further insight into the crystal structure change of the sodium iron hexacyanoferrate nanosphere cathode material during charge and discharge processes.

Tang, Z, Jin, W, Sun, R, Liao, Y, Zhen, T, Chen, H, Wu, Q, Gou, L & Li, C 2018, 'Improved thermostability and enzyme activity of a recombinant phyA mutant phytase from Aspergillus niger N25 by directed evolution and site-directed mutagenesis', Enzyme and Microbial Technology, vol. 108, pp. 74-81.
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© 2017 Elsevier Inc. We previously constructed three recombinant phyA mutant strains (PP-NPm-8, PP-NPep-6A and I44E/T252R-PhyA), showing improved catalytic efficiency or thermostability of Aspergillus niger N25 phytase, by error-prone PCR or site-directed mutagenesis. In this study, directed evolution and site-directed mutagenesis were further applied to improve the modified phytase properties. After one-round error-prone PCR for phytase gene of PP-NPep-6A, a single transformant, T195L/Q368E/F376Y, was obtained with the significant improvements in catalytic efficiency and thermostability. The phytase gene of T195L/Q368E/F376Y, combined with the previous mutant phytase genes of PP-NPep-6A, PP-NPm-8 and I44E/T252R-PhyA, was then sequentially modified by DNA shuffling. Three genetically engineered strains with desirable properties were then obtained, namedQ172R, Q172R/K432R andQ368E/K432R. Among them, Q172R/K432R showed the highest thermostability with the longest half-life and the greatest remaining phytase activity after heat treatment, while Q368E/K432R showed the highest catalytic activity. Five substitutions (Q172R, T195L, Q368E, F376Y, K432R) identified from random mutagenesis were added sequentially to the phytase gene of PP-NPep-6A to investigate how the mutant sites influence the properties of phytase. Characterization and structural analysis demonstrated that these mutations could produce cumulative or synergistic improvements in thermostability or catalytic efficiency of phytase.

Tanner, JD, Deplazes, E & Mancera, RL 2018, 'The Biological and Biophysical Properties of the Spider Peptide Gomesin', Molecules, vol. 23, no. 7, pp. 1733-1733.
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This review summarises the current knowledge of Gomesin (Gm), an 18-residue long, cationic anti-microbial peptide originally isolated from the haemocytes of the Brazilian tarantula Acanthoscurria gomesiana. The peptide shows potent cytotoxic activity against clinically relevant microbes including Gram-positive and Gram-negative bacteria, fungi, and parasites. In addition, Gm shows in-vitro and in-vivo anti-cancer activities against several human and murine cancers. The peptide exerts its cytotoxic activity by permeabilising cell membranes, but the underlying molecular mechanism of action is still unclear. Due to its potential as a therapeutic agent, the structure and membrane-binding properties, as well as the leakage and cytotoxic activities of Gm have been studied using a range of techniques. This review provides a summary of these studies, with a particular focus on biophysical characterisation studies of peptide variants that have attempted to establish a structure-activity relationship. Future studies are still needed to rationalise the binding affinity and cell-type-specific selectivity of Gm and its variants, while more pre-clinical studies are required to develop Gm into a therapeutically useful peptide.

Tanveer Karim, AMM, Rahman, MA, Hossain, MS, Khan, MKR, Rahman, MM, Kamruzzaman, M & Ton‐That, C 2018, 'Multi‐Color Excitonic Emissions in Chemical Dip‐Coated Organolead Mixed‐Halide Perovskite', ChemistrySelect, vol. 3, no. 23, pp. 6525-6530.
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AbstractOrganolead mixed‐halide perovskites capable of emitting multiple colors not only allow the fabrication of compact devices but also improves the functionality of light emitting devices beyond conventional displays. Here we demonstrate a cost‐effective chemical dip‐coating technique to grow highly reproducible methylammonium‐lead‐halide perovskite film, which exhibits highly efficient multi‐color emissions of red, green and ultraviolet. The power‐ and temperature‐resolved cathodoluminescence analyses reveal that these emissions are attributed to localized excitions with thermal activation energies of 27, 29 and 57 meV. The non‐linear fitting of these emission band widths within the frame work of Boson model reveals that excitons are strongly coupled to the lattice with energy of 28 meV, which is consistent with the Raman measurement. This work presents an effective method for the deposition of high‐quality and large‐area perovskite film, which could be useful for high‐performance multi‐color display devices.

Tasena, H, Faiz, A, Timens, W, Noordhoek, J, Hylkema, MN, Gosens, R, Hiemstra, PS, Spira, A, Postma, DS, Tew, GW, Grimbaldeston, MA, van den Berge, M, Heijink, IH & Brandsma, C-A 2018, 'microRNA–mRNA regulatory networks underlying chronic mucus hypersecretion in COPD', European Respiratory Journal, vol. 52, no. 3, pp. 1701556-1701556.
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Chronic mucus hypersecretion (CMH) is a common feature in chronic obstructive pulmonary disease (COPD) and is associated with worse prognosis and quality of life. This study aimed to identify microRNA (miRNA)–mRNA regulatory networks underlying CMH.The expression profiles of miRNA and mRNA in bronchial biopsies from 63 COPD patients were associated with CMH using linear regression. Potential mRNA targets of each CMH-associated miRNA were identified using Pearson correlations. Gene set enrichment analysis (GSEA) and STRING (search tool for the retrieval of interacting genes/proteins) analysis were used to identify key genes and pathways.20 miRNAs and 539 mRNAs were differentially expressed with CMH in COPD. The expression of 10 miRNAs was significantly correlated with the expression of one or more mRNAs. Of these, miR-134-5p, miR-146a-5p and the let-7 family had the highest representation of CMH-associated mRNAs among their negatively correlated predicted targets.KRASandEDN1were identified as key regulators of CMH and were negatively correlated predicted targets of miR-134-5p and let-7a-5p, let-7d-5p, and let-7f-5p, respectively. GSEA suggested involvement ofMUC5AC-related genes and several other relevant gene sets in CMH. The lower expression of miR-134-5p was confirmed in primary airway fibroblasts from COPD patients with CMH.We identified miR-134-5p, miR-146a-5p and let-7 family, along with their potential target genes includingKRASandEDN1, as potential key miRNA–mRNA networks regulating CMH in COPD.

Tawfik, SA, Reimers, JR, Stampfl, C & Ford, MJ 2018, 'van der Waals Forces Control the Internal Chemical Structure of Monolayers within the Lamellar Materials CuInP₂S₆ and CuBiP₂Se₆', The Journal of Physical Chemistry C, vol. 122, no. 39, pp. 22675-22687.
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© 2018 American Chemical Society. Following the recent demonstration that van der Waals forces control the ferroelectric ordering of layers within nanoflakes and bulk samples of CuBiP2Se6 and CuInP2S6, it is demonstrated that they also control the internal geometrical structure of isolated monolayers of these materials. This internal structure involves large displacements of copper atoms, either normal to the layer plane or else within the plane, that change its ligation environment. In both cases, the van der Waals dispersion force out-competes traditional bonding effects to control the structure. However, we find that the aspects of the dispersion force giving rise to each effect are uncorrelated: long-range effects control the interlayer ferroelectric ordering, whereas short-range effects control the internal layer structure. These conclusions are drawn considering the predicted properties of monolayers, bilayers, and bulk materials obtained using 14 density-functional theory-based methods. Although the different methods used often predict starkly different quantitative results, they concur as to the basic nature of ABP2X6 materials. Of the methods used, only the PBE-D3 and optPBEvdW methods were found to predict a wide range of observed properties without serious disparity. Finding optimal computational methods remains a significant challenge for which the unusual multiscale nature of the van der Waals interactions in ABP2X6 materials provides demanding criteria.

Tawfik, SA, Stampfl, C & Ford, MJ 2018, 'Superconductivity in intercalated buckled two-dimensional materials: KGe$_2$', Physical Chemistry Chemical Physics, vol. 20, no. 37, pp. 24027-24032.
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Germanene has emerged as a novel two-dimensional material with variousinteresting properties and applications. Here we report the possibility ofsuperconductivity in a stable potassium intercalated germanene compound,KGe$_2$, with a transition temperature $T_c \sim 11$ K, and an electron-phononcoupling of 1.9. Applying a 5\% tensile strain, which reduces the bucklingheight by 4.5\%, leads to the reduction of the electron-phonon coupling by 11\%and a slight increase in $T_c \sim 12$ K. That is, strong electron-phononcoupling results from the buckled structure of the germanene layers. Despitebeing an intercalated van der Waals material similar to intercalated graphitesuperconductors, it does not possess an occupied interlayer state.

Tekwe, CD, Zoh, RS, Bazer, FW, Wu, G & Carroll, RJ 2018, 'Functional Multiple Indicators, Multiple Causes Measurement Error Models', Biometrics, vol. 74, no. 1, pp. 127-134.
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Summary Objective measures of oxygen consumption and carbon dioxide production by mammals are used to predict their energy expenditure. Since energy expenditure is not directly observable, it can be viewed as a latent construct with multiple physical indirect measures such as respiratory quotient, volumetric oxygen consumption, and volumetric carbon dioxide production. Metabolic rate is defined as the rate at which metabolism occurs in the body. Metabolic rate is also not directly observable. However, heat is produced as a result of metabolic processes within the body. Therefore, metabolic rate can be approximated by heat production plus some errors. While energy expenditure and metabolic rates are correlated, they are not equivalent. Energy expenditure results from physical function, while metabolism can occur within the body without the occurrence of physical activities. In this manuscript, we present a novel approach for studying the relationship between metabolic rate and indicators of energy expenditure. We do so by extending our previous work on MIMIC ME models to allow responses that are sparsely observed functional data, defining the sparse functional multiple indicators, multiple cause measurement error (FMIMIC ME) models. The mean curves in our proposed methodology are modeled using basis splines. A novel approach for estimating the variance of the classical measurement error based on functional principal components is presented. The model parameters are estimated using the EM algorithm and a discussion of the model's identifiability is provided. We show that the defined model is not a trivial extension of longitudinal or functional data methods, due to the presence of the latent construct. Results from its application to data collected on Zucker diabetic fatty rats are provided. Simulation results investigating the properties of our approach are also presented.

Teluguntla, P, Thenkabail, PS, Oliphant, A, Xiong, J, Gumma, MK, Congalton, RG, Yadav, K & Huete, A 2018, 'A 30-m landsat-derived cropland extent product of Australia and China using random forest machine learning algorithm on Google Earth Engine cloud computing platform', ISPRS Journal of Photogrammetry and Remote Sensing, vol. 144, pp. 325-340.
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© 2018 The Author(s) Mapping high resolution (30-m or better) cropland extent over very large areas such as continents or large countries or regions accurately, precisely, repeatedly, and rapidly is of great importance for addressing the global food and water security challenges. Such cropland extent products capture individual farm fields, small or large, and are crucial for developing accurate higher-level cropland products such as cropping intensities, crop types, crop watering methods (irrigated or rainfed), crop productivity, and crop water productivity. It also brings many challenges that include handling massively large data volumes, computing power, and collecting resource intensive reference training and validation data over complex geographic and political boundaries. Thereby, this study developed a precise and accurate Landsat 30-m derived cropland extent product for two very important, distinct, diverse, and large countries: Australia and China. The study used of eight bands (blue, green, red, NIR, SWIR1, SWIR2, TIR1, and NDVI) of Landsat-8 every 16-day Operational Land Imager (OLI) data for the years 2013–2015. The classification was performed by using a pixel-based supervised random forest (RF) machine learning algorithm (MLA) executed on the Google Earth Engine (GEE) cloud computing platform. Each band was time-composited over 4–6 time-periods over a year using median value for various agro-ecological zones (AEZs) of Australia and China. This resulted in a 32–48-layer mega-file data-cube (MFDC) for each of the AEZs. Reference training and validation data were gathered from: (a) field visits, (b) sub-meter to 5-m very high spatial resolution imagery (VHRI) data, and (c) ancillary sources such as from the National agriculture bureaus. Croplands versus non-croplands knowledge base for training the RF algorithm were derived from MFDC using 958 reference-training samples for Australia and 2130 reference-training samples for China. The resultin...

Teng, B, Han, Y, Zhang, X, Xiao, H, Yu, C, Li, H, Cheng, Z, Jin, D, Wong, K-L, Ma, P & Lin, J 2018, 'Phenanthriplatin(iv) conjugated multifunctional up-converting nanoparticles for drug delivery and biomedical imaging', Journal of Materials Chemistry B, vol. 6, no. 31, pp. 5059-5068.
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Platinum-based drugs cisplatin, carboplatin, and oxaliplatin are widely used in the clinical treatment of cancer.

Terlizzi, M, Molino, A, Colarusso, C, Donovan, C, Imitazione, P, Somma, P, Aquino, RP, Hansbro, PM, Pinto, A & Sorrentino, R 2018, 'Activation of the Absent in Melanoma 2 Inflammasome in Peripheral Blood Mononuclear Cells From Idiopathic Pulmonary Fibrosis Patients Leads to the Release of Pro-Fibrotic Mediators', Frontiers in Immunology, vol. 9, no. APR.
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© 2018 Terlizzi, Molino, Colarusso, Donovan, Imitazione, Somma, Aquino, Hansbro, Pinto and Sorrentino. Idiopathic pulmonary fibrosis (IPF) is a chronic fibro-proliferative disease characterized by poor prognosis, with a mean survival of ~2-3 years after definite diagnosis. The cause of IPF is still unknown but it is a heterogeneous condition in which the aberrant deposition of extracellular matrix leads to extensive lung remodeling. This remodeling is a consequence of inflammatory responses, but the mechanisms involved are poorly understood. In this study, we first analyzed a bleomycin-induced mouse model, which showed that higher expression of IL-1β, but not IL-18, was correlated to pulmonary cell infiltration and fibrosis. Then, we found that peripheral blood mononuclear cells (PBMCs) from IPF patients released IL-1α and IL-18 in a NLRP3- and calpain-independent manner after LPS ± ATP stimulation. Instead, the activation of the absent in melanoma 2 (AIM2) inflammasome induced the release of IL-1α in a caspase-1-/caspase-8-independent manner; whereas IL-18 release was caspase-1 dependent. These effects correlated with the release of the pro-fibrotic TGF-β, which was induced by AIM2 activation in a caspase-1- and TLR4-independent manner, but dependent on IL-1α. In this context, the activation of AIM2 induced the release of caspase-4 from IPF-derived PBMCs, which correlated with the mRNA levels of this caspase that was higher in IPF than in healthy PBMCs. In conclusion, our findings identify a novel molecular mechanism whereby the activation of AIM2 could lead to the activation of the non-canonical inflammasome (caspase-4 dependent) that induces the release of IL-1α responsible for the release of TGF-β from PBMCs of IPF patients.

Tharmatt, A, Das, R, Anand, A, Mahajan, S, Mehta, M, Satija, S, Sharma, N, Khatik, GL & Khurana, N 2018, 'Identification of molecular targets of potential antidiabetic drugs using prediction of activity spectra for substances and molecular docking', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 1-10.
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Context: Diabetes mellitus is not a solitary sickness yet is a gathering of metabolic issue influencing countless on the planet. It is essentially described by incessant hyperglycemia because of deformities in insulin discharge or insulin activity. It is predicated that the quantity of diabetes individual on the planet could reach up to 366 million by the year 2030. Even though the instances of diabetes are expanding step by step, aside from insulin and oral hypoglycemic medications, no other method for treatment has been effectively grown up until now. Objective: In the present study, an initiative is tried to delineate the usefulness of prediction of activity spectra for substances (PASS) online software and molecular docking technique for providing new molecular ways of predicting new antidiabetic drug targets of potential phytoconstituents. Materials and Methods: In the study, important phytoconstituents having reported in vitro and in vivo antidiabetic activities have been reviewed. Among them, few phytoconstituents were selected for presenting to PASS online software. Pa and Pi value was predicted for these phytoconstituents on different antidiabetic target sites. Based on PASS prediction, five phytoconstituents were selected for molecular docking study using AutoDock Vina 4.0. Three target sites which were dipeptidyl peptidase-4 (DPP-4), glucagon-like peptide-1 (GLP-1), and α glucosidase were selected for prediction of probable affinities of these 5 selected phytoconstituents. Result and Discussion: Among these five constituents, diosmin showed best binding affinity with DPP-4, GLP-1, and α glucosidase that was −10.2 kcal/mol, −8.3 kcal/mol, and −9.7kcal/mol, followed by kaempferol. Results of the present study can be utilized for designing of further in vitro and in vivo antidiabetic studies for these phytoconstituents. Conclusion: This study suggested the usefulness of these software in predicting the probable antidiabetic targets sites of pote...

Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Editors', Hyperspectral Indices and Image Classifications for Agriculture and Vegetation, pp. xxv-xxviii.

Thien, F, Beggs, PJ, Csutoros, D, Darvall, J, Hew, M, Davies, JM, Bardin, PG, Bannister, T, Barnes, S, Bellomo, R, Byrne, T, Casamento, A, Conron, M, Cross, A, Crosswell, A, Douglass, JA, Durie, M, Dyett, J, Ebert, E, Erbas, B, French, C, Gelbart, B, Gillman, A, Harun, N-S, Huete, A, Irving, L, Karalapillai, D, Ku, D, Lachapelle, P, Langton, D, Lee, J, Looker, C, MacIsaac, C, McCaffrey, J, McDonald, CF, McGain, F, Newbigin, E, O'Hehir, R, Pilcher, D, Prasad, S, Rangamuwa, K, Ruane, L, Sarode, V, Silver, JD, Southcott, AM, Subramaniam, A, Suphioglu, C, Susanto, NH, Sutherland, MF, Taori, G, Taylor, P, Torre, P, Vetro, J, Wigmore, G, Young, AC & Guest, C 2018, 'The Melbourne epidemic thunderstorm asthma event 2016: an investigation of environmental triggers, effect on health services, and patient risk factors', The Lancet Planetary Health, vol. 2, no. 6, pp. e255-e263.
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BACKGROUND: A multidisciplinary collaboration investigated the world's largest, most catastrophic epidemic thunderstorm asthma event that took place in Melbourne, Australia, on Nov 21, 2016, to inform mechanisms and preventive strategies. METHODS: Meteorological and airborne pollen data, satellite-derived vegetation index, ambulance callouts, emergency department presentations, and data on hospital admissions for Nov 21, 2016, as well as leading up to and following the event were collected between Nov 21, 2016, and March 31, 2017, and analysed. We contacted patients who presented during the epidemic thunderstorm asthma event at eight metropolitan health services (each including up to three hospitals) via telephone questionnaire to determine patient characteristics, and investigated outcomes of intensive care unit (ICU) admissions. FINDINGS: Grass pollen concentrations on Nov 21, 2016, were extremely high (>100 grains/m3). At 1800 AEDT, a gust front crossed Melbourne, plunging temperatures 10°C, raising humidity above 70%, and concentrating particulate matter. Within 30 h, there were 3365 (672%) excess respiratory-related presentations to emergency departments, and 476 (992%) excess asthma-related admissions to hospital, especially individuals of Indian or Sri Lankan birth (10% vs 1%, p<0·0001) and south-east Asian birth (8% vs 1%, p<0·0001) compared with previous 3 years. Questionnaire data from 1435 (64%) of 2248 emergency department presentations showed a mean age of 32·0 years (SD 18·6), 56% of whom were male. Only 28% had current doctor-diagnosed asthma. 39% of the presentations were of Asian or Indian ethnicity (25% of the Melbourne population were of this ethnicity according to the 2016 census, relative risk [RR] 1·93, 95% CI 1·74-2·15, p <0·0001). Of ten individuals who died, six were Asian or Indian (RR 4·54, 95% CI 1·28-16·09; p=0·01). 35 individuals were admitted to an intensive care unit, all had asthma, 12 took inhaled preventers, and five d...

Thomson, PG, Fowler, AM, Davis, AR, Pattiaratchi, CB & Booth, DJ 2018, 'Some Old Movies Become Classics – A Case Study Determining the Scientific Value of ROV Inspection Footage on a Platform on Australia’s North West Shelf', Frontiers in Marine Science, vol. 5, no. DEC.
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© 2018 Thomson, Fowler, Davis, Pattiaratchi and Booth. The global oil and gas industry holds a vast archive of Remotely Operated Vehicle (ROV) inspection footage potentially containing useful long-term data on marine biological communities. With the upcoming era of decommissioning of oil and gas structures, it is timely to assess the usefulness of this footage for researching these communities. We used ROV inspection footage to characterize the sessile invertebrates and fishes associated with the Goodwyn Alpha Production Platform (GWA) on the North West Shelf of Australia between depths of 10 and 125 m during 2006 and 2008. Depth was a major driver of invertebrate assemblages, most likely due to specific requirements such as light, and differences between years were most likely from the physical detachment of species by cyclones and internal waves. Phototrophic species were mostly limited to the upper 50 m of the platform, including the hard coral Pocillopora sp. and the soft corals Nephthea sp. and Scleronephthya sp. In contrast, heterotrophic species including sponges, anemones, bryozoans, hydroids, bivalves such as Lopha folium and the hard coral Tubastrea spp., were distributed across all depths. We observed 1791 fish from at least 10 families and 19 species, including commercial species such as crimson seaperch (Lutjanus erythropterus), red emperor (L. sebae), saddle-tailed seaperch (L. malabaricus), mangrove jack (L. argentimaculatus) and trevally (Caranx spp.). Fish density increased significantly with depth during 2008, from a mean of 23 fish/50 m2 between 10 and 25 m to 3373 fish/50 m2 at 125 m, where small unidentified baitfish were abundant. The highest densities of commercial species occurred between 25 and 75 m depth, suggesting that mid-depth platform sections had high habitat value, a consideration when selecting decommissioning options. The greatest difficulties using the video were the poor lighting and resolution that inhibited our abi...

Thummavichai, K, Wang, N, Cheong Lem, L, Phillips, M, Ton-That, C, Chang, H, Hu, C, Xu, F, Xia, Y & Zhu, Y 2018, 'Lanthanide-doped W 18 O 49 nanowires: Synthesis, structure and optical properties', Materials Letters, vol. 214, pp. 232-235.
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© 2017 The effects of Ce- and La-doped WOx nanostructures on the morphology and crystal structures of WOx nanowires are investigated first, then the impact of these dopants on the cathodoluminescence (CL) properties of the WOx nanowires is studied. The dopants induced a morphological evolution and crystalline lattice expansion of the WOx nanostructures. By analyzing the surface composition and oxidation state ratios of W5+/W6+ in each sample using X-ray photoelectron spectroscopy, we attempt to interpret the observed CL spectra shift from ultraviolet to blue emission of the Ce- and La-doped nanowires.

Tian, C, Doblin, MA, Dafforn, KA, Johnston, EL, Pei, H & Hu, W 2018, 'Dinoflagellate cyst abundance is positively correlated to sediment organic carbon in Sydney Harbour and Botany Bay, NSW, Australia', Environmental Science and Pollution Research, vol. 25, no. 6, pp. 5808-5821.
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There is growing public concern about the global expansion of harmful algal bloom species (HABs), with dinoflagellate microalgae comprising the major portion of the harmful taxa. These motile, unicellular organisms have a lifecycle involving sexual reproduction and resting cyst formation whereby cysts can germinate from sediments and 'seed' planktonic populations. Thus, investigation of dinoflagellate cyst (dinocyst) distribution in sediments can provide significant insights into HAB dynamics and contribute to indices of habitat quality. Species composition and abundance of dinocysts in relation to sediment characteristics were studied at 18 stations in two densely populated temperate Australian estuaries, Sydney Harbour (Parramatta River/Port Jackson; PS) and Botany Bay (including Georges River; GB). Eighteen dinocyst taxa were identified, dominated by Protoceratium reticulatum and Gonyaulax sp.1 in the PS estuary, together with Archaeperidinium minutum and Gonyaulax sp.1 in the GB estuary. Cysts of Alexandrium catenella, which is one of the causative species of paralytic shellfish poisoning (PSP), were also detected in both estuaries. Out of the measured sediment characteristics (TOC, Cd, Cr, Cu, Fe, Pb, Mn, Ni, Zn and polycyclic aromatic hydrocarbons), TOC was the parameter explaining most of the variation in dinocyst assemblages and was positively correlated to most of the heavy metals. Given the significant relationship between sediment TOC and dinocyst abundance and heavy metal concentrations, this study suggests that sediment TOC could be broadly used in risk management for potential development of algal blooms and sediment contamination in these estuaries.

Tian, C, Hao, D, Pei, H, Doblin, MA, Ren, Y, Wei, J & Feng, Y 2018, 'Phytoplankton Functional Groups Variation and Influencing Factors in a Shallow Temperate Lake', Water Environment Research, vol. 90, no. 6, pp. 510-519.
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ABSTRACT: The present study was carried out in Luoma Lake, a shallow lake in temperate eastern China. Based on a two‐year study, the dynamics of phytoplankton functional groups and influencing factors were analyzed. A total of 178 taxa were identified and sorted into 20 codons, according to the phytoplankton functional group classification. In order to find the environmental factors driving phytoplankton variations, fifteen groups were analyzed in detail using redundancy analysis. Groups P (Fragilaria crotonensis), X2 (Chlamydomonas globosa, C. microsphaera and Chroomonas acuta), and MP (Navicula rotaeana) were dominant during low temperature periods, whereas groups X2, S1 (Pseudanabaena limnetica), and W1 (Euglena sp.) were dominant during high temperature periods. Water temperature, total phosphorus, and ammonium were the significant driving factors explaining phytoplankton succession. Furthermore, total phosphorus and ammonium could be broadly used in risk management for potential algal blooms in Luoma Lake.

Tian, H, Huang, F, Zhu, Y, Liu, S, Han, Y, Jaroniec, M, Yang, Q, Liu, H, Lu, GQM & Liu, J 2018, 'The Development of Yolk–Shell‐Structured Pd&ZnO@Carbon Submicroreactors with High Selectivity and Stability', Advanced Functional Materials, vol. 28, no. 32, pp. 1801737-1801737.
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AbstractDesign of multicomponent yolk–shell structures is crucial for the fabrication of micro/nanoreactors for a variety of applications. This work reports the rational design and synthesis of yolk–shell‐structured submicroreactors with loaded metal nanoparticles into ZnO–microporous carbon core–shell structures. The solvothermal treatment and carbonization process of uniform zeolitic imidazolate framework‐8 (ZIF‐8)@resin polymer core–shell structures leads to the generation of yolk–shell‐structured ZnO@carbon. The synthesis conditions are optimized to track the evolution of ZIF‐8 in a confined space of resin polymer as a submicroreactor itself. It is found that nanoribbon evolution occurs via the formation of the intermediate needle‐like particles. The Pd&ZnO@carbon submicroreactor is shown to be a highly selective catalyst (selectivity >99%) for hydrogenation of phenylacetylene to phenylethylene. The excellent performance of Pd&ZnO@carbon particles is evidenced by higher conversion and selectivity than that of Pd/ZnO and Pd/C with similar Pd loading. Furthermore, Pd&ZnO@carbon submicroreactors show superior catalytic stability, and no deactivation after 25 h of reaction. The proposed strategy is promising for the design of multifunctional micro/nanoreactors or nanocontainers for construction of artificial cells.

Tian, H, Liang, Y, Repac, J, Zhang, S, Luo, C, Liou, S-C, Wang, G, Ehrman, SH & Han, W 2018, 'Rational Design of Core–Shell-Structured Particles by a One-Step and Template-Free Process for High-Performance Lithium/Sodium-Ion Batteries', The Journal of Physical Chemistry C, vol. 122, no. 39, pp. 22232-22240.
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© 2018 American Chemical Society. Tin (Sn)-based materials are one of most promising candidates for rechargeable (Li+ and Na+ ion) batteries because of their high theoretical capacities (993 mAh/g for Li4.4Sn and 847 mAh/g for Na15Sn4) and reasonable working potentials. However, Sn-based anodes suffer from huge volume changes during cycling that hinder the applications in commercialized rechargeable batteries. Unique particle engineering to fabricate Sncore-carbonshell (Sn@C) particles has been shown to address or circumvent these problems. In this work, a distinct core-shell-structured Sn@C anode material has been successfully developed by using a one-step and template-free process (colloidal spray pyrolysis). A comprehensive analysis of chemical reaction kinetics of core-shell particles assists the product design to control the particle composition and structure by tuning the process variables, such as reaction temperature and cosolvent concentration. The unique Sn@C anode delivers a high capacity of 720 mAh/g after 300 cycles at 0.5C for lithium-ion batteries and a high capacity of >500 mAh/g at 0.2C for sodium-ion batteries. More importantly, this work advances the design of high-performance Sn@C composites for lithium/sodium-ion batteries in scalable process development, particle engineering, and material innovation.

Tian, H, Wang, T, Zhang, F, Zhao, S, Wan, S, He, F & Wang, G 2018, 'Tunable porous carbon spheres for high-performance rechargeable batteries', Journal of Materials Chemistry A, vol. 6, no. 27, pp. 12816-12841.
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A review focusing on the tunable pore structure design, surface chemistry, composition, and electrochemical performances of PCSs in various types of rechargeable batteries in order to provide insight and inspiration for promoting the development of next-generation high-performance batteries.

Toledo, JR, Jesus, DBD, Kianinia, M, Leal, AS, Fantini, C, Cury, LA, Sáfar, GM, Aharonovich, I & Krambrock, K 2018, 'Electron Paramagnetic Resonance signature of point defects in neutron irradiated hexagonal Boron Nitride', Phys. Rev. B, vol. 98, no. 15, p. 155203.
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Hexagonal boron nitride (h-BN) is an attractive van der Waals material forstudying fluorescent defects due to its large bandgap. In this work, wedemonstrate enhanced pink color due to neutron irradiation and perform electronparamagnetic resonance (EPR) measurements. The new point defects aretentatively assigned to doubly- occupied nitrogen vacancies with (S = 1) and azero-field splitting (D = 1.2 GHz). These defects are associated with a broadvisible optical absorption band and near infrared photoluminescence bandcentered at ~ 490 nm and 820 nm, respectively. The EPR signal intensities arestrongly affected by thermal treatments in temperature range between 600 to800{\deg}C, where also the irradiation - induced pink color is lost. Ourresults are important for understanding of point defects in h-BN and theirdeployment for quantum and integrated photonic applications.

Tonkin, RS, Bowles, C, Perera, CJ, Keating, BA, Makker, PGS, Duffy, SS, Lees, JG, Tran, C, Don, AS, Fath, T, Liu, L, O'Carroll, SJ, Nicholson, LFB, Green, CR, Gorrie, C & Moalem-Taylor, G 2018, 'Attenuation of mechanical pain hypersensitivity by treatment with Peptide5, a connexin-43 mimetic peptide, involves inhibition of NLRP3 inflammasome in nerve-injured mice', Experimental Neurology, vol. 300, pp. 1-12.
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© 2017 Elsevier Inc. Connexin43 (Cx43) hemichannels in spinal cord astrocytes are implicated in the maintenance of neuropathic pain following peripheral nerve injury. Peptide5 is a Cx43 mimetic peptide that blocks hemichannels. In this study, we investigated the effects of spinal delivery of Peptide5 on mechanical pain hypersensitivity in two mouse models of neuropathic pain, peripheral nerve injury and chemotherapy-induced peripheral neuropathy (CIPN). We demonstrated that 10 days following a chronic constriction injury (CCI) of the sciatic nerve, Cx43 expression, co-localised predominantly with astrocytes, was increased in the ipsilateral L3–L5 lumbar spinal cord. An intrathecal injection of Peptide5 into nerve-injured mice, on day 10 when pain was well-established, caused significant improvement in mechanical pain hypersensitivity 8 h after injection. Peptide5 treatment resulted in significantly reduced Cx43, and microglial and astrocyte activity in the dorsal horn of the spinal cord, as compared to control saline-treated CCI mice. Further in vitro investigations on primary astrocyte cultures showed that 1 h pre-treatment with Peptide5 significantly reduced adenosine triphosphate (ATP) release in response to extracellular calcium depletion. Since ATP is a known activator of the NOD-like receptor protein 3 (NLRP3) inflammasome complex, a key mediator of neuroinflammation, we examined the effects of Peptide5 treatment on NLRP3 inflammasome expression. We found that NLRP3, its adaptor apoptosis-associated spec-like protein (ASC) and caspase-1 protein were increased in the ipsilateral spinal cord of CCI mice and reduced to naïve levels following Peptide5 treatment. In the models of oxaliplatin- and paclitaxel-induced peripheral neuropathy, treatment with Peptide5 had no effect on mechanical pain hypersensitivity. Interestingly, in these CIPN models, although spinal Cx43 expression was significantly increased at day 13 following chemotherapy, NLRP3 expres...

Toole, K, Philp, M, Krayem, N, Fu, S, Shimmon, R & Taflaga, S 2018, 'Color Tests for the Preliminary Identification of New Psychoactive Substances', Methods in molecular biology (Clifton, N.J.), vol. 1810, pp. 1-11.
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Color tests are a key tool for the rapid and simple identification of seized illicit drugs. This chapter outlines a series of color tests that can be used for the preliminary identification of new psychoactive substances such as cathinones, piperazines, tryptamines, and amphetamine-type stimulants.

Topa, SH, Subramoni, S, Palombo, EA, Kingshott, P, Rice, SA & Blackall, LL 2018, 'Cinnamaldehyde disrupts biofilm formation and swarming motility of Pseudomonas aeruginosa', Microbiology, vol. 164, no. 9, pp. 1087-1097.
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© 2018 The Authors. Bacterial biofilms can cause serious health care complications associated with increased morbidity and mortality. There is an urge to discover and develop new biofilm inhibitors from natural products or by modifying natural compounds or understanding the modes of action of existing compounds. Cinnamaldehyde (CAD), one of the major components of cinnamon oil, has been demonstrated to act as an antimicrobial agent against a number of Gram-negative and Gram-positive pathogens, including Pseudomonas aeruginosa, Helicobacter pylori and Listeria monocytogenes. Despite the mechanism of action of CAD against the model organism P. aeruginosa being undefined, based on its antimicrobial properties, we hypothesized that it may disrupt preformed biofilms of P. aeruginosa. The minimum inhibitory concentration (MIC) of CAD for planktonic P. aeruginosa was determined to be 11.8 mM. Membrane depolarization assays demonstrated disruption of the transmembrane potential of P. aeruginosa. CAD at 5.9mM (0.5 MIC) disrupted preformed biofilms by 75.6% and 3mM CAD (0.25 MIC) reduced the intracellular concentrations of the secondary messenger, bis-(3′–5′)-cyclic dimeric guanosine monophosphate (c-di-GMP), which controls P. aeruginosa biofilm formation. The swarming motility of P. aeruginosa was also reduced by CAD in a concentration-dependent manner. Collectively, these findings show that sub-MICs of CAD can disrupt biofilms and other surface colonization phenotypes through the modulation of intracellular signalling processes.

Torpy, F & Zavattaro, M 2018, 'Bench-Study of Green-Wall Plants for Indoor Air Pollution Reduction', Journal of Living Architecture, vol. 5, no. 1, pp. 1-15.
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Potted-plants have the potential for improving indoor air quality (IAQ), however there has been little research on the performance of green-walls as indoor biofilters. The aim of this investigation was to compare rates of air pollutant reduction with two commonly used indoor species, and to assess the effects of added substrate airflows on the capacity of green-wall modules to remove two prevalent indoor airborne contaminants - particulate matter (PM), and volatile organic compounds (VOCs), using benzene as model. The species tested were Chlorophytum comosum (Spider Plant) and Epipremnum aureum (Pothos). The results showed that each species could significantly reduce increasing doses of PM, with or without augmented substrate airflow, however benzene removal rates decreased with increasing aeration. The findings provide a first assessment of the ability of green-wall plants to reduce indoor air pollution, and responses to two types of pollutant, particulate and gaseous.

Torpy, F, Clements, N, Pollinger, M, Dengel, A, Mulvihill, I, He, C & Irga, P 2018, 'Testing the single-pass VOC removal efficiency of an active green wall using methyl ethyl ketone (MEK)', Air Quality, Atmosphere & Health, vol. 11, no. 2, pp. 163-170.
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© 2017, The Author(s). In recent years, research into the efficacy of indoor air biofiltration mechanisms, notably living green walls, has become more prevalent. Whilst green walls are often utilised within the built environment for their biophilic effects, there is little evidence demonstrating the efficacy of active green wall biofiltration for the removal of volatile organic compounds (VOCs) at concentrations found within an interior environment. The current work describes a novel approach to quantifying the VOC removal effectiveness by an active living green wall, which uses a mechanical system to force air through the substrate and plant foliage. After developing a single-pass efficiency protocol to understand the immediate effects of the system, the active green wall was installed into a 30-m3 chamber representative of a single room and presented with the contaminant 2-butanone (methyl ethyl ketone; MEK), a VOC commonly found in interior environments through its use in textile and plastic manufacture. Chamber inlet levels of MEK remained steady at 33.91 ± 0.541 ppbv. Utilising a forced-air system to draw the contaminated air through a green wall based on a soil-less growing medium containing activated carbon, the combined effects of substrate media and botanical component within the biofiltration system showed statistically significant VOC reduction, averaging 57% single-pass removal efficiency over multiple test procedures. These results indicate a high level of VOC removal efficiency for the active green wall biofilter tested and provide evidence that active biofiltration may aid in reducing exposure to VOCs in the indoor environment.

Torpy, FR, Pettit, T & Irga, PJ 2018, 'Applied Horticultural Biotechnology for the Mitigation of Indoor Air Pollution', Journal of People, Plants, and Environment, vol. 21, no. 6, pp. 445-460.
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Exposure to indoor air pollution is an emerging world-wide problem, with growing evidence that it is a major cause of morbidity worldwide. Whilst most indoor air pollutants are of outdoor origin, these combine with a range of indoor sourced pollutants that may lead to high pollutant levels indoors. The pollutants of greatest concern are volatile organic compounds (VOCs) and particulate matter (PM), both of which are associated with a range of serious health problems. Whilst current buildings usually use ventilation with outdoor air to remove these pollutants, botanical systems are gaining recognition as an effective alternative. Whilst many years research has shown that traditional potted plants and their substrates are capable of removing VOCs effectively, they are inefficient at removing PM, and are limited in their pollutant removal rates by the need for pollutants to diffuse to the active pollutant removal components of these systems. Active botanical biofiltration, using green wall systems combined with mechanical fans to increase pollutant exposure to the plants and substrate, show greatly increased rates of pollutant removal for both VOCs, PM and also carbon dioxide (CO2). A developing body of research indicates that these systems can outperform existing technologies for indoor air pollutant removal, although further research is required before their use will become widespread. Whilst it is known that plant species selection and substrate characteristics can affect the performance of active botanical systems, optimal characteristics are yet to be identified. Once this research has been completed, it is proposed that active botanical biofiltration will provide a cheap and low energy use alternative to mechanical ventilations systems for the maintenance of indoor environmental quality.

TOWNSEND, KD 2018, 'CLASSIFICATION OF REFLECTION SUBGROUPS MINIMALLY CONTAINING -SYLOW SUBGROUPS', Bulletin of the Australian Mathematical Society, vol. 97, no. 1, pp. 57-68.
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Let a prime $p$ divide the order of a finite real reflection group. We classify the reflection subgroups up to conjugacy that are minimal with respect to inclusion, subject to containing a $p$-Sylow subgroup. For Weyl groups, this is achieved by an algorithm inspired by the Borel–de Siebenthal algorithm. The cases where there is not a unique conjugacy class of reflection subgroups minimally containing the $p$-Sylow subgroups are the groups of type $F_{4}$ when $p=2$ and $I_{2}(m)$...

Trevathan-Tackett, SM, Thomson, ACG, Ralph, PJ & Macreadie, PI 2018, 'Fresh carbon inputs to seagrass sediments induce variable microbial priming responses', Science of The Total Environment, vol. 621, pp. 663-669.
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© 2017 Elsevier B.V. Microbes are the ‘gatekeepers’ of the marine carbon cycle, yet the mechanisms for how microbial metabolism drives carbon sequestration in coastal ecosystems are still being defined. The proximity of coastal habitats to runoff and disturbance creates ideal conditions for microbial priming, i.e., the enhanced remineralisation of stored carbon in response to fresh substrate availability and oxygen introduction. Microbial priming, therefore, poses a risk for enhanced CO2 release in these carbon sequestration hotspots. Here we quantified the existence of priming in seagrass sediments and showed that the addition of fresh carbon stimulated a 1.7- to 2.7-fold increase in CO2 release from recent and accumulated carbon deposits. We propose that priming taking place at the sediment surface is a natural occurrence and can be minimised by the recalcitrant components of the fresh inputs (i.e., lignocellulose) and by reduced metabolism in low oxygen and high burial rate conditions. Conversely, priming of deep sediments after the reintroduction to the water column through physical disturbances (e.g., dredging, boat scars) would cause rapid remineralisation of previously preserved carbon. Microbial priming is identified as a process that weakens sediment carbon storage capacity and is a pathway to CO2 release in disturbed or degraded seagrass ecosystems; however, increased management and restoration practices can reduce these anthropogenic disturbances and enhance carbon sequestration capacity.

Trevathan‐Tackett, SM, Wessel, C, Cebrián, J, Ralph, PJ, Masqué, P & Macreadie, PI 2018, 'Effects of small‐scale, shading‐induced seagrass loss on blue carbon storage: Implications for management of degraded seagrass ecosystems', Journal of Applied Ecology, vol. 55, no. 3, pp. 1351-1359.
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AbstractSeagrass meadows are important global blue carbon sinks. Despite a 30% loss of seagrasses globally during the last century, there is limited empirical research investigating the effects of disturbance and loss of seagrass on blue carbon stocks.In this study, we hypothesised that seagrass loss would reduce blue carbon stocks. Using shading cloth, we simulated small‐scale die‐offs of two subtropical seagrass species, Halodule wrightii and Thalassia testudinum, in a dynamic northern Gulf of Mexico lagoon. The change in quantity and quality of sediment organic matter (OM) and organic carbon was compared among die‐off, control and bare plots before the die‐off treatment, shortly after the die‐off treatment and 11 months after the die‐off treatment. 210Pb age dating was performed on bare and Thalassia plots at 11 months to evaluate the impact of sediment erosion in the absence of vegetation.The small‐scale die‐off led to a 50%–65% OM loss in the sediment in the top 8 cm of Halodule plots. Thalassia plots lost significant portions of OM (50%) and organic carbon (Corg; 21%–47%) in only the top 1 cm of sediment. The 210Pb profiles indicated Thalassia die‐off reduced the Corg sequestration rate by 10%, in addition to a loss of c. 1 year's worth of Corg stocks (c. 22 g/m2

Trist, BG, Hare, DJ & Double, KL 2018, 'A Proposed Mechanism for Neurodegeneration in Movement Disorders Characterized by Metal Dyshomeostasis and Oxidative Stress', Cell Chemical Biology, vol. 25, no. 7, pp. 807-816.
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© 2018 Elsevier Ltd Shared molecular pathologies between distinct neurodegenerative disorders offer unique opportunities to identify common mechanisms of neuron death, and apply lessons learned from one disease to another. Neurotoxic superoxide dismutase 1 (SOD1) proteinopathy in SOD1-associated familial amyotrophic lateral sclerosis (fALS) is recapitulated in idiopathic Parkinson disease (PD), suggesting that these two phenotypically distinct disorders share an etiological pathway, and tractable therapeutic target(s). Despite 25 years of research, the molecular determinants underlying SOD1 misfolding and toxicity in fALS remain poorly understood. The absence of SOD1 mutations in PD highlights mounting evidence that SOD1 mutations are not the sole cause of SOD1 protein misfolding occasioning oligomerization and toxicity, reinforcing the importance of non-genetic factors, including protein metallation and post-translational modification in determining SOD1 stability and function. We propose that these non-genetic factors underlie the misfolding and dysfunction of SOD1 and other proteins in both PD and fALS, constituting a shared and tractable pathway to neurodegeneration. Trist et al. propose a shared etiological pathway in Parkinson disease and SOD1-associated familial amyotrophic lateral sclerosis, whereby concomitant changes in cellular copper and oxidative stress within dying neurons contribute to the dysfunction of specific proteins that are essential for maintaining neuronal health, including superoxide dismutase 1.

Truong, M, Monahan, LG, Carter, DA & Charles, IG 2018, 'Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis', PeerJ, vol. 6, pp. e4761-e4761.
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Many infectious diseases disproportionately affect people in the developing world. Cryptococcal meningitis is one of the most common mycoses in HIV-AIDS patients, with the highest burden of disease in sub-Saharan Africa. Current best treatment regimens still result in unacceptably high mortality rates, and more effective antifungal agents are needed urgently. Drug development is hampered by the difficulty of developing effective antifungal agents that are not also toxic to human cells, and by a reluctance among pharmaceutical companies to invest in drugs that cannot guarantee a high financial return. Drug repurposing, where existing drugs are screened for alternative activities, is becoming an attractive approach in antimicrobial discovery programs, and various compound libraries are now commercially available. As these drugs have already undergone extensive optimisation and passed regulatory hurdles this can fast-track their progress to market for new uses. This study screened the Screen-Well Enzo library of 640 compounds for candidates that phenotypically inhibited the growth ofCryptococcus deuterogattii. The anthelminthic agent flubendazole, and L-type calcium channel blockers nifedipine, nisoldipine and felodipine, appeared particularly promising and were tested in additional strains and species. Flubendazole was very active against all pathogenicCryptococcusspecies, with minimum inhibitory concentrations of 0.039–0.156 μg/mL, and was equally effective against isolates that were resistant to fluconazole. While nifedipine, nisoldipine and felodipine all inhibitedCryptococcus, nisoldipine was also effective againstCandida, SaccharomycesandAspergillus. This study validates repurposing as a rapid approach for finding new agents to treat neglected infectious diseases.

Tschitschko, B, Erdmann, S, DeMaere, MZ, Roux, S, Panwar, P, Allen, MA, Williams, TJ, Brazendale, S, Hancock, AM, Eloe-Fadrosh, EA & Cavicchioli, R 2018, 'Genomic variation and biogeography of Antarctic haloarchaea', Microbiome, vol. 6, no. 1, pp. 113-113.
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BACKGROUND:The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS:The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION:The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography o...

Tse, K, Cheng, A, Ma, F & Herrup, K 2018, 'DNA damage‐associated oligodendrocyte degeneration precedes amyloid pathology and contributes to Alzheimer's disease and dementia', Alzheimer's & Dementia, vol. 14, no. 5, pp. 664-679.
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AbstractIntroductionIn looking for novel non‐amyloid‐based etiologies for Alzheimer's disease, we explore the hypothesis that age‐related myelin loss is an attractive explanation for age‐associated cognitive decline and dementia.MethodsWe performed a meta‐analysis of data in the National Alzheimer's Coordinating Center database accompanied by quantitative histopathology of myelin and oligodendrocytes (OLs) in frontal cortices of 24 clinically characterized individuals. Pathological findings were further validated in an Alzheimer's disease mouse model and in culture.ResultsMyelin lesions increased with cognitive impairment in an amyloid‐independent fashion with signs of degeneration appearing before neuronal loss. Myelinating OLs in the gray matter showed greater vulnerability than those in white matter, and the degenerative changes correlated with evidence of DNA damage. Similar results were found in myelinating OL cultures where DNA damage caused aberrant OL cell cycle re‐entry and death.DiscussionWe present the first comprehensive analysis of the cell biology of early myelin loss in sporadic Alzheimer's disease.

Tsoli, M, Liu, J, Franshaw, L, Shen, H, Cheng, C, Jung, M, Joshi, S, Ehteda, A, Khan, A, Montero-Carcabosso, A, Dilda, PJ, Hogg, P & Ziegler, DS 2018, 'Dual targeting of mitochondrial function and mTOR pathway as a therapeutic strategy for diffuse intrinsic pontine glioma', Oncotarget, vol. 9, no. 7, pp. 7541-7556.
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Ueland, M, Forbes, SL & Stuart, BH 2018, 'Seasonal variation of fatty acid profiles from textiles associated with decomposing pig remains in a temperate Australian environment', Forensic Chemistry, vol. 11, pp. 120-127.
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© 2018 Elsevier B.V. A methodology to examine the human post-mortem decomposition process has been developed through the monitoring of chemical changes to decomposition fluids absorbed by clothing. Model surface burials using clothed pigs were established during summer and winter seasons in a temperate region of Australia. Three clothing materials were investigated: cotton, polyester and cotton-polyester. Lipid decomposition products were extracted from the textiles and the fatty acid composition measured as a function of burial time using gas chromatography – mass spectrometry (GC-MS). Two derivatisation methods for the fatty acids were compared to establish the most effective approach and it was established that a trimethylsilylation derivatisation method is the optimal preparation technique. The summer trials revealed two rates of transformation of fatty acids from unsaturated to saturated forms, with a faster rate of change occurring earlier in the trials. A different pattern of behaviour was observed for the fatty acids detected during the winter trial, with a decrease in saturated fatty acids initially observed, followed by the conversion of unsaturated to saturated fatty acids until the end of trial. The initial change observed during the winter trial was attributed to a dehydrogenation process caused by microbiological enyzymatic activity. The study has demonstrated the feasibility of examining lipid decomposition products collected in clothing from burials to provide insight into the conditions and length of burial.

Valderrama Ballesteros, L, Matthews, JL & Hoeksema, BW 2018, 'Pollution and coral damage caused by derelict fishing gear on coral reefs around Koh Tao, Gulf of Thailand', Marine Pollution Bulletin, vol. 135, pp. 1107-1116.
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van de Water, JAJM, Chaib De Mares, M, Dixon, GB, Raina, J, Willis, BL, Bourne, DG & van Oppen, MJH 2018, 'Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef‐building coral', Molecular Ecology, vol. 27, no. 4, pp. 1065-1080.
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AbstractGlobal increases in coral disease prevalence have been linked to ocean warming through changes in coral‐associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase‐activating system and multiple immune system‐related genes. Elevated seawater temperatures did not induce shifts in the coral‐associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocy...

Van Deynze, A, Zamora, P, Delaux, P-M, Heitmann, C, Jayaraman, D, Rajasekar, S, Graham, D, Maeda, J, Gibson, D, Schwartz, KD, Berry, AM, Bhatnagar, S, Jospin, G, Darling, A, Jeannotte, R, Lopez, J, Weimer, BC, Eisen, JA, Shapiro, H-Y, Ané, J-M & Bennett, AB 2018, 'Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota', PLOS Biology, vol. 16, no. 8, pp. e2006352-e2006352.
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© 2018 Van Deynze et al. http://creativecommons.org/licenses/by/4.0/. Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15 N 2 incorporation assays. Field experiments in Sierra Mixe using 15 N natural abundance or 15 N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%–82% of the nitrogen nutrition of Sierra Mixe maize.

van Geldermalsen, M, Quek, L-E, Turner, N, Freidman, N, Pang, A, Guan, YF, Krycer, JR, Ryan, R, Wang, Q & Holst, J 2018, 'Benzylserine inhibits breast cancer cell growth by disrupting intracellular amino acid homeostasis and triggering amino acid response pathways', BMC Cancer, vol. 18, no. 1.
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van Gorsel, E, Cleverly, J, Beringer, J, Cleugh, H, Eamus, D, Hutley, LB, Isaac, P & Prober, S 2018, 'Preface: OzFlux: a network for the study of ecosystem carbon and water dynamics across Australia and New Zealand', Biogeosciences, vol. 15, no. 1, pp. 349-352.
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van Zyl, VL, Muller, A & Williams, DBG 2018, 'Charge-tagged polar phosphine ligands in Pd-catalysed reactions in aqueous and ionic media', Tetrahedron Letters, vol. 59, no. 10, pp. 918-921.
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© 2018 Elsevier Ltd A new range of polar imidazolium and phosphate-containing ligands was synthesised from readily available starting materials in high yielding multi-step transformations. These ligands were used to generate Pd catalysts for Suzuki and Heck C–C coupling reactions in organic and organic/aqueous media. The catalysts performed well in aqueous media in the Suzuki reaction and less well in the Heck reaction, related to substrate solubility in the aqueous media. When moving to ionic liquids, the Heck reaction dramatically improved, especially in media compatible with the polar catalysts and the non-polar reagents. In all cases, the catalysts were stable to the formation of Pd black, a form of degradation that frequently befalls Pd catalysts. The catalysts could be successfully recycled without loss of activity.

Varkey, D, Mazard, S, Jeffries, TC, Hughes, DJ, Seymour, J, Paulsen, IT & Ostrowski, M 2018, 'Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary', PLOS ONE, vol. 13, no. 12, pp. e0209857-e0209857.
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© 2018 Varkey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the ...

Velazquez-Salinas, L, Ramirez-Medina, E, Bracht, AJ, Hole, K, Brito, BP, Gladue, DP & Carrillo, C 2018, 'Phylodynamics of parapoxvirus genus in Mexico (2007–2011)', Infection, Genetics and Evolution, vol. 65, pp. 12-14.
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© 2018 In this study we report for the first time the phylodynamics of the parapoxvirus (PPV) genus in Mexico. Based on the analysis by PCR of 124 epithelial samples collected between 2007 and 2011 from naturally infected goats, sheep and cows in Mexico, we found that different PPV were present in 21 out of the 24 states sampled during this study. Our phylogenetic analysis confirmed the presence of different PPV species in Mexico, and their phylogenetic relationship with other PPV circulating in the US and Canada. Furthermore, we describe the existence of two different ORFV phylogenetic groups that are clearly host associated (sheep or goat). Evidence of directional selection at five specific amino acid residues in the enveloped glycoprotein B2L might help to support this host predilection. Collectively, the results generated in this study highlight the importance of PPV genus in Mexico and open the possibility for future studies describing with more detail the importance of this genus in North America.

Vellemu, EC, Mensah, PK, Griffin, NJ, Odume, ON, Palmer, CG & Dowse, R 2018, 'Using a Risk-based Approach for Derivation of Water Quality Guidelines for Sulphate', Mine Water and the Environment, vol. 37, no. 1, pp. 166-173.
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© 2017, Springer-Verlag GmbH Germany. Sulphate is a major salt component in acid mine drainage and a crucial ecological concern in most coal and gold mining regions, globally. However, there remains a paucity of data on sulphate salinity toxicity on freshwater taxa. In this study, we hypothesised sensitivity differences for five freshwater species (Adenophlebia auriculata, Burnupia stenochorias, Caridina nilotica, Pseudokirchneriella subcapitata, and Oreochromis mossambicus) to increasing sulphate salinity concentrations after 240 h of exposure. Species sensitivity distributions (SSDs) were used to rank the sensitivity of tested species to the inorganic sulphate salts, which included magnesium sulphate (MgSO 4 ), sodium sulphate (Na 2 SO 4 ), and calcium sulphate (CaSO 4 ) as models of mining salinisation in South Africa. The SSDs were also used to estimate appropriate protective concentrations of the salts for the tested species. Sensitivity differences were measured and Na 2 SO 4 was the most toxic of the tested salts. A concentration of 0.020 g/L Na 2 SO 4 , 0.055 g/L CaSO 4 , and 0.108 g/L MgSO 4 or a combined salts limit of 0.067 g/L would be protective of 95% of the populations of the five species tested; these all suggest that the 0.25 g/L compliance limit for South Africa is insufficient. Future studies should incorporate more species in the SSD approach to be coupled by field validations to further improve the ecological relevance of these findings.

Verzosa, DMB, De Las Peñas, MLAN, Aberin, MAQ & Garces, LPDM 2018, 'App for Addition and Subtraction of Integers', International Journal for Technology in Mathematics Education, vol. 25, no. 4, pp. 21-33.
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This paper presents a mobile app, AlgeOps, created to assist students in understanding addition and subtraction of integers. The design of the app amalgamated the neutralization model (based on cancelling integers of opposite signs) and the number line model to offer a more holistic representation of integers. Furthermore, since AlgeOps presents two objects, boxes and balloons, the learning objective may be extended to adding and subtracting polynomials. Pre- and post-assessments, student observations and interviews with teachers and students revealed the app can increase performance, facilitate conceptual development, and increase engagement in tasks involving integer addition and subtraction.

Vo Hoang Nhat, P, Ngo, HH, Guo, WS, Chang, SW, Nguyen, DD, Nguyen, PD, Bui, XT, Zhang, XB & Guo, JB 2018, 'Can algae-based technologies be an affordable green process for biofuel production and wastewater remediation?', Bioresource Technology, vol. 256, pp. 491-501.
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© 2018 Elsevier Ltd Algae is a well-known organism that its characteristic is prominent for biofuel production and wastewater remediation. This critical review aims to present the applicability of algae with in-depth discussion regarding three key aspects: (i) characterization of algae for its applications; (ii) the technical approaches and their strengths and drawbacks; and (iii) future perspectives of algae-based technologies. The process optimization and combinations with other chemical and biological processes have generated efficiency, in which bio-oil yield is up to 41.1%. Through life cycle assessment, algae bio-energy achieves high energy return than fossil fuel. Thus, the algae-based technologies can reasonably be considered as green approaches. Although selling price of algae bio-oil is still high (about $2 L−1) compared to fossil fuel's price of $1 L−1, it is expected that the algae bio-oil's price will become acceptable in the next coming decades and potentially dominate 75% of the market.

Vo, H-N-P, Bui, X-T, Nguyen, T-M-H, Koottatep, T & Bandyopadhyay, A 2018, 'Insights of the Removal Mechanisms of Pharmaceutical and Personal Care Products in Constructed Wetlands', Current Pollution Reports, vol. 4, no. 2, pp. 93-103.
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Vonk, JM, Nieuwenhuis, MAE, Dijk, FN, Boudier, A, Siroux, V, Bouzigon, E, Probst‐Hensch, N, Imboden, M, Keidel, D, Sin, D, Bossé, Y, Hao, K, van den Berge, M, Faiz, A, Koppelman, GH & Postma, DS 2018, 'Novel genes and insights in complete asthma remission: A genome‐wide association study on clinical and complete asthma remission', Clinical & Experimental Allergy, vol. 48, no. 10, pp. 1286-1296.
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SummaryBackgroundAsthma is a chronic respiratory disease without a cure, although there exists spontaneous remission. Genome‐wide association (GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission.ObjectiveWe performed a GWA study to develop insights in asthma remission.MethodsClinical remission (ClinR) was defined by the absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR). A GWA study on both ClinR and ComR was performed in 790 asthmatics with initial doctor diagnosis of asthma and BHR and long‐term follow‐up. We assessed replication of the 25 top single nucleotide polymorphisms (SNPs) in 2 independent cohorts (total n = 456), followed by expression quantitative loci (eQTL) analyses of the 4 replicated SNPs in lung tissue and epithelium.ResultsOf the 790 asthmatics, 178 (23%) had ClinR and 55 ComR (7%) after median follow‐up of 15.5 (range 3.3‐47.8) years. In ClinR, 1 of the 25 SNPs, rs2740102, replicated in a meta‐analy...

Vuppaladadiyam, AK, Yao, JG, Florin, N, George, A, Wang, X, Labeeuw, L, Jiang, Y, Davis, RW, Abbas, A, Ralph, P, Fennell, PS & Zhao, M 2018, 'Impact of Flue Gas Compounds on Microalgae and Mechanisms for Carbon Assimilation and Utilization', ChemSusChem, vol. 11, no. 2, pp. 334-355.
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AbstractTo shift the world to a more sustainable future, it is necessary to phase out the use of fossil fuels and focus on the development of low‐carbon alternatives. However, this transition has been slow, so there is still a large dependence on fossil‐derived power, and therefore, carbon dioxide is released continuously. Owing to the potential for assimilating and utilizing carbon dioxide to generate carbon‐neutral products, such as biodiesel, the application of microalgae technology to capture CO2 from flue gases has gained significant attention over the past decade. Microalgae offer a more sustainable source of biomass, which can be converted into energy, over conventional fuel crops because they grow more quickly and do not adversely affect the food supply. This review focuses on the technical feasibility of combined carbon fixation and microalgae cultivation for carbon reuse. A range of different carbon metabolisms and the impact of flue gas compounds on microalgae are appraised. Fixation of flue gas carbon dioxide is dependent on the selected microalgae strain and on flue gas compounds/concentrations. Additionally, current pilot‐scale demonstrations of microalgae technology for carbon dioxide capture are assessed and its future prospects are discussed. Practical implementation of this technology at an industrial scale still requires significant research, which necessitates multidisciplinary research and development to demonstrate its viability for carbon dioxide capture from flue gases at the commercial level.

Wadhwa, S, Sharma, DS, Mehta, M, Thakur, D, Mahajan, S, Singh, SK & Satija, S 2018, 'Vitamin D deficiency, skin, and sunshine: A review', International Journal of Green Pharmacy, vol. 12, no. 2, pp. S345-S353.
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The sunshine vitamin - “Vitamin D” is a subject of interest that attracted researcher’s attention in the past few decades. Vitamin D is a fat-soluble vitamin and also a nutrient which increases the calcium absorption and plays an important part in the maintenance of body’s immune system and bone formation. However, the deficiency of Vitamin D, also known as hypovitaminosis D, will affect various body parts such as the brain, heart, muscle, immune system, and bones. Thus, the deficiency leads to severe conditions such as osteopenia, osteoporosis, rickets (in children), hypertension, fractures and falls in adults, cancers, diabetes, autoimmune diseases, infections, and neurological disorders. An effective approach for the deficiency prevention is the thorough understanding of Vitamin D sources, Vitamin D serum levels, and deficiency symptoms, linked with different pathological conditions, requirement and maintenance in the body, sunlight exposure duration, and effective treatment dose. Therefore, the present review will lay an emphasis on the role of Vitamin D, the reasons for its deficiency, available sources, and treatment options reported so far.

WANG De-jiang, 王, DI Xiang-jun, 狄, WANG Bao-ming, 王, WANG Fan, 王帆, GUO Zhi-yong, 郭 & JIN Da-yong, 金 2018, 'Advances in single particle tracking in living cells', Chinese Optics, vol. 11, no. 3, pp. 281-295.
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© 2018, China Science Publishing & Media LTD. All right reserved. Single particle tracking(SPT) technique locates and tracks individual fluorescent or scattering particles within a cell with the help of microscope system. Based on the ability of real-time monitoring of the complex and highly dynamic changes in tissue structure within living cells and the ability to provide dynamic relationships between structure and function, SPT has important applications in cell biology. In this review,the mechanism of SPT and its application on cells are summarized. Firstly, the dynamics of SPT are introduced, including single particle localization, trajectory reconstruction and analysis. Then the optical materials and instruments that SPT technology focuses on at the present stage are described. Finally, the application of SPT in cell membrane, intracellular signaling pathway, molecular transport mechanism, genetic information expression, and viral infection mechanism are proposed. In addition, the advance of SPT technology are prospected in this paper.

Wang, B, Liu, DL, O'Leary, GJ, Asseng, S, Macadam, I, Lines‐Kelly, R, Yang, X, Clark, A, Crean, J, Sides, T, Xing, H, Mi, C & Yu, Q 2018, 'Australian wheat production expected to decrease by the late 21st century', Global Change Biology, vol. 24, no. 6, pp. 2403-2415.
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AbstractClimate change threatens global wheat production and food security, including the wheat industry in Australia. Many studies have examined the impacts of changes in local climate on wheat yield per hectare, but there has been no assessment of changes in land area available for production due to changing climate. It is also unclear how total wheat production would change under future climate when autonomous adaptation options are adopted. We applied species distribution models to investigate future changes in areas climatically suitable for growing wheat in Australia. A crop model was used to assess wheat yield per hectare in these areas. Our results show that there is an overall tendency for a decrease in the areas suitable for growing wheat and a decline in the yield of the northeast Australian wheat belt. This results in reduced national wheat production although future climate change may benefit South Australia and Victoria. These projected outcomes infer that similar wheat‐growing regions of the globe might also experience decreases in wheat production. Some cropping adaptation measures increase wheat yield per hectare and provide significant mitigation of the negative effects of climate change on national wheat production by 2041–2060. However, any positive effects will be insufficient to prevent a likely decline in production under a high CO2 emission scenario by 2081–2100 due to increasing losses in suitable wheat‐growing areas. Therefore, additional adaptation strategies along with investment in wheat production are needed to maintain Australian agricultural production and enhance global food security. This scenario analysis provides a foundation towards understanding changes in Australia's wheat cropping systems, which will assist in developing adaptation strategies to mitigate climate change impacts on global wheat production.

Wang, F, Wen, S, He, H, Wang, B, Zhou, Z, Shimoni, O & Jin, D 2018, 'Microscopic inspection and tracking of single upconversion nanoparticles in living cells', Light: Science & Applications, vol. 7, no. 4, pp. 18007-18007.
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© 2018 The Author(s). Nanoparticles have become new tools for cell biology imaging, sub-cellular sensing, super-resolution imaging, and drug delivery. Long-term 3D tracking of nanoparticles and their intracellular motions have advanced the understanding of endocytosis and exocytosis as well as of active transport processes. The sophisticated operation of correlative optical-electron microscopy and scientific-grade cameras is often used to study intercellular processes. Nonetheless, most of these studies are still limited by the insufficient sensitivity for separating a single nanoparticle from a cluster of nanoparticles or their aggregates8. Here we report that our eyes can track a single fluorescent nanoparticle that emits over 4000 photons per 100 milliseconds under a simple microscope setup. By tracking a single nanoparticle with high temporal, spectral and spatial resolution, we show the measurement of the local viscosity of the intracellular environment. Moreover, beyond the colour domain and 3D position, we introduce excitation power density as the fifth dimension for our eyes to simultaneously discriminate multiple sets of single nanoparticles.

Wang, G 2018, 'Renewable Energy Technologies for Sustainable Development', Advanced Sustainable Systems, vol. 2, no. 8-9, pp. 1800109-1800109.
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Wang, J, Faiz, A, Ge, Q, Vermeulen, CJ, Van der Velden, J, Snibson, KJ, van de Velde, R, Sawant, S, Xenaki, D, Oliver, B, Timens, W, ten Hacken, N, van den Berge, M, James, A, Elliot, JG, Dong, L, Burgess, JK & Ashton, AW 2018, 'Unique mechanisms of connective tissue growth factor regulation in airway smooth muscle in asthma: Relationship with airway remodelling', Journal of Cellular and Molecular Medicine, vol. 22, no. 5, pp. 2826-2837.
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AbstractNeovascularization, increased basal membrane thickness and increased airway smooth muscle (ASM) bulk are hallmarks of airway remodelling in asthma. In this study, we examined connective tissue growth factor (CTGF) dysregulation in human lung tissue and animal models of allergic airway disease. Immunohistochemistry revealed that ASM cells from patients with severe asthma (A) exhibited high expression of CTGF, compared to mild and non‐asthmatic (NA) tissues. This finding was replicated in a sheep model of allergic airways disease. In vitro, transforming growth factor (TGF)‐β increased CTGF expression both in NA‐ and A‐ASM cells but the expression was higher in A‐ASM at both the mRNA and protein level as assessed by PCR and Western blot. Transfection of CTGF promoter‐luciferase reporter constructs into NA‐ and A‐ASM cells indicated that no region of the CTGF promoter (−1500 to +200 bp) displayed enhanced activity in the presence of

Wang, JTH, Huston, WM, Johanesen, P, Lloyd, M & Waller, KL 2018, 'A laboratory competency examination in microbiology', FEMS Microbiology Letters, vol. 365, no. 20.
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© FEMS 2018. All rights reserved. The American Society for Microbiology's curricular guidelines for Introductory Microbiology highlighted key laboratory skills in the isolation, visualization and identification of microorganisms as core learning objectives in the discipline. Since the publication of these guidelines in 2012, there has been a paucity of diagnostic assessment tools in the literature that can be used to assess competencies in the microbiology laboratory. This project aimed to establish a laboratory competency examination for introductory microbiology, with tasks specifically aligned to laboratory skills and learning outcomes outlined in curricular guidelines for microbiology. A Laboratory Competency Examination assessing student skills in light microscopy, Gram-staining, pure culture, aseptic technique, serial dilution, dilution calculations and pipetting was developed at The University of Queensland, Australia. The Laboratory Competency Examination was field-tested in a large introductory microbiology subject (~400 students), and student performance and learning gains data were collected from 2016 to 2017 to evaluate the validity of the assessment. The resulting laboratory assessment is presented as an endpoint diagnostic tool for assessing laboratory competency that can be readily adapted towards different educational contexts.

Wang, K, Titchener, JG, Kruk, SS, Xu, L, Chung, H-P, Parry, M, Kravchenko, II, Chen, Y-H, Solntsev, AS, Kivshar, YS, Neshev, DN & Sukhorukov, AA 2018, 'Quantum metasurface for multiphoton interference and state reconstruction', Science, vol. 361, no. 6407, pp. 1104-1108.
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Going quantum with metamaterials Metasurfaces should allow wafer-thin surfaces to replace bulk optical components. Two reports now demonstrate that metasurfaces can be extended into the quantum optical regime. Wang et al. determined the quantum state of multiple photons by simply passing them through a dielectric metasurface, scattering them into single-photon detectors. Stav et al. used a dielectric metasurface to generate entanglement between spin and orbital angular momentum of single photons. The results should aid the development of integrated quantum optic circuits operating on a nanophotonic platform. Science , this issue p. 1104 , p. 1101

Wang, M, Chen, M, Zhanghao, K, Zhang, X, Jing, Z, Gao, J, Zhang, MQ, Jin, D, Dai, Z, Xi, P & Dai, Q 2018, 'Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information', Nanoscale, vol. 10, no. 42, pp. 19757-19765.
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Super-resolution imaging and orientation detection of surface enhanced Raman scattering nanoparticles using polarization modulation.

Wang, S, Liu, S, Li, X, Li, C, Zang, R, Man, Z, Wu, Y, Li, P & Wang, G 2018, 'SnS₂/Sb₂S₃ Heterostructures Anchored on Reduced Graphene Oxide Nanosheets with Superior Rate Capability for Sodium‐Ion Batteries', Chemistry – A European Journal, vol. 24, no. 15, pp. 3873-3881.
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AbstractTin disulfide, as a promising high‐capacity anode material for sodium‐ion batteries, exhibits high theoretical capacity but poor practical electrochemical properties due to its low electrical conductivity. Constructing heterostructures has been considered to be an effective approach to enhance charge transfer and ion‐diffusion kinetics. In this work, composites of SnS2/Sb2S3 heterostructures with reduced graphene oxide nanosheets were synthesized by a facile one‐pot hydrothermal method. When applied as anode material in sodium‐ion batteries, the composite showed a high reversible capacity of 642 mA h g−1 at a current density of 0.2 A g−1 and good cyclic stability without capacity loss in 100 cycles. In particular, SnS2/Sb2S3 heterostructures exhibited outstanding rate performance with capacities of 593 and 567 mA h g−1 at high current densities of 2 and 4 A g−1, respectively, which could be ascribed to the dramatically improved Na+ diffusion kinetics and electrical conductivity.

Wang, S, Teng, Z, Wang, C & Wang, G 2018, 'Stable and Efficient Nitrogen‐Containing Carbon‐Based Electrocatalysts for Reactions in Energy‐Conversion Systems', ChemSusChem, vol. 11, no. 14, pp. 2267-2295.
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AbstractHigh activity and stability are crucial for the practical use of electrocatalysts in fuel cells, metal–air batteries, and water electrolysis, including the oxygen reduction reaction, hydrogen evolution reaction, oxygen evolution reaction, and oxidation reactions of formic acid and alcohols. Electrocatalysts based on nitrogen‐containing carbon (N‐C) materials show promise in catalyzing these reactions; however, there is no systematic review of strategies for the engineering of active and stable N‐C‐based electrocatalysts. Herein, a comprehensive comparison of recently reported N‐C‐based electrocatalysts regarding both electrocatalytic activity and long‐term stability is presented. In the first part of this review, the relationships between the electrocatalytic reactions and selection of the element to modify the N‐C‐based materials are discussed. Afterwards, synthesis methods for N‐C‐based electrocatalysts are summarized, and strategies for the synthesis of highly stable N‐C‐based electrocatalysts are presented. Multiple tables containing data on crucial parameters for both electrocatalytic activity and stability are displayed in this review. Finally, constructing M‐Nx moieties is proposed as the most promising engineering strategy for stable N‐C‐based electrocatalysts.

Wang, T, Su, D, Shanmukaraj, D, Rojo, T, Armand, M & Wang, G 2018, 'Electrode Materials for Sodium-Ion Batteries: Considerations on Crystal Structures and Sodium Storage Mechanisms', Electrochemical Energy Reviews, vol. 1, no. 2, pp. 200-237.
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Abstract: Sodium-ion batteries have been emerging as attractive technologies for large-scale electrical energy storage and conversion, owing to the natural abundance and low cost of sodium resources. However, the development of sodium-ion batteries faces tremendous challenges, which is mainly due to the difficulty to identify appropriate cathode materials and anode materials. In this review, the research progresses on cathode and anode materials for sodium-ion batteries are comprehensively reviewed. We focus on the structural considerations for cathode materials and sodium storage mechanisms for anode materials. With the worldwide effort, high-performance sodium-ion batteries will be fully developed for practical applications. Graphical Abstract: [Figure not available: see fulltext.]

Wang, X, Qi, Q, Wang, Y, Wu, H, Jin, X, Yao, H, Jin, D, Liu, Y & Wang, C 2018, 'Gut microbiota was modulated by moxibustion stimulation in rats with irritable bowel syndrome', Chinese Medicine, vol. 13, no. 1.
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Ward, J 2018, 'The past, present and future state of missing persons investigations in Australia', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-15.
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Watanabe, S, Kuzhiumparambil, U & Fu, S 2018, 'In vitro metabolism of synthetic cannabinoid AM1220 by human liver microsomes and Cunninghamella elegans using liquid chromatography coupled with high resolution mass spectrometry', Forensic Toxicology, vol. 36, no. 2, pp. 435-446.
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© 2018, The Author(s). Purpose: Identifying intake of synthetic cannabinoids generally requires the metabolism data of the drugs so that appropriate metabolite markers can be targeted in urine testing. However, the continuous appearance of new cannabinoids during the last decade has made it difficult to keep up with all the compounds including {1-[(1-methylpiperidin-2-yl)methyl]-1H-indol-3-yl}(naphthalen-1-yl)methanone (AM1220). In this study, metabolism of AM1220 was investigated with human liver microsomes and the fungus Cunninghamella elegans. Methods: Metabolic stability of AM1220 was analysed by liquid chromatography–tandem mass spectrometry in multiple reaction monitoring mode after 1 µM incubation in human liver microsomes for 30 min. Tentative structure elucidation of metabolites was performed on both human liver microsome and fungal incubation samples using liquid chromatography–high-resolution mass spectrometry. Results: Half-life of AM1220 was estimated to be 3.7 min, indicating a high clearance drug. Nine metabolites were detected after incubating human liver microsomes while seven were found after incubating Cunninghamella elegans, leading to 11 metabolites in total (five metabolites were common to both systems). Demethylation, dihydrodiol formation, combination of the two, hydroxylation and dihydroxylation were the observed biotransformations. Conclusions: Three most abundant metabolites in both human liver microsomes and Cunninghamella elegans were desmethyl, dihydrodiol and hydroxy metabolites, despite different isomers of dihydrodiol and hydroxy metabolites in each model. These abundant metabolites can potentially be useful markers in urinalysis for AM1220 intake.

Watanabe, S, Kuzhiumparambil, U & Fu, S 2018, 'Structural Elucidation of Metabolites of Synthetic Cannabinoid UR-144 by Cunninghamella elegans Using Nuclear Magnetic Resonance (NMR) Spectroscopy', The AAPS Journal, vol. 20, no. 2.
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© 2018, American Association of Pharmaceutical Scientists. The number of new psychoactive substances keeps on rising despite the controlling efforts by law enforcement. Although metabolism of the newly emerging drugs is continuously studied to keep up with the new additions, the exact structures of the metabolites are often not identified due to the insufficient sample quantities for techniques such as nuclear magnetic resonance (NMR) spectroscopy. The aim of the study was to characterise several metabolites of the synthetic cannabinoid (1-pentyl-1H-indol-3-yl) (2,2,3,3-tetramethylcyclopropyl) methanone (UR-144) by NMR spectroscopy after the incubation with the fungus Cunninghamella elegans. UR-144 was incubated with C. elegans for 72 h, and the resulting metabolites were chromatographically separated. Six fractions were collected and analysed by NMR spectroscopy. UR-144 was also incubated with human liver microsomes (HLM), and the liquid chromatography-high resolution mass spectrometry analysis was performed on the HLM metabolites with the characterised fungal metabolites as reference standards. Ten metabolites were characterised by NMR analysis including dihydroxy metabolites, carboxy and hydroxy metabolites, a hydroxy and ketone metabolite, and a carboxy and ketone metabolite. Of these metabolites, dihydroxy metabolite, carboxy and hydroxy metabolites, and a hydroxy and ketone metabolite were identified in HLM incubation. The results indicate that the fungus is capable of producing human-relevant metabolites including the exact isomers. The capacity of the fungus C. elegans to allow for NMR structural characterisation by enabling production of large amounts of metabolites makes it an ideal model to complement metabolism studies.

Waters, L, Cameron, M, Padula, MP, Marks, DC & Johnson, L 2018, 'Refrigeration, cryopreservation and pathogen inactivation: an updated perspective on platelet storage conditions', Vox Sanguinis, vol. 113, no. 4, pp. 317-328.
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AbstractConventional storage of platelet concentrates limits their shelf life to between 5 and 7 days due to the risk of bacterial proliferation and the development of the platelet storage lesion. Cold storage and cryopreservation of platelets may facilitate extension of the shelf life to weeks and years, and may also provide the benefit of being more haemostatically effective than conventionally stored platelets. Further, treatment of platelet concentrates with pathogen inactivation systems reduces bacterial contamination and provides a safeguard against the risk of emerging and re‐emerging pathogens. While each of these alternative storage techniques is gaining traction individually, little work has been done to examine the effect of combining treatments in an effort to further improve product safety and minimize wastage. This review aims to discuss the benefits of alternative storage techniques and how they may be combined to alleviate the problems associated with conventional platelet storage.

Watherston, J, McNevin, D, Gahan, ME, Bruce, D & Ward, J 2018, 'Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification', Forensic Science International: Genetics, vol. 37, pp. 270-282.
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© 2018 Elsevier B.V. DNA profiling has emerged as the gold standard for the identification of victims in mass disaster events providing an ability to identify victims, reassociate remains and provide investigative leads at a relatively low cost, and with a high degree of discrimination. For the majority of samples, DNA-based identification can be achieved in a fast, streamlined and high-throughput manner. However, a large number of remains will be extremely compromised, characteristic of mass disasters. Advances in technology and in the field of forensic biology have increased the options for the collection, sampling, preservation and processing of samples for DNA profiling. Furthermore, recent developments now allow a vast array of new genetic markers and genotyping techniques to extract as much genetic information from a sample as possible, ensuring that identification is not only accurate but also possible where material is degraded, or limited. Where historically DNA profiling has involved comparison with ante mortem samples or relatives, now DNA profiling can direct investigators towards putative victims or relatives, for comparison through the determination of externally visible characteristics, or biogeographical ancestry. This paper reviews the current and emerging tools available for maximising the recovery of genetic information from post mortem samples in a disaster victim identification context.

Wee, BA, Thomas, M, Sweeney, EL, Frentiu, FD, Samios, M, Ravel, J, Gajer, P, Myers, G, Timms, P, Allan, JA & Huston, WM 2018, 'A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women', Australian and New Zealand Journal of Obstetrics and Gynaecology, vol. 58, no. 3, pp. 341-348.
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BackgroundWe know very little about the microbiota inhabiting the upper female reproductive tract and how it impacts on fertility.AimsThis pilot study aimed to examine the vaginal, cervical and endometrial microbiota for women with a history of infertility compared to women with a history of fertility.Materials and methodsUsing a retrospective case–control study design, women were recruited for collection of vaginal, cervical and endometrial samples. The microbiota composition was analysed by 16S ribosomal RNA (rRNA) gene amplification and endometrial expression of selected human genes by quantitative reverse transcription polymerase chain reaction.ResultsSixty‐five specimens from the reproductive tract of 31 women were successfully analysed using 16S rRNA gene amplicon sequencing (16 controls and 15 cases). The dominant microbial community members were consistent in the vagina and cervix, and generally consistent with the endometrium although the relative proportions varied. We detected three major microbiota clusters that did not group by tissue location or case–control status. There was a trend that infertile women more often had Ureaplasma in the vagina and Gardnerella in the cervix. Testing for the expression of selected genes in the endometrium did not show evidence of correlation with case–control status, or with microbial community composition, although Tenascin‐C expression correlated with a history of miscarriage.ConclusionsThere is a need for further exploration of the endometrial microbiota, and how the microbiota members or profile interplays with fertility or assisted reproductive technologies.

Wei, Z, Piantavigna, S, Holt, SA, Nelson, A, Spicer, PT & Prescott, SW 2018, 'Comparing Surfactant Structures at “Soft” and “Hard” Hydrophobic Materials: Not All Interfaces Are Equivalent', Langmuir, vol. 34, no. 31, pp. 9141-9152.
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Welford, A, Maniam, S, Gann, E, Thomsen, L, Langford, SJ & McNeill, CR 2018, 'Thionation of naphthalene diimide molecules: Thin-film microstructure and transistor performance', Organic Electronics, vol. 53, pp. 287-295.
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Wen, S, Zhou, J, Zheng, K, Bednarkiewicz, A, Liu, X & Jin, D 2018, 'Advances in highly doped upconversion nanoparticles', Nature Communications, vol. 9, no. 1, pp. 2415-2415.
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AbstractLanthanide-doped upconversion nanoparticles (UCNPs) are capable of converting near-infra-red excitation into visible and ultraviolet emission. Their unique optical properties have advanced a broad range of applications, such as fluorescent microscopy, deep-tissue bioimaging, nanomedicine, optogenetics, security labelling and volumetric display. However, the constraint of concentration quenching on upconversion luminescence has hampered the nanoscience community to develop bright UCNPs with a large number of dopants. This review surveys recent advances in developing highly doped UCNPs, highlights the strategies that bypass the concentration quenching effect, and discusses new optical properties as well as emerging applications enabled by these nanoparticles.

Wenzel, R, Major, D, Hesp, K & Doble, P 2018, 'Determination of vitamin B12 in equine urine by liquid chromatography – inductively coupled plasma – mass spectrometry', Journal of Trace Elements in Medicine and Biology, vol. 50, pp. 634-639.
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© 2018 Elsevier GmbH Regulating authorities in the racing industry have restricted the administration of potentially performance enhancing cobalt salts to horses. There are severe penalties for trainers presenting horses with elevated urine cobalt concentrations, and compliance is ensured via analysis of total urinary cobalt at thresholds of 100 μg/L. When cobalt is present as part of the cobalamin molecule it is not considered performance enhancing. This paper demonstrates that a horse can excrete a significant proportion of a commercially available vitamin B12 injection in urine without metabolic modification. A liquid chromatography – inductively coupled plasma – mass spectrometry (LC-ICP-MS) method is presented for urinary cobalt speciation. Given the serious nature surrounding performance enhancing drug offences, we conclude that presumptive positives identified by urine total cobalt measurements require further analysis to differentiate inorganic cobalt from vitamin B12.

Winters, BL, Rawling, T, Vandenberg, RJ, Christie, MJ, Bhola, RF & Imlach, WL 2018, 'Activity of novel lipid glycine transporter inhibitors on synaptic signalling in the dorsal horn of the spinal cord', British Journal of Pharmacology, vol. 175, no. 12, pp. 2337-2347.
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Background and PurposeInhibitory neurotransmission plays an important role in controlling excitability within nociceptive circuits of the spinal cord dorsal horn. Loss of inhibitory signalling is thought to contribute to the development of pathological pain. Preclinical studies suggest that increasing inhibitory glycinergic signalling is a good therapeutic strategy for treating pain. One approach to increase synaptic glycine is to inhibit the activity of the glycine transporter 2 (GlyT2) on inhibitory nerve terminals. These transporters are involved in regulating glycine concentrations and recycling glycine into presynaptic terminals. Inhibiting activity of GlyT2 increases synaptic glycine, which decreases excitability in nociceptive circuits and provides analgesia in neuropathic and inflammatory pain models.Experimental ApproachWe investigated the effects of reversible and irreversible GlyT2 inhibitors on inhibitory glycinergic and NMDA receptor‐mediated excitatory neurotransmission in the rat dorsal horn. The effect of these drugs on synaptic signalling was determined using patch‐clamp electrophysiology techniques to measure glycine‐ and NMDA‐mediated postsynaptic currents in spinal cord slices in vitro.Key ResultsWe compared activity of four compounds that increase glycinergic tone with a corresponding increase in evoked glycinergic postsynaptic currents. These compounds did not deplete synaptic glycine release over time. Interestingly, none of these compounds increased glycine‐mediated excitatory signalling through NMDA receptors. The results suggest that these compounds preferentially inhibit GlyT2 over G1yT1 with no potentiation of the glycine receptor and without inducing spillover from inhibitory to excitatory synapses.

Wong, MG, The, NL & Glastras, S 2018, 'Maternal obesity and offspring risk of chronic kidney disease', Nephrology, vol. 23, no. S4, pp. 84-87.
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ABSTRACTIt is increasingly recognized that maternal obesity is implicated in developmental programming, contributing to the future risk of chronic disease development in offspring. The exact mechanisms of the role of maternal obesity in the development of chronic kidney disease in offspring remain unclear and animal models used are not without limitation. Human studies are limited by the effects of postnatal environmental conditions, which may have a direct impact on disease phenotype; and animal models are limited by use of species that differ significantly. This review will examine the most recent evidence from animal models on the impact of maternal factors during pregnancy/lactation on the future risk of chronic kidney disease development in offspring, emphasising the role of maternal obesity in exacerbating the deleterious effects of diet‐induced obesity and/or diabetes on renal health.

Wong, SL, To, J, Santos, J, Allam, VSRR, Dalton, JP, Djordjevic, SP, Donnelly, S, Padula, MP & Sukkar, MB 2018, 'Proteomic Analysis of Extracellular HMGB1 Identifies Binding Partners and Exposes Its Potential Role in Airway Epithelial Cell Homeostasis', Journal of Proteome Research, vol. 17, no. 1, pp. 33-45.
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© 2017 American Chemical Society. The release of damage-associated molecular patterns (DAMPs) by airway epithelial cells is believed to play a crucial role in the initiation and development of chronic airway conditions such as asthma and chronic obstructive pulmonary disease (COPD). Intriguingly, the classic DAMP high-mobility group box-1 (HMGB1) is detected in the culture supernatant of airway epithelial cells under basal conditions, indicating a role for HMGB1 in the regulation of epithelial cellular and immune homeostasis. To gain contextual insight into the potential role of HMGB1 in airway epithelial cell homeostasis, we used the orthogonal and complementary methods of high-resolution clear native electrophoresis, immunoprecipitation, and pull-downs coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) to profile HMGB1 and its binding partners in the culture supernatant of unstimulated airway epithelial cells. We found that HMGB1 presents exclusively as a protein complex under basal conditions. Moreover, protein network analysis performed on 185 binding proteins revealed 14 that directly associate with HMGB1: amyloid precursor protein, F-actin-capping protein subunit alpha-1 (CAPZA1), glyceraldehyde-3 phosphate dehydrogenase (GAPDH), ubiquitin, several members of the heat shock protein family (HSPA8, HSP90B1, HSP90AA1), XRCC5 and XRCC6, high mobility group A1 (HMGA1), histone 3 (H3F3B), the FACT (facilitates chromatin transcription) complex constituents SUPT1H and SSRP1, and heterogeneous ribonucleoprotein K (HNRNPK). These studies provide a new understanding of the extracellular functions of HMGB1 in cellular and immune homeostasis at the airway mucosal surface and could have implications for therapeutic targeting.

Wonoputri, V, Gunawan, C, Liu, S, Barraud, N, Yee, LH, Lim, M & Amal, R 2018, 'Ferrous ion as a reducing agent in the generation of antibiofilm nitric oxide from a copper-based catalytic system', Nitric Oxide, vol. 75, pp. 8-15.
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© 2018 Elsevier Inc. The work found that the electron-donating properties of ferrous ions (Fe2+) can be used for the conversion of nitrite (NO2−) into the biofilm-dispersing signal nitric oxide (NO) by a copper(II) complex (CuDTTCT) catalyst, a potentially applicable biofilm control technology for the water industries. The availability of Fe2+ varied depending on the characteristics of the aqueous systems (phosphate- and carbonate-containing nitrifying bacteria growth medium, NBGM and phosphate buffered saline, PBS at pH 6 to 8, to simulate conditions typically present in the water industries) and was found to affect the production of NO from nitrite by CuDTTCT (casted into PVC). Greater amounts of NO were generated from the CuDTTCT-nitrite-Fe2+ systems in PBS compared to those in NBGM, which was associated with the reduced extent of Fe2+-to-Fe3+ autoxidation by the iron-precipitating moieties phosphates and carbonate in the former system. Further, acidic conditions at pH 6.0 were found to favor NO production from the catalytic system in both PBS and NBGM compared to neutral or basic pH (pH 7.0 or 8.0). Lower pH was shown to stabilize Fe2+ and reduce its autoxidation to Fe3+. These findings will be beneficial for the potential implementation of the NO-generating catalytic technology and indeed, a ‘non-killing’ biofilm dispersal activity of CuDTTCT-nitrite-Fe2+ was observed on nitrifying bacteria biofilms in PBS at pH 6.

Woodcock, S 2018, 'Sdrawkcab scitamehtam: The case for understanding mathematics backwards', ANZIAM Journal, vol. 59, pp. 143-143.
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Woodhall, SC, Gorwitz, RJ, Migchelsen, SJ, Gottlieb, SL, Horner, PJ, Geisler, WM, Winstanley, C, Hufnagel, K, Waterboer, T, Martin, DL, Huston, WM, Gaydos, CA, Deal, C, Unemo, M, Dunbar, JK & Bernstein, K 2018, 'Advancing the public health applications of Chlamydia trachomatis serology', The Lancet Infectious Diseases, vol. 18, no. 12, pp. e399-e407.
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© 2018 Elsevier Ltd Genital Chlamydia trachomatis infection is the most commonly diagnosed sexually transmitted infection. Trachoma is caused by ocular infection with C trachomatis and is the leading infectious cause of blindness worldwide. New serological assays for C trachomatis could facilitate improved understanding of C trachomatis epidemiology and prevention. C trachomatis serology offers a means of investigating the incidence of chlamydia infection and might be developed as a biomarker of scarring sequelae, such as pelvic inflammatory disease. Therefore, serological assays have potential as epidemiological tools to quantify unmet need, inform service planning, evaluate interventions including screening and treatment, and to assess new vaccine candidates. However, questions about the performance characteristics and interpretation of C trachomatis serological assays remain, which must be addressed to advance development within this field. In this Personal View, we explore the available information about C trachomatis serology and propose several priority actions. These actions involve development of target product profiles to guide assay selection and assessment across multiple applications and populations, establishment of a serum bank to facilitate assay development and evaluation, and development of technical and statistical methods for assay evaluation and analysis of serological findings. The field of C trachomatis serology will benefit from collaboration across the public health community to align technological developments with their potential applications.

Wright, ST, Ryan, LM & Pham, T 2018, 'A novel case‐control subsampling approach for rapid model exploration of large clustered binary data', Statistics in Medicine, vol. 37, no. 6, pp. 899-913.
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In many settings, an analysis goal is the identification of a factor, or set of factors associated with an event or outcome. Often, these associations are then used for inference and prediction. Unfortunately, in the big data era, the model building and exploration phases of analysis can be time‐consuming, especially if constrained by computing power (ie, a typical corporate workstation). To speed up this model development, we propose a novel subsampling scheme to enable rapid model exploration of clustered binary data using flexible yet complex model set‐ups (GLMMs with additive smoothing splines). By reframing the binary response prospective cohort study into a case‐control–type design, and using our knowledge of sampling fractions, we show one can approximate the model estimates as would be calculated from a full cohort analysis. This idea is extended to derive cluster‐specific sampling fractions and thereby incorporate cluster variation into an analysis. Importantly, we demonstrate that previously computationally prohibitive analyses can be conducted in a timely manner on a typical workstation. The approach is applied to analysing risk factors associated with adverse reactions relating to blood donation.

Wu, J, Kobayashi, H, Stark, SC, Meng, R, Guan, K, Tran, NN, Gao, S, Yang, W, Restrepo‐Coupe, N, Miura, T, Oliviera, RC, Rogers, A, Dye, DG, Nelson, BW, Serbin, SP, Huete, AR & Saleska, SR 2018, 'Biological processes dominate seasonality of remotely sensed canopy greenness in an Amazon evergreen forest', New Phytologist, vol. 217, no. 4, pp. 1507-1520.
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SummarySatellite observations of Amazon forests show seasonal and interannual variations, but the underlying biological processes remain debated.Here we combined radiative transfer models (RTMs) with field observations of Amazon forest leaf and canopy characteristics to test three hypotheses for satellite‐observed canopy reflectance seasonality: seasonal changes in leaf area index, in canopy‐surface leafless crown fraction and/or in leaf demography.Canopy RTMs (PROSAIL and FLiES), driven by these three factors combined, simulated satellite‐observed seasonal patterns well, explaining c. 70% of the variability in a key reflectance‐based vegetation index (MAIAC EVI, which removes artifacts that would otherwise arise from clouds/aerosols and sun–sensor geometry). Leaf area index, leafless crown fraction and leaf demography independently accounted for 1, 33 and 66% of FLiES‐simulated EVI seasonality, respectively. These factors also strongly influenced modeled near‐infrared (NIR) reflectance, explaining why both modeled and observed EVI, which is especially sensitive to

Wu, P-J, Masouleh, MI, Dini, D, Paterson, C, Torok, P, Overby, DR & Kabakova, IV 2018, 'Detection of Proteoglycan Loss from Articular Cartilage using Brillouin Microscopy, with Applications to Osteoarthritis', Biomedical Optics Express, vol. 10, no. 5, pp. 2457-2466.
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The degeneration of articular cartilage (AC) occurs in osteoarthritis (OA),which is a leading cause of pain and disability in middle-aged and olderpeople. The early disease related changes in cartilage extra-cellular matrix(ECM) start with depletion of proteoglycan(PG), leading to an increase intissue hydration and permeability. These early compositional changes are small(<10%) and hence difficult to register with conventional non-invasive imagingtechnologies (magnetic resonance and ultrasound imaging). Here we applyBrillouin microscopy for detecting changes in the mechanical properties andcomposition of porcine AC. OA-like degradation is mimicked by enzymatic tissuedigestion, and we compare Brillouin microscopy measurements againsthistological staining of PG depletion over varying digestion times and enzymeconcentrations. The non-destructive nature of Brillouin imaging technologyopens new avenues for creating minimally invasive arthroscopic devices for OAdiagnostics and therapeutic monitoring.

Wu, X, Howe, ENW & Gale, PA 2018, 'Supramolecular Transmembrane Anion Transport: New Assays and Insights', Accounts of Chemical Research, vol. 51, no. 8, pp. 1870-1879.
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Wu, Y, Li, S, Liu, J, Liu, X, Ruan, W, Lu, J, Liu, Y, Lawson, T, Shimoni, O, Lovejoy, DB, Walker, AK, Cong, Y & Shi, B 2018, 'Stilbenes from Veratrum maackii Regel Protect against Ethanol-Induced DNA Damage in Mouse Cerebellum and Cerebral Cortex', ACS Chemical Neuroscience, vol. 9, no. 7, pp. 1616-1624.
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© Copyright 2018 American Chemical Society. Ethanol is a principle ingredient of alcoholic beverages with potential neurotoxicity and genotoxicity, and the ethanol-associated oxidative DNA damage in the central nervous system is well documented. Natural source compounds may offer new options to protect the brain against ethanol-induced genotoxicity. Veratrum maackii Regel is a toxic rangeland plant linked to teratogenicity which is also used in traditional Chinese medicine as 'Lilu' and is reported to contain a family of compounds called stilbenes that can have positive biological activity. In this study, nine stilbenes were isolated from the aerial parts of V. maackii Regel, and their structures were identified as cis-mulberroside A (1), resveratrol-4,3′-O-β-d-diglucopyranoside (2), mulberroside A (3), gentifolin K (4), resveratrol-3,5-O-β-d-diglucopyranoside (5), oxyresveratrol- 4′-O-β-d-glucopyranoside (6), oxyresveratrol-3-O-β-d-glucopyranoside (7), oxyresveratrol (8), and resveratrol (9) using ESI-MS and NMR techniques. The total concentration of extracted compounds 2-9 was 2.04 mg/g, suggesting that V. maackii Regel is a novel viable source of these compounds. In an in vivo comet assay, compounds 1-9 were observed to decrease DNA damage in mouse cerebellum and cerebral cortex caused by acute ethanol administration. Histological observation also revealed decreased brain injury in mice administered with compounds 1-9 after acute ethanol administration. The protective effects of compound 6 were associated with increasing T-SOD and GSH-PX activities and a decrease in NO and MDA concentrations. These findings suggest that these compounds are potent inhibitors of ethanol-induced brain injury possibly via the inhibition of oxidative stress and may be valuable leads for future therapeutic development.

Xiao, H, Zaslawski, C, Vardy, J & Oh, B 2018, 'Treatment of Sciatica Following Uterine Cancer with Acupuncture: A Case Report', Medicines, vol. 5, no. 1, pp. 6-6.
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For women, gynaecological or obstetrical disorders are second to disc prolapse as the most common cause of sciatica. As not many effective conventional treatments can be found for sciatica following uterine cancer, patients may seek assistance from complementary and alternative medicine. Here, we present a case of a woman with severe and chronic sciatica secondary to uterine cancer who experienced temporary relief from acupuncture.

Xiao, L, Alder, R, Mehta, M, Krayem, N, Cavasinni, B, Laracy, S, Cameron, S & Fu, S 2018, 'Development of a quantitative method for the analysis of cocaine analogue impregnated into textiles by Raman spectroscopy', Drug Testing and Analysis, vol. 10, no. 4, pp. 761-767.
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AbstractCocaine trafficking in the form of textile impregnation is routinely encountered as a concealment method. Raman spectroscopy has been a popular and successful testing method used for in situ screening of cocaine in textiles and other matrices. Quantitative analysis of cocaine in these matrices using Raman spectroscopy has not been reported to date. This study aimed to develop a simple Raman method for quantifying cocaine using atropine as the model analogue in various types of textiles. Textiles were impregnated with solutions of atropine in methanol. The impregnated atropine was extracted using less hazardous acidified water with the addition of potassium thiocyanate (KSCN) as an internal standard for Raman analysis. Despite the presence of background matrix signals arising from the textiles, the cocaine analogue could easily be identified by its characteristic Raman bands. The successful use of KSCN normalised the analyte signal response due to different textile matrix background interferences and thus removed the need for a matrix‐matched calibration. The method was linear over a concentration range of 6.25–37.5 mg/cm2 with a coefficient of determination (R2) at 0.975 and acceptable precision and accuracy. A simple and accurate Raman spectroscopy method for the analysis and quantification of a cocaine analogue impregnated in textiles has been developed and validated for the first time. This proof‐of‐concept study has demonstrated that atropine can act as an ideal model compound to study the problem of cocaine impregnation in textile. The method has the potential to be further developed and implemented in real world forensic cases.

Xiao, L, Bhadbhade, M & Baker, AT 2018, 'Reversible five-coordinate ⇄ six-coordinate transformation in cobalt(II) complexes', Journal of Molecular Structure, vol. 1157, pp. 112-118.
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© 2017 Elsevier B.V. The heterocyclic ligands 2,6-bis(pyrazol-1-yl)pyridine (L1) and 2,6-bis(benzimidazol-2-yl)pyridine (L2) and their cobalt(II) complexes were synthesized. The blue five-coordinate complex [Co(L1)Cl2] isolated initially from the reaction mixture rapidly absorbed water vapour from the atmosphere to yield the pink six-coordinate complex [Co(L1)(H2O)3]Cl2. This change is reversible upon desiccation or transferring [Co(L1)(H2O)3]Cl2 into acetonitrile. The five coordinate complex [Co(L2)Cl2], however, remains stable under similar conditions. The structures of the complexes [Co(L1)Cl2], [Co(L1)(H2O)3]Cl2 and [Co(L2)Cl2] have been determined by x-ray crystallography. The magnetic susceptibilities and the electronic spectra for [Co(L1)Cl2], [Co(L2)Cl2] and [Co(L1)(H2O)3]Cl2 are presented.

Xie, X, Kretschmer, K, Anasori, B, Sun, B, Wang, G & Gogotsi, Y 2018, 'Porous Ti₃C₂T_x MXene for Ultrahigh-Rate Sodium-Ion Storage with Long Cycle Life', ACS Applied Nano Materials, vol. 1, no. 2, pp. 505-511.
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The development of anode materials remains a challenge to satisfy the requirements of sodium-ion storage for large-scale energy-storage applications, which is ascribed to the low kinetics of ionic/electron transfer of electrode materials. Here we show that the controlled anisotropic assembly of highly conductive Ti3C2Tx MXene nanosheets to form a porous structure can enhance the sodium-ion storage kinetics. At high current densities of 1 and 10 A g-1, the porous Ti3C2Tx electrode delivered capacities of 166 and 124 mA h g-1, respectively. Even at an extremely high current density of 100 A g-1, a capacity of 24 mA h g-1 could be achieved. The porous Ti3C2Tx electrode also exhibited a long cycle life that can be extended to 1000 cycles with no capacity decay at a current density of 1 A g-1. This work demonstrates successful control of the Ti3C2Tx architecture to push electrochemical sodium-ion storage closer to large-scale applications and is expected to shed light on the rational utilization of the outstanding properties of MXenes by controlling their microscopic assembly.

Xiong, P, Zhang, X, Zhang, F, Yi, D, Zhang, J, Sun, B, Tian, H, Shanmukaraj, D, Rojo, T, Armand, M, Ma, R, Sasaki, T & Wang, G 2018, 'Two-Dimensional Unilamellar Cation-Deficient Metal Oxide Nanosheet Superlattices for High-Rate Sodium Ion Energy Storage', ACS Nano, vol. 12, no. 12, pp. 12337-12346.
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Cation-deficient two-dimensional (2D) materials, especially atomically thin nanosheets, are highly promising electrode materials for electrochemical energy storage that undergo metal ion insertion reactions, yet they have rarely been achieved thus far. Here, we report a Ti-deficient 2D unilamellar lepidocrocite-type titanium oxide (Ti0.87O2) nanosheet superlattice for sodium storage. The superlattice composed of alternately restacked defective Ti0.87O2 and nitrogen-doped graphene monolayers exhibits an outstanding capacity of ∼490 mA h g-1 at 0.1 A g-1, an ultralong cycle life of more than 10000 cycles with ∼0.00058% capacity decay per cycle, and especially superior low-temperature performance (100 mA h g-1 at 12.8 A g-1 and -5 °C), presenting the best reported performance to date. A reversible Na+ ion intercalation mechanism without phase and structural change is verified by first-principles calculations and kinetics analysis. These results herald a promising strategy to utilize defective 2D materials for advanced energy storage applications.

Xu, J, Fan, H, Su, D & Wang, G 2018, 'Nitrogen doped yolk-shell carbon spheres as cathode host for lithium-sulfur battery', Journal of Alloys and Compounds, vol. 747, pp. 283-292.
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© 2018 Elsevier B.V. Suppressing the shuttle effect while maintaining high sulfur content is the primary challenge for the development of lithium-sulfur (Li-S) batteries. An effective encapsulator for Li-S battery is supposed to have enough void space for sulfur accommodation and alleviation of volume expansion. Moreover, an excellent electronic conductivity is also crucial for high sulfur utilization. Thus, we designed mesoporous nitrogen doped yolk-shell carbon (NYSC) spheres as novel sulfur encapsulators. This unique structure design greatly fulfills the synergistic effect of chemisorption and physisorption for polysulfides, specially at high sulfur loading. The inner mesoporous “yolk” acts as a sulfur reservoir to entrap polysulfide species. Meanwhile, the outer “shell” serves as a physical barrier to alleviate the dissolution of polysulfides. Additionally, the doped nitrogen atom in carbon lattice can modify the electron distribution, introduce more defects and active sites for the chemisorption of polysulfides, improve the reversibility of Li2S/polysulfide/S conversion and the electronic conductivity, contributing to the enhanced electrochemical performance for Li-S batteries (a high specific capacity of 1329 mA h g−1 at 0.2 C and an extended cycle life).

Xu, J, Lawson, T, Fan, H, Su, D & Wang, G 2018, 'Updated Metal Compounds (MOFs, S, OH, N, C) Used as Cathode Materials for Lithium–Sulfur Batteries', Advanced Energy Materials, vol. 8, no. 10, pp. 1702607-1702607.
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AbstractLithium–sulfur (Li–S) batteries have the potential to be as efficient and as widespread as lithium‐ion (Li‐ion) batteries, since sulfur electrode has high theoretical capacity (1672 mA h gsul−1) and this element is affordable. However, unlike their ubiquitous lithium ion (Li‐ion) counterparts, it is difficult to realize the commercialization of Li‐S battery. Because the shuttle effect of polysulfide inevitably results in the serious capacity degradation. Tremendous progress is devoted to approach this problem from the aspect of physical confinement and chemisorption of polysulfide. Owing to weak intermolecular interactions, physical confinement strategy, however is not effective when the battery is cycled long‐term. Chemisorption of polysulfide that derived from polar–polar interaction, Lewis acid–base interaction, and sulfur‐chain catenation, are proven to significantly suppress the shuttle effect of polysulfide. It is also discovered that the metal compounds have strong chemical interactions with polysulfide. Therefore, this review focuses on latest metal–organic frameworks metal sulfides, metal hydroxides, metal nitrides, metal carbides, and discusses how the chemical interactions couple with the unique properties of these metal compounds to tackle the problem of polysulfide shuttle effect.

Xu, J, Zhang, W, Chen, Y, Fan, H, Su, D & Wang, G 2018, 'MOF-derived porous N–Co₃O₄@N–C nanododecahedra wrapped with reduced graphene oxide as a high capacity cathode for lithium–sulfur batteries', Journal of Materials Chemistry A, vol. 6, no. 6, pp. 2797-2807.
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N–Co₃O₄@N–C nanododecahedra combine the advantages of strong affinity for polysulfides and excellent electronic conductivity.

Xu, J, Zhang, W, Fan, H, Cheng, F, Su, D & Wang, G 2018, 'Promoting lithium polysulfide/sulfide redox kinetics by the catalyzing of zinc sulfide for high performance lithium-sulfur battery', Nano Energy, vol. 51, pp. 73-82.
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© 2018 Entrapping polysulfide from dissolution into electrolyte by strong chemisorption of polar materials has been widely reported in lithium-sulfur (Li-S) battery. Here, for the first time, zinc sulfide (ZnS) was demonstrated as an activation catalyst in Li-S battery to suppress the soluble polysulfide shuttle effect by powering kinetics redox reactions of lithium polysulfide/sulfide. Kinetic analyses comprehensively identify that ZnS not only facilities polysulfide redox kinetics in liquid phase (Li2S8→Li2S6→Li2S4), but also promotes the effective decompositions of lithium sulfide (Li2S). Furthermore, first-principle calculations confirm that the low lithium ion diffusion barrier on the surface of ZnS promotes the redox reaction between lithium ion and sulfur species; and the low migration energy barrier of polysulfide on its surface guarantees the fast diffussion of polysulfides from the ZnS surface to the nearby conductive substrate, thus effectively smoothes polysulfides’ entrapping-diffusion-conversion mechanism across the ZnS interface, resulting in the highly reversible electrochemical performance. As evidenced by the ex situ SEM and visible experiment, the reaction between migrated sulfur species and lithium anode was significantly alleviated, and the insulating Li2S/Li2S2 was uniformly deposited on the ZnS-CB/S cathode. This ZnS cathode based Li-S battery exhibits outstanding performance including an excellent retained discharge specific capacity of 589 mA h gsul−1 with the high sulfur loading of 7 mg cm−2 (200 cycles) and extended cycling stability at the high current rate of 2 C, 5 C (632, 388 mA h gsul−1 after 1000 cycles).

Xu, X, Zhou, D, Qin, X, Lin, K, Kang, F, Li, B, Shanmukaraj, D, Rojo, T, Armand, M & Wang, G 2018, 'A room-temperature sodium–sulfur battery with high capacity and stable cycling performance', Nature Communications, vol. 9, no. 1, pp. 3870-3870.
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AbstractHigh-temperature sodium–sulfur batteries operating at 300–350 °C have been commercially applied for large-scale energy storage and conversion. However, the safety concerns greatly inhibit their widespread adoption. Herein, we report a room-temperature sodium–sulfur battery with high electrochemical performances and enhanced safety by employing a “cocktail optimized” electrolyte system, containing propylene carbonate and fluoroethylene carbonate as co-solvents, highly concentrated sodium salt, and indium triiodide as an additive. As verified by first-principle calculation and experimental characterization, the fluoroethylene carbonate solvent and high salt concentration not only dramatically reduce the solubility of sodium polysulfides, but also construct a robust solid-electrolyte interface on the sodium anode upon cycling. Indium triiodide as redox mediator simultaneously increases the kinetic transformation of sodium sulfide on the cathode and forms a passivating indium layer on the anode to prevent it from polysulfide corrosion. The as-developed sodium–sulfur batteries deliver high capacity and long cycling stability.

Yam, J, Gestier, S, Bryant, B, Campbell-Ward, M, Bogema, D & Jenkins, C 2018, 'The identification of Theileria bicornis in captive rhinoceros in Australia', International Journal for Parasitology: Parasites and Wildlife, vol. 7, no. 1, pp. 85-89.
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Yan, K, Sun, B, Munroe, P & Wang, G 2018, 'Three-dimensional pie-like current collectors for dendrite-free lithium metal anodes', Energy Storage Materials, vol. 11, pp. 127-133.
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© 2017 Lithium (Li) metal possesses very high specific capacity and low electrochemical potential, which shows great advantages to be used in next generation rechargeable Li metal batteries (LMBs). However, poor cyclability of Li metal anodes caused by inhomogeneous and uncontrolled Li deposition hinders the practical applications of rechargeable LMBs. Here, in order to effectively suppress Li dendrite growth without degrading the specific capacity, a three-dimensional (3D) pie-like porous current collector was prepared based on copper nanowires (CuNWs) and graphene (GE). The inter-spaces inside the CuNWs framework efficiently accommodate Li deposition. Meanwhile, the GE layer wrapped outside CuNWs functions as flexible interfacial protective layer that could protect extra Li deposition. Furthermore, the GE shell can also decelerate the oxidation of CuNWs in ambient atmosphere. The CuNWs@GE current collectors demonstrated several merits to achieve better Li metal anodes with significantly improved Coulombic efficiency and cyclability for rechargeable LMBs.

Yang, CH, Zhang, JY, Wang, GX & Zhang, C 2018, 'Dependence of the optical conductivity on the uniaxial and biaxial strains in black phosphorene', Physical Review B, vol. 97, no. 24.
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© 2018 American Physical Society. By using the Kubo formula, the optical conductivity of strained black phosphorene was studied. The anisotropic band dispersion gives rise to an orientation dependent optical conductivity. The energy gap can be tuned by the uniaxial and biaxial strains which can be observed from the interband optical conductivity polarized along the armchair (x) direction. The preferential conducting direction is along the x direction. The dependence of the intraband optical conductivity along the zigzag (y) direction on the Fermi energy and strain exhibits increasing or decreasing monotonously. However, along the x direction this dependence is complicated which originates from the carriers' inverse-direction movements obtained by two types of the nearest phosphorus atom interactions. The modification of the biaxial strain on the energy structure and optical-absorption property is more effective. The imaginary part of the total optical conductivity (Imσ) can be negative around the threshold of the interband optical transition by modifying the chemical potential. Away from this frequency region, Imσ exhibits positive value. It can be used in the application of the surface plasmon propagations in multilayer dielectric structures.

Yang, T, Liu, Y, Huang, Z, Liu, J, Bian, P, Ling, CD, Liu, H, Wang, G & Zheng, R 2018, 'In situ growth of ZnO nanodots on carbon hierarchical hollow spheres as high-performance electrodes for lithium-ion batteries', Journal of Alloys and Compounds, vol. 735, pp. 1079-1087.
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© 2017 Elsevier B.V. Metal-organic frameworks (MOFs) is an ideal class of precursors or templates to build up transition metal based composites with unique architectures and high electrochemical performance for energy storage applications. In this work, a hybrid hollow nanoarchitecture made of ultrasmall zinc oxide nanodots (less than 5 nm in diameter) and carbon with 3D ordered hollow structure have been synthesized through a simple surfactant-assisted hydrothermal method followed by thermal annealing treatment. This 3D ordered hollow structure not only offers good electronic transportation routes and ionic conductive channels, but also effectively relieves the stress and mitigates the volume variation during lithiation/delithiation process as reflected by the high cycle stability and excellent rate capability as anode materials for lithium ion batteries. Benefitting from the rational design of 3D hollow structure and the synergistic effect between the ultrasmall ZnO nanodots and carbon framework, the ZnO/C hollow structures exhibit decent electrochemical performance of lithium storage with excellent cycling stability (a reversible capacity of 919 mA h/g over 100 cycles at 100 mA/g) and enhanced rate capability (567 mA h/g at high current density of 2 A/g). In addition, it also can deliver a capacity of 741 mA h/g at 500 mA/g after 120 cycles. These results uncover a facile route for the material design for energy application.

Yang, W, Yang, W, Sun, B, Di, S, Yan, K, Wang, G & Shao, G 2018, 'Mixed Lithium Oxynitride/Oxysulfide as an Interphase Protective Layer To Stabilize Lithium Anodes for High-Performance Lithium–Sulfur Batteries', ACS Applied Materials & Interfaces, vol. 10, no. 46, pp. 39695-39704.
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Copyright © 2018 American Chemical Society. Lithium metal is strongly recognized as a promising anode material for next-generation high-energy-density systems. However, unstable solid electrolyte interphase and uncontrolled lithium dendrites growth induce severe capacity decay and short cycle life accompanied by high security risks. Here, we propose a simple method for constructing an artificial solid electrolyte interphase layer on the surface of lithium metal through spontaneous reaction, where ammonium persulfate and lithium nitrate are exploited as oxidants. The satisfactory artificial protective layer with uniform and dense morphology is composed of mixed lithium compounds, mainly including LixSOy and LixNOy species, which could effectively stabilize the interphase between electrolyte and lithium metal anode and restrain the 'shuttle effect' of polysulfides. By employing the premodified lithium metal as anodes for lithium-sulfur batteries, the resulting cells exhibit excellent cycle stability (capacity decay of 0.09% per cycle over 300 cycles at 1 C and Coulombic efficiency of over 98%) and outstanding rate capability (850.8 mAh g-1 even at 4 C). Hence, introducing a stable artificial protective layer to protect lithium anode delivers a new strategy for solving the issues related to lithium-metal batteries.

Yang, W, Yang, W, Zhang, F, Wang, G & Shao, G 2018, 'Hierarchical Interconnected Expanded Graphitic Ribbons Embedded with Amorphous Carbon: An Advanced Carbon Nanostructure for Superior Lithium and Sodium Storage', Small, vol. 14, no. 39, pp. 1802221-1802221.
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AbstractCarbon materials have attracted considerable attention as anodes for lithium‐ion and sodium‐ion batteries due to their low cost and environmental friendliness. This work reports an advanced carbon nanostructure that takes advantage of the chelation effect of glucose and metal ions, which ensures the uniform dispersion of metal in the precursor. Thus, an effective catalytic conversion from sp3 to sp2 carbon occurs, enabling simultaneously formation of pores with catalyzed graphitic structures. Due to the low carbonization temperature and short carbonization time as well as the different catalytic degree of various metals, a series of expanded graphitic layers from 0.34 to 0.44 nm with defects and amorphous carbon structure are obtained. The structure not only offers accessible graphitic spacings for reversible lithium/sodium ion insertion, but also provides abundant active sites for lithium/sodium ion adsorption in the defects and amorphous structure. Moreover, the hierarchical interconnected porous structure combining graphitic ribbons is beneficial for fast electronic/ionic transport and favorable electrolyte permeation. More importantly, such advanced carbon materials prove their feasibility for balancing the pore structure and degree of graphitization. When serving as the electrode material for lithium‐ion and sodium‐ion batteries, excellent electrochemical performance along with fast kinetics and long cycle life is achieved.

Yang, X, Gray, J, Chapman, G, Zhu, Q, Tulau, M & McInnes-Clarke, S 2018, 'Digital mapping of soil erodibility for water erosion in New South Wales, Australia', Soil Research, vol. 56, no. 2, pp. 158-158.
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Soil erodibility represents the soil’s response to rainfall and run-off erosivity and is related to soil properties such as organic matter content, texture, structure, permeability and aggregate stability. Soil erodibility is an important factor in soil erosion modelling, such as the Revised Universal Soil Loss Equation (RUSLE), in which it is represented by the soil erodibility factor (K-factor). However, determination of soil erodibility at larger spatial scales is often problematic because of the lack of spatial data on soil properties and field measurements for model validation. Recently, a major national project has resulted in the release of digital soil maps (DSMs) for a wide range of key soil properties over the entire Australian continent at approximately 90-m spatial resolution. In the present study we used the DSMs and New South Wales (NSW) Soil and Land Information System to map and validate soil erodibility for soil depths up to 100 cm. We assessed eight empirical methods or existing maps on erodibility estimation and produced a harmonised high-resolution soil erodibility map for the entire state of NSW with improvements based on studies in NSW. The modelled erodibility values were compared with those from field measurements at soil plots for NSW soils and revealed good agreement. The erodibility map shows similar patterns as that of the parent material lithology classes, but no obvious trend with any single soil property. Most of the modelled erodibility values range from 0.02 to 0.07 t ha h ha–1 MJ–1 mm–1 with a mean (± s.d.) of 0.035 ± 0.007 t ha h ha–1 MJ–1 mm–1. The validated K-factor map was further used along with other RUSLE factors to assess soil loss across NSW for preventing and managing soil erosion.

Yang, Z, Li, P, McDonagh, A, Li, S, Lv, M, Li, Y, Yu, Z & Feng, C 2018, 'Chitosan-based Nano-biocomposites and their Applications in Medicine and Pharmaceutics', Current Organic Chemistry, vol. 22, no. 7, pp. 628-640.
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© 2018 Bentham Science Publishers. Background: Chitosan-based nano-biocomposite has received more and more attentions in the past few years because of the outstanding merits that chitosan is a natural polymer with biodegradable and biocompatible. Objective: The purpose of the present study is to summarize the different preparation methods of chitosan-based nano-biocomposites, such as electrostatic interaction method, preparation of chitosan-based nano-biocomposites from modified chitosan using selfassembly technique, chemical crosslinking approach, metal ions coordination and metal nanoparticles compound methods. In addition, the applications of chitosan-based nanobiocomposites in wound dressing, drug delivery, tissue engineering and biosensors are also discussed. Results: The results show that chitosan-based nano-biocomposites based on nanoparticles or nanohydrogel that can deliver drugs directly to cancer cells at a sustained and controlled rate may provide better efficacy and lower toxicity for the treatment of cancer. Furthermore, chitosan-based nano-biocomposites can enhance the properties of unmodified chitosan and improve the amphipathy, physical and mechanical properties of chitosan and produce new biological functions. Conclusion: It is believed that the rapid development of nano-science and technology must brought broad application prospects for the chitosan-based nano-biocomposites.

Yousaf, M, Wang, Y, Chen, Y, Wang, Z, Aftab, W, Mahmood, A, Wang, W, Guo, S & Han, RPS 2018, 'Tunable Free-Standing Core–Shell CNT@MoSe₂ Anode for Lithium Storage', ACS Applied Materials & Interfaces, vol. 10, no. 17, pp. 14622-14631.
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Yu, C, Ding, B, Zhang, X, Deng, X, Deng, K, Cheng, Z, Xing, B, Jin, D, Ma, P & Lin, J 2018, 'Targeted iron nanoparticles with platinum-(IV) prodrugs and anti-EZH2 siRNA show great synergy in combating drug resistance in vitro and in vivo', Biomaterials, vol. 155, pp. 112-123.
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© 2017 Elsevier Ltd Resistance to platinum agents is challenging in cancer treatment with platinum drugs. Such resistant cells prevent effective platinum accumulation intracellular and alter cellular adaptations to survive from cytotoxicity by regulating corresponding proteins expression. Ideal therapeutics should combine resolution to these pump and non-pump relevant resistance of cancer cells to achieve high efficacy and low side effect. Fe3O4 nanocarrier loaded with drugs could enter cells in a more efficient endocytosis manner which circumvents pump-relevant drug resistance. EZH2 protein which was previously found to be over-expressed in drug-resistant cancer cells was reported to be involved in platinum drug resistance and play a vital role in anti-apoptosis pathways. Here, we report Fe3O4 nanoparticles loaded with siEZH2 (siRNA), a platinum prodrug in +4 oxidation state (cis, cis, trans-diamminedichlorodisuccinato-platinum-(IV), namely Pt(IV)) and luteinizing hormone-releasing hormone (LHRH) targeting polypeptides. Results show that targeted nanoparticles loading with siEZH2 synergize with Pt(IV) and result in similar cell killing performance to A2780/DDP cells (cisplatin resistant) compared with non-siEZH2 loaded nanoparticles to A2780 cells (cisplatin sensitive). Thus, this Fe3O4@PEI-Pt(IV)-PEG-LHRH@siEZH2 nanoparticles reverse the cisplatin resistance from the pump and non-pump relevant aspects, fully taking advantage of nanocarrier system.

Zavřel, T, Chmelík, D, Sinetova, MA & Červený, J 2018, 'Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium <em>Synechocystis</em>', Journal of Visualized Experiments, no. 139.
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Zavřel, T, Očenášová, P, Sinetova, M & Červený, J 2018, 'Determination of Storage (Starch/Glycogen) and Total Saccharides Content in Algae and Cyanobacteria by a Phenol-Sulfuric Acid Method', BIO-PROTOCOL, vol. 8, no. 15.
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Zavřel, T, Szabó, M, Tamburic, B, Evenhuis, C, Kuzhiumparambil, U, Literáková, P, Larkum, AWD, Raven, JA, Červený, J & Ralph, PJ 2018, 'Effect of carbon limitation on photosynthetic electron transport in Nannochloropsis oculata', Journal of Photochemistry and Photobiology B: Biology, vol. 181, pp. 31-43.
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© 2018 Elsevier B.V. This study describes the impacts of inorganic carbon limitation on the photosynthetic efficiency and operation of photosynthetic electron transport pathways in the biofuel-candidate microalga Nannochloropsis oculata. Using a combination of highly-controlled cultivation setup (photobioreactor), variable chlorophyll a fluorescence and transient spectroscopy methods (electrochromic shift (ECS) and P700 redox kinetics), we showed that net photosynthesis and effective quantum yield of Photosystem II (PSII) decreased in N. oculata under carbon limitation. This was accompanied by a transient increase in total proton motive force and energy-dependent non-photochemical quenching as well as slightly elevated respiration. On the other hand, under carbon limitation the rapid increase in proton motive force (PMF, estimated from the total ECS signal) was also accompanied by reduced conductivity of ATP synthase to protons (estimated from the rate of ECS decay in dark after actinic illumination). This indicates that the slow operation of ATP synthase results in the transient build-up of PMF, which leads to the activation of fast energy dissipation mechanisms such as energy-dependent non-photochemical quenching. N. oculata also increased content of lipids under carbon limitation, which compensated for reduced NAPDH consumption during decreased CO2 fixation. The integrated knowledge of the underlying energetic regulation of photosynthetic processes attained with a combination of biophysical methods may be used to identify photo-physiological signatures of the onset of carbon limitation in microalgal cultivation systems, as well as to potentially identify microalgal strains that can better acclimate to carbon limitation.

Zhand, S, Hosseini, SM, Tabarraei, A, Saeidi, M, Saghaeian Jazi, M, Kalani, MR & Moradi, A 2018, 'Oral poliovirus vaccine-induced programmed cell death involves both intrinsic and extrinsic pathways in human colorectal cancer cells', Oncolytic Virotherapy, vol. Volume 7, pp. 95-105.
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PURPOSE: Colorectal cancer (CRC) is one of the most common causes of cancer death throughout the world. Replication-competent viruses, which are naturally able to infect and lyse tumor cells, seem to be promising in this field. The aim of this study was to evaluate the potential of oral poliovirus vaccine (OPV) on human CRC cells and elucidate the mechanism of apoptosis induction. MATERIALS AND METHODS: Protein and gene expression of poliovirus (PV) receptor (CD155) on four human CRC cell lines including HCT116, SW480, HT-29, and Caco-2 and normal fetal human colon (FHC) cell line as a control were examined by flow cytometry and SYBR Green Real-Time PCR, respectively. Cytotoxicity of OPV on indicated cell lines was tested using MTT assay. The ability of OPV on apoptosis induction for both intrinsic and extrinsic pathways was examined using caspase-8 and caspase-9 colorimetric assay kits. The PV propagation in mentioned cell lines was investigated, and the quantity of viral yields (cells associated and extracellular) was determined using TaqMan PCR. RESULTS: CD155 mRNA and protein were expressed significantly higher in studied CRC cell lines rather than the normal cell line (P=0). OPV induced cell death in a time- and dose-dependent manner in human CRC cells. Apoptosis through both extrinsic and intrinsic pathways was detected in CRC cells with the minimum level found in FHC. PV viral load was significantly correlated with apoptosis via extrinsic (R=0.945, P=0.0001) and intrinsic (R=0.756, P=0.001) pathways. CONCLUSION: This study suggests that OPV has potential for clinical treatment of CRC. However further studies in animal models (tumor xenografts) are needed to be certain that it is qualified enough for treatment of CRC.

Zhang, J, Zhao, Y, Guo, X, Chen, C, Dong, C-L, Liu, R-S, Han, C-P, Li, Y, Gogotsi, Y & Wang, G 2018, 'Single platinum atoms immobilized on an MXene as an efficient catalyst for the hydrogen evolution reaction', Nature Catalysis, vol. 1, no. 12, pp. 985-992.
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© 2018, The Author(s), under exclusive licence to Springer Nature Limited. Single-atom catalysts offer a pathway to cost-efficient catalysis using the minimal amount of precious metals. However, preparing and keeping them stable during operation remains a challenge. Here we report the synthesis of double transition metal MXene nanosheets—Mo 2 TiC 2 T x , with abundant exposed basal planes and Mo vacancies in the outer layers—by electrochemical exfoliation, enabled by the interaction between protons and the surface functional groups of Mo 2 TiC 2 T x . The as-formed Mo vacancies are used to immobilize single Pt atoms, enhancing the MXene’s catalytic activity for the hydrogen evolution reaction. The developed catalyst exhibits a high catalytic ability with low overpotentials of 30 and 77 mV to achieve 10 and 100 mA cm −2 and a mass activity about 40 times greater than the commercial platinum-on-carbon catalyst. The strong covalent interactions between positively charged Pt single atoms and the MXene contribute to the exceptional catalytic performance and stability.

Zhang, Q, Yan, D, Nie, Z, Qiu, X, Wang, S, Yuan, J, Su, D, Wang, G & Wu, Z 2018, 'Iron-Doped NiCoP Porous Nanosheet Arrays as a Highly Efficient Electrocatalyst for Oxygen Evolution Reaction', ACS Applied Energy Materials, vol. 1, no. 2, pp. 571-579.
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© 2018 American Chemical Society. There is a great challenge to employ an electrocatalyst that has high efficiency, is earth-abundant, and is a non-noble metal for oxygen evolution reaction (OER). Herein, we reported a low-cost and highly efficient OER catalyst, Fe-doped NiCoP nanosheet arrays in situ grown on nickel foam (NiCoFeP/NF), which was synthesized via a simple and mild hydrothermal and phosphorization method. In 1 M KOH solution, the as-prepared NiCoFeP/NF produces a larger current density of 200 mA·cm-2 at a low overpotential of 271 mV and exhibits a low Tafel slope of 45 mV·dec-1, which is superior to commercial RuO2. The outstanding OER performance of the as-prepared NiCoFeP/NF can be attributed to the synergetic effects among Fe, Ni, and Co elements, unique nanosheet arrays structure, and the great intrinsic electrocatalytic activity. On the basis of the above factors, the as-prepared NiCoFeP/NF may work as a promising OER electrocatalyst.

Zhang, X, Wang, N, Xie, Z, Ma, X & Huete, A 2018, 'Water Loss Due to Increasing Planted Vegetation over the Badain Jaran Desert, China', Remote Sensing, vol. 10, no. 1, pp. 134-134.
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Water resources play a vital role in ecosystem stability, human survival, and social development in drylands. Human activities, such as afforestation and irrigation, have had a large impact on the water cycle and vegetation in drylands over recent years. The Badain Jaran Desert (BJD) is one of the driest regions in China with increasing human activities, yet the connection between human management and the ecohydrology of this area remains largely unclear. In this study, we firstly investigated the ecohydrological dynamics and their relationship across different spatial scales over the BJD, using multi-source observational data from 2001 to 2014, including: total water storage anomaly (TWSA) from Gravity Recovery and Climate Experiment (GRACE), normalized difference vegetation index (NDVI) from Moderate Resolution Imaging Spectroradiometer (MODIS), lake extent from Landsat, and precipitation from in situ meteorological stations. We further studied the response of the local hydrological conditions to large scale vegetation and climatic dynamics, also conducting a change analysis of water levels over four selected lakes within the BJD region from 2011. To normalize the effect of inter-annual variations of precipitation on vegetation, we also employed a relationship between annual average NDVI and annual precipitation, or modified rain-use efficiency, termed the RUEmo. A focus of this study is to understand the impact of the increasing planted vegetation on local ecohydrological systems over the BJD region. Results showed that vegetation increases were largely found to be confined to the areas intensely influenced by human activities, such as croplands and urban areas. With precipitation patterns remaining stable during the study period, there was a significant increasing trend in vegetation greenness per unit of rainfall, or RUEmo over the BJD, while at the same time, total water storage as measured by satellites has been continually decreasing sin...

Zhang, Y, Aughterson, R, Karatchevtseva, I, Kong, L, Tran, TT, Čejka, J, Aharonovich, I & Lumpkin, GR 2018, 'Uranyl oxide hydrate phases with heavy lanthanide ions: [Ln(UO₂)₂O₃(OH)]·0.5H₂O (Ln = Tb, Dy, Ho and Yb)', New Journal of Chemistry, vol. 42, no. 15, pp. 12386-12393.
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Four iso-structured uranyl oxide hydrate phases containing heavy lanthanide ions have been synthesized under hydrothermal conditions and characterized.

Zhanghao, K, Gao, J, Jin, D, Zhang, X & Xi, P 2018, 'Super-resolution fluorescence polarization microscopy', Journal of Innovative Optical Health Sciences, vol. 11, no. 01, pp. 1730002-1730002.
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Fluorescence polarization is related to the dipole orientation of chromophores, making fluorescence polarization microscopy possible to reveal structures and functions of tagged cellular organelles and biological macromolecules. Several recent super resolution techniques have been applied to fluorescence polarization microscopy, achieving dipole measurement at nanoscale. In this review, we summarize both diffraction limited and super resolution fluorescence polarization microscopy techniques, as well as their applications in biological imaging.

Zhao, C, Hao, X, Liu, C, Yu, J & Mitrovic, SM 2018, 'ASSESSMENT OF WATER RELATED ECOLOGICAL SECURITY UNDER CHANGING ENVIRONMENT IN CHINA', Environmental Engineering and Management Journal, vol. 17, no. 6, pp. 1399-1410.
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© 2018, Gheorghe Asachi Technical University of Iasi, Romania. All rights reserved. Over the last few decades intensive human activities and climate changing have stressed ecological systems impeding sustainable development of the social economy in many regions in China. The importance of ecological security has gained greater prominence. Sustaining or restoring natural functions of water ecosystems is also crucial for human welfare. To assess water related ecological security (WES), this paper constructed a framework based on the Pressure-State-Response (PSR) model with indicators in terms of society, economy, water resources, water environment and ecology. The Entropy Method was used to determine the weighting of each indicator. Spatial distribution and temporal trend of WES was then analyzed in China. With weighting analyses, dominant factors threatening eco-security were identified. Results show that the basin of Inland Rivers in the Northwest (IRNW) and the basin of Rivers in the Southwest (RSW) are the most ecologically threatened regions in China. In the IRNW basin, the WES is mostly affected by the factors of water consumption ratio and soil erosion area ratio, while in the RSW basin it was influenced by the natural population increase ratio and the investment percent of GDP in environmental pollution treatment. Most WES indexes (WESIs) in the ten basins show an increasing trend, except for that in the basin of Rivers in Southeast (RSE) which has a decreasing trend due to the reduced investment ratio of environmental pollution treatment. These results will provide valuable information to water resources management.

Zhao, C, Yang, S, Liu, J, Liu, C, Hao, F, Wang, Z, Zhang, H, Song, J, Mitrovic, SM & Lim, RP 2018, 'Linking fish tolerance to water quality criteria for the assessment of environmental flows: A practical method for streamflow regulation and pollution control', Water Research, vol. 141, pp. 96-108.
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The survival of aquatic biota in stream ecosystems depends on both water quantity and quality, and is particularly susceptible to degraded water quality in regulated rivers. Maintenance of environmental flows (e-flows) for aquatic biota with optimum water quantity and quality is essential for sustainable ecosystem services, especially in developing regions with insufficient stream monitoring of hydrology, water quality and aquatic biota. Few e-flow methods are available that closely link aquatic biota tolerances to pollutant concentrations in a simple and practical manner. In this paper a new method was proposed to assess e-flows that aimed to satisfy the requirements of aquatic biota for both the quantity and quality of the streamflow by linking fish tolerances to water quality criteria, or the allowable concentration of pollutants. For better operation of water projects and control of pollutants discharged into streams, this paper presented two coefficients for streamflow adjustment and pollutant control. Assessment of e-flows in the Wei River, the largest tributary of the Yellow River, shows that streamflow in dry seasons failed to meet e-flow requirements. Pollutant influx exerted a large pressure on the aquatic ecosystem, with pollutant concentrations much higher than that of the fish tolerance thresholds. We found that both flow velocity and water temperature exerted great influences on the pollutant degradation rate. Flow velocity had a much greater influence on pollutant degradation than did the standard deviation of flow velocity. This study provides new methods to closely link the tolerance of aquatic biota to water quality criteria for e-flow assessment. The recommended coefficients for streamflow adjustment and pollutant control, to dynamically regulate streamflow and control pollutant discharge, are helpful for river management and ecosystems rehabilitation. The relatively low data requirement also makes the method easy to use efficiently in developi...

Zhao, C, Zhang, Y, Yang, S, Xiang, H, Sun, Y, Yang, Z, Yu, Q & Lim, RP 2018, 'Quantifying effects of hydrological and water quality disturbances on fish with food-web modeling', Journal of Hydrology, vol. 560, pp. 1-10.
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© 2018 Elsevier B.V. Accurately delineating the effects of hydrological and water quality habitat factors on the aquatic biota will significantly assist the management of water resources and restoration of river ecosystems. However, current models fail to comprehensively consider the effects of multiple habitat factors on the development of fish species. In this study, a dynamic framework for river ecosystems was set up to explore the effects of multiple habitat factors in terms of hydrology and water quality on the fish community in rivers. To achieve this the biomechanical forms of the relationships between hydrology, water quality, and aquatic organisms were determined. The developing processes of the food web without external disturbance were simulated by 208 models, constructed using Ecopath With Ecosim (EWE). These models were then used to analyze changes in biomass (ΔB) of two representative fish species, Opsariichthys bidens and Carassius auratus, which are widely distributed in Asia, and thus have attracted the attention of scholars and stakeholders, due to the consequence of habitat alteration. Results showed that the relationship between the changes in fish biomass and key habitat factors can be expressed in a unified form. T-tests for the unified form revealed that the means of the two data sets of simulated and observed ΔB for these two fish species (O. bidens and C. auratus) were equal at the significance level of 5%. Compared with other ecological dynamic models, our framework includes theories that are easy to understand and has modest requirements for assembly and scientific expertise. Moreover, this framework can objectively assess the influence of hydrological and water quality variance on aquatic biota with simpler theory and little expertise. Therefore, it is easy to be put into practice and can provide a scientific support for decisions in ecological restoration made by river administrators and stakeholders across the world.

Zhao, CS, Yang, ST, Sun, Y, Zhang, HT, Sun, CL, Xu, TR, Lim, RP & Mitrovic, SM 2018, 'Estimating river accommodation capacity for organic pollutants in data-scarce areas', Journal of Hydrology, vol. 564, pp. 442-451.
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© 2018 Elsevier B.V. Globally, water quality degradation severely threatens the security of water resources. Understanding a river's capacity to accommodate pollutants (or water environmental capacity: WEC) can help efficiently protect rivers. However, the requirement for comprehensive ground-observed hydrological and water quality data in previous methods makes it difficult to estimate WEC in areas with limited ground observations. This paper proposes a new framework for WEC estimation in data-scarce areas based on remotely sensed skin water temperature and limited ground observations. Two new models were developed to calculate the two critical parameters for WEC estimation: water temperature, and integrated pollutant degradation coefficients (k). Images of ASTER Surface Kinetic Temperature (AST_08) 90 m grid product were used to retrieve water temperatures. The above results were subsequently used to calculate a river's capacity to accommodate pollutants, or WEC, in agriculturally dominated areas. The use of remote sensing techniques enables the methods to be applied over large spatial scales and to areas with limited ground observations. The application and testing of the framework in four rivers, including two Chinese rivers (the Huai and the Wei Rivers) and two Australian rivers (the Ovens and the Gwydir Rivers), suggest that the models performed well to calculate the real-time water temperature and the coefficient k based on limited ground-observations. Uncertainty analysis on water temperature calculated from remotely sensed land surface temperature and ground-observed meteorological air temperature suggests that remotely sensed water temperature had high concurrence with ground observations (RMSE = 3.08 °C with R2= 0.88), while the sparse-spatially distributed meteorological stations reduced the accuracy in estimating water temperature (RMSE = 4.39 °C with R2= 0.91). We found that the coefficient (k) increased with water temperature over different seasons...

Zhao, F, Lin, Y, Zhai, L, Gao, C, Zhang, J, Ye, Q, Zaslawski, CJ, Ma, F, Wang, Y & Liang, C 2018, 'Effects of cardiac rehabilitation qigong exercise in patients with stable coronary artery disease undergoing phase III rehabilitation: A randomized controlled trial (with video)', Journal of Traditional Chinese Medical Sciences, vol. 5, no. 4, pp. 420-430.
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Zhao, L, Ge, X, Zhao, H, Shi, L, Capobianco, JA, Jin, D & Sun, L 2018, 'Double-Sensitive Drug Release System Based on MnO₂ Assembled Upconversion Nanoconstruct for Double-Model Guided Chemotherapy', ACS Applied Nano Materials, vol. 1, no. 4, pp. 1648-1656.
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A double-sensitive drug release system based on MnO2 nanosheets was synthesized using a facile method for imaging guided chemotherapy in cancer cells. The upconversion nanoparticles (UCNPs) as core are used for upconversion luminescence (UCL) imaging, and the coating of mesoporous silica shows excellent ability for loading drug. The assembly with MnO2 nanosheets can respond to low intracellular pH and GSH in cancer cells. The obtained UCNPs@mSiO2-MnO2 nanoparticles with excellent biocompatibility can be applied as drug carriers. As expected, the UCNPs@mSiO2(DOX)-MnO2 (UCDMs) nanoconstruct loading with DOX offer practical chemotherapeutic effects in vitro, suggesting the active drug release in cancer cells. The luminescence intensity and magnetic resonance signals increased with the decomposition of the MnO2 nanosheets and the release of DOX under low pH and high levels of GSH. In addition, the UCDMs exhibit excellent intracellular UCL imaging, indicating that they can be used as a selective imaging agent in a cancerous environment. Thus, the UCDMs present potential application for use as theranostic agents in imaging guided therapy.

Zhao, L, Wen, S, Zhu, M, Li, D, Xing, Y, Shen, M, Shi, X & Zhao, J 2018, '^99mTc-labelled multifunctional polyethylenimine-entrapped gold nanoparticles for dual mode SPECT and CT imaging', Artificial Cells, Nanomedicine, and Biotechnology, vol. 46, no. sup1, pp. 488-498.
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© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group. In this study, we report the synthesis, characterization and utilization of 99m Tc-labelled polyethylenimine-entrapped gold nanoparticles ( 99m Tc-Au-PENPs) for dual mode single-photon emission computed tomography/computed tomography (SPECT/CT) imaging applications. Polyethylenimine (PEI) was selected as a platform to conjugate with diethylene triamine pentacetate acid (DTPA) and polyethylene glycol monomethyl ether to synthesize Au PENPs, followed by acetylation or hydroxylation modification of the remaining PEI surface amine groups and radiolabelling of 99m Tc. The generated multifunctional 99m Tc-Au-PENPs with different surface groups (acetyl or hydroxyl) were characterized via different methods. The Au PENPs before 99m Tc labelling are colloidally stable, haemocompatibility and noncytotoxic at an Au concentration up to 100 μM. The 99m Tc-labelled Au PENPs exhibit high radiochemical purity, good stability and SPECT/CT imaging performance of different organs and lymph node. The designed strategy to use the radionuclide labelling technique and PEI-facilitated versatile nanoplatform may be extended to develop various novel nanoprobes for precision imaging applications.

Zhao, S, Sun, B, Yan, K, Zhang, J, Wang, C & Wang, G 2018, 'Aegis of Lithium-Rich Cathode Materials via Heterostructured LiAlF₄ Coating for High-Performance Lithium-Ion Batteries', ACS Applied Materials & Interfaces, vol. 10, no. 39, pp. 33260-33268.
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Lithium-rich oxides have been regarded as one of the most competitive cathode materials for next-generation lithium-ion batteries due to their high theoretical specific capacity and high discharge voltage. However, they are still far from being commercialized due to low rate capability and poor cycling stability. In this study, we propose a heterostructured LiAlF₄ coating strategy to overcome those obstacles. The as-developed lithium-rich cathode material shows outstanding performance including a high reversible capacity (246 mA h g^-1 at 0.1C), excellent rate capability (133 mA h g^-1 at 5C), and ultralong cycling stability (3000 cycles). Comparing with those of pristine and AlF₃-coated lithium-rich cathode materials, the enhanced performances can be attributed to the introduction of the lithium-ion-conductive nanolayer and the generation of nonbonding O ^n- species in the active material lattice, which enable rapid and effective lithium ion transport and diffusion. Our work provides a new strategy to develop high-performance lithium-rich cathode materials for high-energy-density lithium-ion batteries.

Zhao, Y, Zhang, J, Wu, W, Guo, X, Xiong, P, Liu, H & Wang, G 2018, 'Cobalt-doped MnO2 ultrathin nanosheets with abundant oxygen vacancies supported on functionalized carbon nanofibers for efficient oxygen evolution', Nano Energy, vol. 54, pp. 129-137.
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© 2018 Elsevier Ltd Developing low-cost and efficient catalysts for oxygen evolution reactions (OER) with both excellent activity and robust stability remains a great challenge. Herein, we report a facile spontaneous redox reaction to grow cobalt-doped MnO2 ultrathin nanosheets in situ with abundant oxygen vacancies vertically aligned on cobalt/nitrogen co-functionalized carbon nanofibers (Co-MnO2|OV) as an efficient OER catalyst. It is confirmed that metallic cobalt plays a critical role in the formation of long and ultrathin MnO2 nanosheets during the redox reaction. Furthermore, the cobalt ions doped into MnO2 significantly enhance the catalytic activity of MnO2 nanosheets. Benefiting from the collaborative advantages of doping strategy, fast charge transfer kinetics and strong synergistic coupling effects, Co-MnO2|OV composites exhibit an excellent catalytic activity and a good durability for electrochemical water oxidation, reaching 10 mA cm−2 at an overpotential of 279 mV. According to the density functional theory (DFT) calculations, the enhanced catalytic activity mainly originates from a better conductivity and the decreased adsorption energy barrier of OH- on the O sites neighboring the doped Co and oxygen vacancies. Our findings suggest that the control over the structure and composition of the materials can achieve highly efficient oxygen evolution electrocatalysts.

Zheng, L, Zhu, J, Lu, DD-C, Wang, G & He, T 2018, 'Incremental capacity analysis and differential voltage analysis based state of charge and capacity estimation for lithium-ion batteries', Energy, vol. 150, pp. 759-769.
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© 2018 Elsevier Ltd The reliability and safety of battery operations necessitate an efficient battery management system (BMS) with accurate battery state of charge (SOC) and capacity estimation techniques. This paper investigates the incremental capacity analysis (ICA) and differential voltage analysis (DVA) methods for onboard battery SOC and capacity estimation. Since the conventional cell terminal voltage based ICA/DVA methods are sensitive to the changed battery resistance and polarization during battery aging processes, the SOC based ICA/DVA methods are proposed to address this problem as so to accurately identify features of interest on incremental capacity (IC) and differential voltage (DV) curves for applications. Three feature points (FPs) that are potential to be easily identified by battery management systems are extracted from the SOC based IC/DV curves, and then the relations between FPs and cell SOCs/capacities are quantified and applied for battery SOC and capacity estimation. The robustness of the proposed approach against various aging levels and erroneous cumulative capacities is evaluated. Promising results with the maximum absolute error of 1.0% and the relative error of 2.0% can be achieved for battery SOC and capacity estimation, respectively.

Zheng, L, Zhu, J, Wang, G, Lu, DD-C & He, T 2018, 'Differential voltage analysis based state of charge estimation methods for lithium-ion batteries using extended Kalman filter and particle filter', Energy, vol. 158, pp. 1028-1037.
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© 2018 Elsevier Ltd Accurate battery state of charge (SOC) estimation can contribute to safe and reliable utilization of the battery. However, commonly used battery model-based SOC estimation methods suffer from the lack of a universal battery model for cells in a battery pack since the model parameters of each cell are inevitably different from each other and variable with battery aging, leading to difficulties in promoting the model-based methods for real applications. To solve this problem, a differential voltage (DV) analysis based universal battery model and two associated SOC estimation algorithms using extended Kalman filter (EKF) and particle filter (PF), respectively, are proposed in this paper. By means of a natural cubic interpolation approach, a battery SOC-DV model is firstly derived from the SOC based DV curves of various cells at different aging levels. A novel battery model-based scheme is then proposed to incorporate the SOC-DV model for the estimation. The robustness of the proposed approaches against different cell aging levels is evaluated, and the promising SOC estimates with the maximum absolute error of 1.75% and the root mean square error of less than 1.10% can be achieved.

Zheng, L, Zhu, J, Wang, G, Lu, DD-C & He, T 2018, 'Lithium-ion Battery Instantaneous Available Power Prediction Using Surface Lithium Concentration of Solid Particles in a Simplified Electrochemical Model', IEEE Transactions on Power Electronics, vol. 33, no. 11, pp. 9551-9560.
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© 1986-2012 IEEE. Accurate battery power capability prediction can contribute to reliable and sufficient utilization of the battery to absorb or deliver a certain amount of power within its safe operating area. The power capability of a battery is a finite quantity that is limited by the electrochemical reaction properties occurring inside the battery. Note that the instantaneous available power of the battery is strongly related to the surface lithium concentration of solid particles in battery electrodes, but their relationship has not been explored sufficiently yet. This paper proposes a novel method for battery instantaneous available power prediction using a practical physical limit (i.e., lithium concentration limit) rather than the limits of macroscopically observed variables, such as the cell terminal voltage and current, thus providing a direct insight into electrochemical processes inside batteries. The surface lithium concentration of the solid particle is derived from a simplified battery electrochemical model, and a relationship between battery instantaneous available power and surface lithium concentration is quantified for the power capability prediction. Promising results with small forecast errors can be achieved for battery charging and discharging at different cell aging levels and ambient temperatures, which highlights the superior accuracy and robustness of the proposed method.

Zheng, S, Kim, C, Lal, S, Meier, P, Sibbritt, D & Zaslawski, C 2018, 'The Effects of Twelve Weeks of Tai Chi Practice on Anxiety in Stressed But Healthy People Compared to Exercise and Wait‐List Groups–A Randomized Controlled Trial', Journal of Clinical Psychology, vol. 74, no. 1, pp. 83-92.
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ObjectiveThis randomized controlled trial was undertaken to determine whether 12 weeks of Tai Chi (TC) practice can reduce anxiety in healthy but stressed people.MethodFifty participants were randomized into TC (n=17), exercise (n=17), and wait‐list (WL) groups (n=16). Outcome measures used were State Trait Anxiety Inventory, Perceived Stress Scale 14 (PSS14), blood pressure and heart rate variability, visual analogue scale (VAS), and Short Form 36.ResultsSignificant improvements were observed from baseline for both TC and exercise groups for both state (p <0.01) and trait (p <0.01) anxiety, PSS14 (p <0.01), VAS (p <0.01), mental health domain (p <0.01), and vitality domain (p <0.01). Superior outcomes were also observed for TC when compared with WL for state and trait anxiety (p <0.01) and mental health domain (p <0.05).ConclusionTC reduces stress levels in healthy individuals and provides a safer, cost effective, and less physically vigorous alternative to exercise.

Zhou, D, Chen, Y, Li, B, Fan, H, Cheng, F, Shanmukaraj, D, Rojo, T, Armand, M & Wang, G 2018, 'A Stable Quasi‐Solid‐State Sodium–Sulfur Battery', Angewandte Chemie, vol. 130, no. 32, pp. 10325-10329.
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AbstractAmbient‐temperature sodium–sulfur (Na–S) batteries are considered a promising energy storage system due to their high theoretical energy density and low costs. However, great challenges remain in achieving a high rechargeable capacity and long cycle life. Herein we report a stable quasi‐solid‐state Na‐S battery enabled by a poly(S‐pentaerythritol tetraacrylate (PETEA))‐based cathode and a (PETEA‐tris[2‐(acryloyloxy)ethyl] isocyanurate (THEICTA))‐based gel polymer electrolyte. The polymeric sulfur electrode strongly anchors sulfur through chemical binding and inhibits the shuttle effect. Meanwhile, the in situ formed polymer electrolyte with high ionic conductivity and enhanced safety successfully stabilizes the Na anode/electrolyte interface, and simultaneously immobilizes soluble Na polysulfides. The as‐developed quasi‐solid‐state Na‐S cells exhibit a high reversible capacity of 877 mA h g−1 at 0.1 C and an extended cycling stability.

Zhou, D, Chen, Y, Li, B, Fan, H, Cheng, F, Shanmukaraj, D, Rojo, T, Armand, M & Wang, G 2018, 'A Stable Quasi‐Solid‐State Sodium–Sulfur Battery', Angewandte Chemie International Edition, vol. 57, no. 32, pp. 10168-10172.
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AbstractAmbient‐temperature sodium–sulfur (Na–S) batteries are considered a promising energy storage system due to their high theoretical energy density and low costs. However, great challenges remain in achieving a high rechargeable capacity and long cycle life. Herein we report a stable quasi‐solid‐state Na‐S battery enabled by a poly(S‐pentaerythritol tetraacrylate (PETEA))‐based cathode and a (PETEA‐tris[2‐(acryloyloxy)ethyl] isocyanurate (THEICTA))‐based gel polymer electrolyte. The polymeric sulfur electrode strongly anchors sulfur through chemical binding and inhibits the shuttle effect. Meanwhile, the in situ formed polymer electrolyte with high ionic conductivity and enhanced safety successfully stabilizes the Na anode/electrolyte interface, and simultaneously immobilizes soluble Na polysulfides. The as‐developed quasi‐solid‐state Na‐S cells exhibit a high reversible capacity of 877 mA h g−1 at 0.1 C and an extended cycling stability.

Zhou, J & Jin, D 2018, 'Triplet state brightens upconversion', Nature Photonics, vol. 12, no. 7, pp. 378-379.
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© 2018 The Publisher. Efficient photon upconversion is desired for applications ranging from molecular sensing to solar-energy harvesting. Now, the population of hidden triplet state electrons, created on dye antennas and rare-earth-doped nanoparticles, has been amplified to brighten upconversion by five orders of magnitude.

Zhou, J, Leaño, JL, Liu, Z, Jin, D, Wong, K, Liu, R & Bünzli, JG 2018, 'Impact of Lanthanide Nanomaterials on Photonic Devices and Smart Applications', Small, vol. 14, no. 40, pp. 1801882-1801882.
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AbstractHalf a century after its initial emergence, lanthanide photonics is facing a profound remodeling induced by the upsurge of nanomaterials. Lanthanide‐doped nanomaterials hold promise for bioapplications and photonic devices because they ally the unmatched advantages of lanthanide photophysical properties with those arising from large surface‐to‐volume ratios and quantum confinement that are typical of nanoobjects. Cutting‐edge technologies and devices have recently arisen from this association and are in turn promoting nanophotonic materials as essential tools for a deeper understanding of biological mechanisms and related medical diagnosis and therapy, and as crucial building blocks for next‐generation photonic devices. Here, the recent progress in the development of nanomaterials, nanotechnologies, and nanodevices for clinical uses and commercial exploitation is reviewed. The candidate nanomaterials with mature synthesis protocols and compelling optical uniqueness are surveyed. The specific fields that are directly driven by lanthanide doped nanomaterials are emphasized, spanning from in vivo imaging and theranostics, micro‐/nanoscopic techniques, point‐of‐care medical testing, forensic fingerprints detection, to micro‐LED devices.

Zhou, J, Wen, S, Liao, J, Clarke, C, Tawfik, SA, Ren, W, Mi, C, Wang, F & Jin, D 2018, 'Activation of the surface dark-layer to enhance upconversion in a thermal field', Nature Photonics, vol. 12, no. 3, pp. 154-158.
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© 2018 The Author(s). Thermal quenching, in which light emission experiences a loss with increasing temperature, broadly limits luminescent efficiency at higher temperature in optical materials, such as lighting phosphors 1-3 and fluorescent probes 4-6 . Thermal quenching is commonly caused by the increased activity of phonons that leverages the non-radiative relaxation pathways. Here, we report a kind of heat-favourable phonons existing at the surface of lanthanide-doped upconversion nanomaterials to combat thermal quenching. It favours energy transfer from sensitizers to activators to pump up the intermediate excited-state upconversion process. We identify that the oxygen moiety chelating Yb3+ ions, [Yb···O], is the key underpinning this enhancement. We demonstrate an approximately 2,000-fold enhancement in blue emission for 9.7 nm Yb3+-Tm3+ co-doped nanoparticles at 453 K. This strategy not only provides a powerful solution to illuminate the dark layer of ultra-small upconversion nanoparticles, but also suggests a new pathway to build high-efficiency upconversion systems.

Zhou, Y, Mu, Z, Adamo, G, Bauerdick, S, Rudzinski, A, Aharonovich, I & Gao, W-B 2018, 'Direct writing of single germanium vacancy center arrays in diamond', New Journal of Physics, vol. 20, no. 12, pp. 125004-125004.
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© 2018 The Author(s). Color centers in diamond are promising solid-state qubits for scalable quantum photonics applications. Amongst many defects, those with inversion symmetry are of an interest due to their promising optical properties. In this work, we demonstrate a maskless implantation of an array of bright, single germanium vacancy (GeV) centers in diamond. Employing the direct focused ion beam technique, single GeV emitters are engineered with the spatial accuracy of tens of nanometers. The single GeV creation ratio reaches as high as 53% with the dose of 200 Ge + ions per spot. The presented fabrication method is promising for future nanofabrication of integrated photonic structures with GeV emitters as a leading platform for spin-spin interactions.

Zhou, Y, Wang, Z, Rasmita, A, Kim, S, Berhane, A, Bodrog, Z, Adamo, G, Gali, A, Aharonovich, I & Gao, W-B 2018, 'Room temperature solid-state quantum emitters in the telecom range', Science Advances, vol. 4, no. 3, pp. eaar3580-eaar3580.
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An optically stable, room temperature single-photon emitter operating in telecom wavelength range is discovered in GaN.

Zhu, L, Lockrey, M, Phillips, MR & Ton‐That, C 2018, 'Spatial Distribution of Defect Luminescence in ZnO Nanorods: An Investigation by Spectral Cathodoluminescence Imaging', physica status solidi (a), vol. 215, no. 19, pp. 1800389-1800389.
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The spatial distribution of ubiquitous green luminescence (GL) in ZnO nanorods is investigated using cathodoluminescence (CL) spectral imaging. The vertically aligned, single‐crystal nanorods exhibit a strong GL emission at 2.42 eV at 80 K, attributable to oxygen vacancies. The spectral imaging reveals the GL emission is predominantly located in the surface layer of nanorods; the thickness and intensity of this layer decreases rapidly at elevated temperatures. On the other hand, the near‐band‐edge emission is weakest near the nanorod edges. The temperature‐dependent CL maps are consistent with the properties of a model in which singly ionized oxygen vacancies are stabilized by the surface band bending, which leads to the GL enhancement at the expense of near‐band‐edge emission. These results demonstrate the utility of spectral CL imaging to map the spatial distribution of defect luminescence in nanostructured materials.

Zhu, T, Wu, C, Song, J, Reimers, JR & Li, Y 2018, 'Polarization effect within a protein crystal: A molecular dynamics simulation study', Chemical Physics Letters, vol. 706, pp. 303-307.
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Systematical molecular dynamics with different force fields are performed to simulate the structure and dynamics of crystal of hen egg-white lysozyme, including AMBER and three versions of protein-specific charge, PPC. The electrostatic polarization within the crystal is studied with the comparison among four 250 ns trajectories under them. Results show that under appropriate parameterized PPC, the protein can be stable during simulations, indicated by both smaller root-mean-square deviation and closer crystallographic B-factors to the experimental values. This work also shows how the selection of dielectric constant affects the results of utilizing PPC.

Zhu, X, Oh, H-S, Ng, YCB, Tang, PYP, Barraud, N & Rice, SA 2018, 'Nitric Oxide-Mediated Induction of Dispersal in Pseudomonas aeruginosa Biofilms Is Inhibited by Flavohemoglobin Production and Is Enhanced by Imidazole', Antimicrobial Agents and Chemotherapy, vol. 62, no. 3.
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ABSTRACT The biological signal molecule nitric oxide (NO) was found to induce biofilm dispersal across a range of bacterial species, which led to its consideration for therapeutic strategies to treat biofilms and biofilm-related infections. However, biofilms are often not completely dispersed after exposure to NO. To better understand this phenomenon, we investigated the response of Pseudomonas aeruginosa biofilm cells to successive NO treatments. When biofilms were first pretreated with a low, noneffective dose of NO, a second dose of the signal molecule at a concentration usually capable of inducing dispersal did not have any effect. Amperometric analysis revealed that pretreated P. aeruginosa cells had enhanced NO-scavenging activity, and this effect was associated with the production of the flavohemoglobin Fhp. Further, quantitative real-time reverse transcription-PCR (qRT-PCR) analysis showed that fhp expression increased by over 100-fold in NO-pretreated biofilms compared to untreated biofilms. Biofilms of mutant strains harboring mutations in fhp or fhpR , encoding a NO-responsive regulator of fhp , were not affected in their dispersal response after the initial pretreatment with NO. Overall, these results suggest that FhpR can sense NO to trigger production of the flavohemoglobin Fhp and inhibit subsequent dispersal responses to NO. Finally, the addition of imidazole, which can inhibit the NO dioxygenase activity of flavohemoglobin, attenuated the prevention of dispersal after NO pretreatment and improved ...

Ziklo, N, Vidgen, ME, Taing, K, Huston, WM & Timms, P 2018, 'Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections', Frontiers in Cellular and Infection Microbiology, vol. 8, no. JAN.
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© 2018 Ziklo, Vidgen, Taing, Huston and Timms. The natural course of Chlamydia trachomatis urogenital tract infections varies between individuals. While protective immunity can occur, some women can become reinfected, contributing to the development of severe pathology. While the reasons for these differences are unknown, an individual's response to induced interferon-γ (IFN-γ) is suggested to be critical. IFN-γ induction of the enzyme indoleamine 2,3-dioxygenase, which depletes tryptophan, may be the key. One hypothesis suggests that indole-producing bacteria in the vaginal microbiota can provide a substrate for the Chlamydia to synthesize tryptophan, rescuing the Chlamydia from host IFN-γ attack. We studied a cohort of 25 women who were either, Chlamydia negative, Chlamydia positive with a single infection, or Chlamydia positive with repeated infection, to test our hypothesis. We characterized their vaginal microbiota, cytokine response, as well as their tryptophan, kynurenine and indole concentrations directly in vaginal secretions. We found that C. trachomatis urogenital tract infections either initial or repeat infections, were associated with elevated vaginal kynurenine/tryptophan ratios, primarily as a result of elevated kynurenine levels. In addition, vaginal microbiota of community state type (CST) IV showed significantly lower vaginal tryptophan levels compared to CST I and III, which might be related to a higher abundance of indole producers found within this group. Furthermore, we found a higher abundance of indole producers in women who cleared their Chlamydia infection post antibiotic treatment. This study demonstrates for the first time in vivo, the association between high vaginal kynurenine/tryptophan ratios and C. trachomatis infections. In addition, tryptophan depletion was associated with vaginal microbiota of CST IV.

Zinder, Y, Lazarev, AA, Musatova, EG & Tarasov, IA 2018, 'Scheduling the Two-Way Traffic on a Single-Track Railway with a Siding', Automation and Remote Control, vol. 79, no. 3, pp. 506-523.
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© 2018, Pleiades Publishing, Ltd. The paper is concerned with scheduling the two-way traffic between two stations connected by a single-track railway with a siding. It is shown that if, for each station, the order in which trains leave this station is known or can be found, then for various objective functions an optimal schedule can be constructed in polynomial time using the method of dynamic programming. Based on this result, the paper also presents a polynomial-time algorithm minimising the weighted number of late trains.

Zoh, RS, Sarkar, A, Carroll, RJ & Mallick, BK 2018, 'A Powerful Bayesian Test for Equality of Means in High Dimensions', Journal of the American Statistical Association, vol. 113, no. 524, pp. 1733-1741.
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© 2018, © 2018 American Statistical Association. We develop a Bayes factor-based testing procedure for comparing two population means in high-dimensional settings. In ‘large-p-small-n” settings, Bayes factors based on proper priors require eliciting a large and complex p × p covariance matrix, whereas Bayes factors based on Jeffrey’s prior suffer the same impediment as the classical Hotelling T2 test statistic as they involve inversion of ill-formed sample covariance matrices. To circumvent this limitation, we propose that the Bayes factor be based on lower dimensional random projections of the high-dimensional data vectors. We choose the prior under the alternative to maximize the power of the test for a fixed threshold level, yielding a restricted most powerful Bayesian test (RMPBT). The final test statistic is based on the ensemble of Bayes factors corresponding to multiple replications of randomly projected data. We show that the test is unbiased and, under mild conditions, is also locally consistent. We demonstrate the efficacy of the approach through simulated and real data examples. Supplementary materials for this article are available online.

Zou, L, Zhang, S, Wang, B & Tan, J 2018, 'High-order super-resolution optical fluctuation imaging based on low-pass denoising', Optics Letters, vol. 43, no. 4, pp. 707-707.
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