Publications

Harezlak, J, Ruppert, D & Wand, MP 2019, Semiparametric Regression with R, 1, Springer, New York.
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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.

Aggarwal, T, Wadhwa, R, Thapliyal, N, Gupta, R, Hansbro, PM, Dua, K & Maurya, PK 2019, 'Nanotechnology in Modern Animal Biotechnology' in Singh, S & Maurya, PK (eds), Nanotechnology in Modern Animal Biotechnology, Springer Singapore, Singapore, pp. 173-193.
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Nanomaterial has been employed as an alternative to antibiotics, diagnostic tools and delivery of therapeutics. In particular, nanomaterial has grabbed the attention of researchers due to their antimicrobial properties due to the emergence of multi-drug resistance of several micro-organisms. The present chapter highlights the antimicrobial nanomaterials with their mechanism of action along with their broad spectrum applications such as silver nanomaterial is antimicrobial in nature and is effective in drug delivery. Metallic, non-metallic and natural/ biodegradable nanomaterials have been discussed as potential antimicrobial and their mode of action. The mechanism of antimicrobial nanomaterial is poorly understood, but oxidative stress, non-oxidative action, inhibition of cell adhesion, decline in biofilm formation, obstructed quoram sensing and metal ion release are attributed to be as the major reasons. In addition, the limitation and toxicity with the clinical and environmental applications are also described.

Aggarwal, T, Wadhwa, R, Thapliyal, N, Gupta, R, Hansbro, PM, Dua, K & Maurya, PK 2019, 'Recent Trends of Nano-material as Antimicrobial Agents' in Nanotechnology in Modern Animal Biotechnology, Springer Singapore, pp. 173-193.
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© Springer Nature Singapore Pte Ltd. 2019. Nanomaterial has been employed as an alternative to antibiotics, diagnostic tools and delivery of therapeutics. In particular, nanomaterial has grabbed the attention of researchers due to their antimicrobial properties due to the emergence of multi-drug resistance of several micro-organisms. The present chapter highlights the antimicrobial nanomaterials with their mechanism of action along with their broad spectrum applications such as silver nanomaterial is antimicrobial in nature and is effective in drug delivery. Metallic, non-metallic and natural/ biodegradable nanomaterials have been discussed as potential antimicrobial and their mode of action. The mechanism of antimicrobial nanomaterial is poorly understood, but oxidative stress, non-oxidative action, inhibition of cell adhesion, decline in biofilm formation, obstructed quoram sensing and metal ion release are attributed to be as the major reasons. In addition, the limitation and toxicity with the clinical and environmental applications are also described.

Ajani, PA, Eriksen, R & Rissik, D 2019, 'Coastal and marine phytoplankton: diversity and ecology' in Suthers, I & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, 2nd Edition, CSIRO Publishing.

Ben-Nissan, B, Cazalbou, S & Choi, AH 2019, 'Bioceramics' in Encyclopedia of Biomedical Engineering, Elsevier, pp. 16-33.
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© 2019 Elsevier Inc. All rights reserved. During the last five decades, the capability to engineer or repair new functional tissues by using porous and monolithic ceramics has been a very effective approach to improve the quality of life of patients. Although the use of natural and synthetic materials in body reconstruction and repair goes back to pre-historic times their use have been accelerated considerable during the last few decades in both scientific research and clinical applications. Over the years, many questions concerning their interactions with both hard and soft tissues have been answered with multidisciplinary teams of surgeons, scientists, and engineers. Since 1970s monolithic ceramics such as alumina and partially stabilized zirconia, silicon nitride and sialon ceramics have been used and investigated clinically. Ceramics can be both inert and modified to be bioactive, they have good wettability hence ideal for lubrication under articulating conditions and they have high wear resistance. Although pure zirconia or PSZ is not currently used commercially, alumina and mixtures and their composites with zirconia have been clinically applied widely. In addition a number of clinical glasses such as Bioglass® and other similar compositions are being also used for bone augmentation and restoration in orthopedic, dental and maxillofacial surgery. They have proved to be efficient and effective and in some instances even much better than current metal prostheses. Calcium phosphates, although arguably most important bioceramic in most cases, is used in porous form and it is not covered in this article which was aimed to be on monolithic bioceramics. It is our aim in this article to present the development of these important monolithic bioceramics focusing on the history, synthesis, properties and the current development in clinical applications.

Ben-Nissan, B, Choi, AH & Green, DW 2019, 'Marine Derived Biomaterials for Bone Regeneration and Tissue Engineering: Learning from Nature' in Springer Series in Biomaterials Science and Engineering, Springer Singapore, Switzerland, pp. 51-78.
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Marine structures, biogenic materials, and biomimetic approaches applied to the fabrication of advanced biomaterials and implants are used to address the shortcomings of existing scaffold designs that are biologically un-responsive throughout the regeneration process and lack necessary versatility. Bioactive ceramics converted from biostructures or natural marine-based materials such as corals, sea urchin, sponges and shells are being designed into functional scaffolds that can adapt and evolve to changing environment during regeneration process. They can regulate cell responses at nanostructured surfaces, and as modules for self-assembling by the patient’s own cells and as smart devices that possess tissue specific homing capabilities. These natural structures can be converted to bioactive ceramics such as hydroxyapatite to assist osseointegration. This chapter covers biomimicry, evolution of marine structures, and their specific use and current research on natural materials such as coral, sponge, sea urchin, sponge nacre, and foraminifera as models and raw materials for bioactive bone scaffolding materials and tissue engineering.

Ben-Nissan, B, Choi, AH, Green, DW, Karacan, I, Akyol, S & Cazalbou, S 2019, 'Thoughts and Tribulations on Bioceramics and Marine Structures' in Springer Series in Biomaterials Science and Engineering, Springer Singapore, pp. 1-25.
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Bernardes, S, Madden, M, Astuti, I, Bernardes, S, Chuvieco, E, Cotten, D, Dennison, PE, Dronova, I, Gitas, I, Gong, P, Franch-Gras, B, Hancher, M, Hirano, A, Howard, A, Hu, X, Huete, A, Jordan, T, Justice, C, Lawrence, RL, Lu, L, Madden, M, Mishra, DR, Mishra, S, Miura, T, Mountrakis, G, Pal, M, Remillard, C, Roberts, DA, Roger, J-C, Singh, KK, Somers, B, Stavrakoudis, D, Sun, W, Sun, G, Thau, D, Tits, L, Usery, EL, Vermote, E, Wang, C, Wang, M, Weng, Q, Xu, W, Yao, T, Yoshioka, H, Zhang, L, Zhang, Q & Zhang, Z 2019, 'Image Processing and Analysis Methods' in Manual of Remote Sensing, 4th Edition, American Society for Photogrammetry and Remote Sensing, pp. 631-868.
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Booth, DJ & Biro, P 2019, 'Adaptation' in Encyclopedia of Ecology, Elsevier, pp. 1-5.
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© 2019 Elsevier B.V. All rights reserved. While adaptations to local environments are well recognized, their actual influence on the dynamics of organisms (e.g., demography of mortality, growth, and reproduction) at a population level are less studied. We discuss some of the ways in which evolutionary adaptation can occur. We then review some of the evidence that morphological, behavioral, life-history, and physiological adaptations can affect populations. We emphasize the fact that adaptations and adaptive changes can be both a cause and consequence of observed population dynamics. Individual responses to the environment integrate to affect dynamics of populations but may also indicate how well the individual is adapted. We also note how adaptations at larger scales (e.g., clinal differences in energy budgets across latitudes) affect population dynamics and may act as a buffer for species against recent human-caused climate change.

Booth, DJ & Biro, P 2019, 'Adaptation' in Encyclopedia of Ecology: Volume 1-4, Second Edition, pp. 1-5.
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While adaptations to local environments are well recognized, their actual influence on the dynamics of organisms (e.g., demography of mortality, growth, and reproduction) at a population level are less studied. We discuss some of the ways in which evolutionary adaptation can occur. We then review some of the evidence that morphological, behavioral, life-history, and physiological adaptations can affect populations. We emphasize the fact that adaptations and adaptive changes can be both a cause and consequence of observed population dynamics. Individual responses to the environment integrate to affect dynamics of populations but may also indicate how well the individual is adapted. We also note how adaptations at larger scales (e.g., clinal differences in energy budgets across latitudes) affect population dynamics and may act as a buffer for species against recent human-caused climate change.

Booth, DJ & Murray, BR 2019, 'Coexistence' in Encyclopedia of Ecology: Volume 1-4, Second Edition, pp. 37-41.
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Theoretical arguments regarding the difficulties of similar species coexisting, many habitats support large numbers of species and populations in high densities. In this article, we discuss the mechanisms by which populations and species coexist. Most of the types of interactions between species and individuals, including predation and competition, have the potential to promote or reduce coexistence. For instance, strongly asymmetrical competition may cause one species to go extinct, but competitive networks may promote coexistence of three or more species. Explanations for coexistence of huge numbers of species on coral reefs or rainforests have expanded from niche diversification hypotheses to, more recently, disturbance-mediated regimes and random recruitment from larval assemblages. Life-history tradeoffs and resting stages such as seed banks in plants can also promote coexistence, and neutral models that assume that the above forces are not important can also lead to a level of coexistence.

Booth, DJ & Murray, BR 2019, 'Coexistence' in Fath, BD (ed), Encyclopedia of Ecology, Elsevier, Oxford, UK, pp. 37-41.
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Červený, J, Šalagovič, J, Muzika, F, Šafránek, D & Schreiber, I 2019, 'Influence of Circadian Clocks on Optimal Regime of Central C-N Metabolism of Cyanobacteria' in Cyanobacteria, Elsevier, pp. 193-206.
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Chen, H, Chan, YL, Oliver, BG, Pollock, CA & Saad, S 2019, 'Maternal Smoking and Fetal Brain Outcome: Mechanisms and Possible Solutions' in Preedy, V (ed), Neuroscience of Nicotine, Elsevier, New York, pp. 9-16.
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Although it is well known that maternal cigarette smoke exposure (SE) is detrimental to the health of children, more than 20% of women continue to smoke during pregnancy. Children exposed to maternal smoking in utero have changes in their brain structure and size, often accompanied by cognitive defects. This may be due to increased brain oxidative stress and inflammatory response in the neonatal period, leading to neuron damage in adulthood. The mitochondria, a major source of cellular oxidative stress, are particularly vulnerable to the damage caused by the free radicals they produce. Interestingly, the female offspring seem to be protected by such adverse impact of maternal smoking. This chapter will specifically review the changes in brain inflammation and oxidative stress and the mechanism of mitophagy machinery. Potential therapeutic strategies will be suggested to mitigate the impact of maternal smoking.

Choi, AH & Ben-Nissan, B 2019, 'Marine-Derived Biomaterials for Tissue Engineering Applications' in Marine-Derived Biomaterials for Tissue Engineering Applications, Springer, pp. 99-111.
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This book presents the latest advances in marine structures and related biomaterials for applications in both soft- and hard-tissue engineering, as well as controlled drug delivery.

Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Industry-Specific Utilization of Solar Industrial Process Heat (SHIP)' in Nanostructured Materials for Next-Generation Energy Storage and Conversion, Springer Berlin Heidelberg, pp. 409-438.
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Fu, S 2019, 'How Do People Try to Beat Drugs Test? Effects of Synthetic Urine, Substituted Urine, Diluted Urine, and In Vitro Urinary Adulterants on Drugs of Abuse Testing' in Dasgupta, A (ed), Critical Issues in Alcohol and Drugs of Abuse Testing, Elsevier, London, UK, pp. 359-389.
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This updated edition is a must-have for clinical pathologists, toxicologists, clinicians, and medical review officers and regulators, bridging the gap between technical and clinical information.

Gerace, D, Ren, B, Martiniello-Wilks, R & Simpson, AM 2019, 'High-Efficiency Lentiviral Gene Modification of Primary Murine Bone-Marrow Mesenchymal Stem Cells' in Methods in Molecular Biology, Springer New York, Switzerland, pp. 197-214.
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Lentiviral vectors are the method of choice for stable gene modification of a variety of cell types. However, the efficiency with which they transduce target cells varies significantly, in particular their typically poor capacity to transduce primary stem cells. Here we describe the isolation and enrichment of murine bone-marrow mesenchymal stem cells (MSCs) via fluorescence-activated cell sorting (FACS); the cloning, production, and concentration of high-titer second generation lentiviral vectors via combined tangential flow filtration (TFF) and ultracentrifugation; and the subsequent high-efficiency gene modification of MSCs into insulin-producing cells via overexpression of the furin-cleavable human insulin (INS-FUR) gene.

Karacan, I, Ben-Nissan, B & Sinutok, S 2019, 'Marine-Based Calcium Phosphates from Hard Coral and Calcified Algae for Biomedical Applications' in Springer Series in Biomaterials Science and Engineering, Springer Singapore, Switzerland, pp. 137-153.
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The materials that are developed from the different kind of marine organisms have a broad range of properties and characteristics that can explain their potential functions in the biomedical area. Accordingly, new opportunities are created by biomaterials produced from marine-based sources such as calcium phosphate-based bioceramics, composites, and polymers within the biomedical fields such as new drug delivery systems, the design of novel implantable devices, and various applications in tissue engineering. The major aim of this chapter is to explain the importance of marine structures applicable for biomedical applications as well as choosing the appropriate conversion technique in order to obtain designs and structures best suited for their intended use. Therefore, we will highlight various conversion techniques used in the synthesis of calcium phosphate bioceramics from various marine sources such as Tubipora musica , Foraminifera , Porites Hard Corals and Halimeda cylindracea calcified algae, and their biomedical applications in this chapter.

Macha, IJ, Ben-Nissan, B, Müller, WH & Cazalbou, S 2019, 'Marine Nanopharmaceuticals for Drug Delivery and Targeting' in Springer Series in Biomaterials Science and Engineering, Springer Singapore, pp. 207-221.
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Malik, S, Liu, C-G, Zhao, X-Q & Mehmood, MA 2019, 'Long-Chain Liquid Biofuels' in Comprehensive Biotechnology, Elsevier, pp. 101-109.
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The rate at which fossil fuels are being consumed today has never been so high in human history. In addition to rapid depletion of the reserves for fossil fuels, the increased consumption also results in the enhanced carbon emissions, raising serious environmental concerns. Therefore, a significant amount of efforts has been devoted to developing fossil fuel alternatives, which are sustainable and environmentally friendly. The first-generation biofuels such as fuel ethanol and biodiesel have been produced through fermentation and enzymatic catalysis from grains and sugarcane and vegetable oils. Due to low energy density, these fuels are not compatible with jet engines, which require energy-rich long-chain fuels that can be produced through microbial platforms either by the manipulation of resident metabolic pathways or engineering the novel ones. However, currently, the production of such fuels is not commercially feasible due to low product yields, fuel-induced toxicity, and complex extraction processes. This article discusses strategies employed to enhance the carbon assimilation pathways of host organisms for directing the metabolic flux more effectively toward the synthesis of desired biofuels via natural or synthetic pathways, along with remodeling of metabolic pathways to achieve the enhanced titer and productivity, and the feasibility of designing biofuel secretion systems are also addressed.

Ngo, HH, Vo, HNP, Guo, W, Bui, X-T, Nguyen, PD, Nguyen, TMH & Zhang, X 2019, 'Advances of Photobioreactors in Wastewater Treatment: Engineering Aspects, Applications and Future Perspectives' in Bui, X-T, Chiemchaisri, C, Fujioka, T & Varjani, S (eds), Energy, Environment, and Sustainability, Springer Singapore, Germany, pp. 297-329.
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The photobioreactor is an efficient artificial system in terms of biomass cultivation and removing pollutants. Compared to other conventional technologies, its design and operational processes are superior. Therefore, the photobioreactor specifically targets and tailors for the increasing demand for biomass and stringent pollutants removal standards. Since the early 1950s, there has been a variety of photobioreactor types, and these have been addressing the different technical issues over time and others more recently. As well, diverse applications of the photobioreactor process are becoming more widespread, and this opens for a good opportunity for future sustainable developments. This book chapter discusses advances being made in photobioreactor technology, encompassing: (1) modelling; (2) designs and classifications; (3) applications and (4) future perspectives.

Oliver, BGG 2019, 'Techniques for detection and research' in Rhinovirus Infections, Elsevier, pp. 265-283.
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© 2019 Elsevier Inc. All rights reserved. This chapter contains practical concepts pertaining to the sampling of the upper and lower airways for human rhinovirus.

Ribaux, O, Delemont, O, Roux, C & Crispino, F 2019, 'La science forensique au service de l’action de sécurité [Forensic science at the service of security action]' in Cusson, M, Ribaux, O, Blais, E & Raynaud, MM (eds), Nouveau traité de sécurité: Sécurité intérieure et sécurité urbaine [New security treaty: Internal security and urban security], Hurtubise, Montreal, pp. 114-125.

Rickert, W, Morozova, A, Müller, WH, Vilchevskaya, EN, Ben-Nissan, B & Macha, I 2019, 'Drug Delivery from Polymer-Based Nanopharmaceuticals—Simulations of Selected Diffusion Processes' in Advanced Structured Materials, Springer International Publishing, Switzerland, pp. 207-226.
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© 2019, Springer Nature Switzerland AG. Knowledge about the release behavior of drugs into the human body is essential for correct long-term medication. This paper complements a previous work by providing details of the numerical methods that were used before. Therefore, we shortly explain the experimental setup and state the governing equations. For the numerical solution, two different methods, the finite element method and the finite volume technique, are used. In addition, three different boundary conditions are employed: Dirichlet conditions and classical as well as non-classical convection Robin-type boundary conditions.

Rissik, D, Ajani, P, Bowling, L, gibbs, M, Kobayashi, T, Pitt, K, Richardson, A & Suthers, I 2019, 'Use of Plankton for Management' in Plankton A Guide to Their Ecology and Monitoring for Water Quality, CSIRO PUBLISHING.
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This Second Edition of Plankton is a fully updated introduction to the biology, ecology and identification of plankton and their use in monitoring water quality.

Rissik, D, van Senden, D, Doherty, M, Ingleton, I, Ajani, P, Bowling, L, Gibbs, M, Gladstone, M, Kobayashi, T, Suthers, I & Froneman, W 2019, 'Plankton-related water quality issues' in Suthers, I, Richardson, A & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, 2nd Edition, CSIRO Publishing.

Samson, RY, Duggin, IG & Bell, SD 2019, 'Analysis of the Archaeal ESCRT Apparatus' in Methods in Molecular Biology, Springer New York, pp. 1-11.
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Members of the archaeal domain of life that lack homologs of actin and tubulin divide by binary fission in a process that is dependent upon orthologs of eukaryotic ESCRT components. Many of these archaeal organisms are hyperthermophilic acidophiles with unique cell wall structures, which create technical challenges for performing traditional cell biological techniques. Here, we describe the 'baby machine' method for synchronizing microorganisms at high temperatures in order to study cell cycle-related processes. We also provide details for fixing, permeabilizing, and staining archaeal cells and ESCRT assemblies for observation by light microscopy.

Shahid, A, Malik, S, Alam, MA, Nahid, N & Mehmood, MA 2019, 'The Culture Technology for Freshwater and Marine Microalgae' in Microalgae Biotechnology for Development of Biofuel and Wastewater Treatment, Springer Singapore, pp. 21-44.
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Microalgae are promising eco-friendly source of food, feed, biofuels, and chemicals. There has been substantial progress at the lab and industrial scales to develop efficient and sustainable microalgae culturing techniques. However, several constraints must be addressed to make the overall process economically viable. Chemo-genetics elements can play a pivotal role in achieving the commercial goals because microalgae grow more efficiently in high concentrations of essential nutrients like nitrogen, phosphorus, and carbon in addition to enhance by-product formation. Moreover, alteration in culturing conditions also activates lipid accumulation. Recent strategies have combined these approaches to enhance lipid accumulation and along with enhanced biomass productivity. It is necessary to optimize inoculum production and culture management to avoid contamination, especially at commercial scales. Furthermore, prevailing outdoor conditions of rainfall, variable temperature, and irradiation, which are entirely different from small lab-scale facilities, pose additional challenges during outdoor cultivation. This chapter highlights the nutritional requirements of culturing media and their impact along with possible challenges on microalgae cultivation to ensure the stable and high productivities of large-scale cultures. Media recycling not only reduces the dependency on freshwater but also increases the economic viability of the process. Recent advances regarding media recycling and strategies to control biological contaminants are also discussed.

Suggett, DJ & Moore, CM 2019, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, Third Edition: Volume 1-5, p. V5-87-V5-93.
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Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change.

Wadhwa, R, Aggarwal, T, Thapliyal, N, Chellappan, DK, Gupta, G, Gulati, M, Collet, T, Oliver, B, Williams, K, Hansbro, PM, Dua, K & Maurya, PK 2019, 'Nanoparticle-Based Drug Delivery for Chronic Obstructive Pulmonary Disorder and Asthma' in Nanotechnology in Modern Animal Biotechnology, Elsevier, The Netherlands, pp. 59-73.
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Pulmonary diseases including chronic obstructive pulmonary disease (COPD) and asthma affect millions of people all over the world. Conventional treatment methodologies are not sufficient to cure or prevent the disease. With the advent of nanotechnology, drug delivery to specific target site is still challenging, but targeted delivery can be achieved by physiochemical properties of the nanoparticles. Delivery of nanoparticles, liposomes, dendrimers, and others has been extensively studied for successful delivery by inhalation and aerosols. Several factors such as size, density, surface, and physical-chemical properties of nanoparticle are essential to cross airway barriers. In this chapter, different nanoparticle-mediated drug delivery systems have been highlighted along with their applications and toxicity in COPD and asthma.

Wadhwa, R, Shukla, SD, Chellappan, DK, Gupta, G, Collet, T, Hansbro, N, Oliver, B, Williams, K, Hansbro, PM, Dua, K & Maurya, PK 2019, 'Phytotherapy in Inflammatory Lung Diseases: An Emerging Therapeutic Interventional Approach' in Phytochemistry: An in-silico and in-vitro Update, Springer Singapore, Singapore, pp. 331-347.
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Chronic obstructive pulmonary disease (COPD) and asthma are the most common inflammatory respiratory diseases related to an increase in mortality and morbidity. Generally, bronchodilators, ß- agonists, anticholinergics and theophylline used for treatment in these conditions and administered by inhalation for delivery, have localized and systematic effects. The adverse effects are due to pharmacodynamic and pharmacokinetic changes and especially drug-drug and drug-disease interactions. However, phytotherapy is classical and widespread throughout the world for the treatment of ailments. This chapter highlights cellular and molecular mediators involved in COPD and asthma, the shortcomings of current therapies and the emerging need of phytomedicines. Phytomedicine supports respiratory physiology, bronchial action and possesses antioxidants to maintain homeostasis.

Wu, D, Hin, LY, Kordzakhia, N & Novikov, A 2019, 'Numerical Approximations to Distributions of Weighted Kolmogorov-Smirnov Statistics via Integral Equations' in 2017 MATRIX Annals, Springer International Publishing, pp. 579-589.
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Abayarathna, T, Murray, BR & Webb, JK 2019, 'Higher incubation temperatures produce long-lasting upward shifts in cold tolerance, but not heat tolerance, of hatchling geckos', Biology Open, vol. 8, no. 4.
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ABSTRACT Heatwaves are a regular occurrence in Australia, and are predicted to increase in intensity and duration in the future. These changes may elevate temperatures inside lizard nests, shortening the incubation period, so that hatchlings are more likely to emerge during heatwaves. Potentially, developmental plasticity or heat hardening could buffer hatchings from future warming. For example, higher incubation temperatures could shift critical thermal maxima upwards, enabling lizards to withstand higher temperatures. To investigate whether developmental plasticity affects hatchling thermal tolerance, we incubated eggs of the velvet gecko Amalosia lesueurii under two fluctuating incubation treatments to mimic current (mean=24.3°C, range 18.4–31.1°C) and future ‘hot’ (mean=28.9°C, range 19.1–38.1°C) nest temperatures. We maintained the hatchlings under identical conditions, and measured their thermal tolerance (CTmax) aged 14 days and 42 days. We then released hatchlings at field sites, and recaptured individually marked lizards aged 6 months, to determine whether incubation induced shifts in thermal tolerance were transitory or long-lasting. We found that at age 14 days, hatchlings from hot-temperature incubation had higher CTmax [mean=39.96±0.25°C (s.d.)] than hatchlings from current-temperature incubation [mean=39.70±0.36°C (s.d.)]. Hatchlings from the current-incubation treatment also had significantly higher heat hardening capacity [mean=0.79±0.37°C (s.d.)] than hatchlings from hot-temperature incubation treatment [mean=0.47±0.17°C (s.d. )]. However, both of these incubation-induced effects did not persist into later life. By contrast, incubation treatment had significant and long-lasting effects on the cold tolerance of hatchlings. At age 14 days, current-incubated hatchlings tolerated colder temperatures [CTmin=11.24±0.41°C (s.d.)] better than hot-incubated hatchlings [CTmin=14.11±0.25°C (s.d.)]. T...

Abdo, P, Huynh, BP, Irga, PJ & Torpy, FR 2019, 'Evaluation of air flow through an active green wall biofilter', Urban Forestry & Urban Greening, vol. 41, pp. 75-84.
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© 2019 Elsevier GmbH Green walls show promise as active bio-filters to improve indoor air quality by removing both gaseous and particulate air pollutants. The current work represents a detailed assessment of airflow through an active green wall module. Airflow distribution through the module, the effect of wetting the substrate, and the effect of introducing a cover to the module's open top face were investigated, with the aim to improve the module's design and achieve more appropriate and effective airflow. Four cases of both planted and unplanted modules under both dry and wet conditions are considered. This work's primary observation is that more air will pass through a typical green wall substrate, and hence become cleansed, when the substrate is saturated wet more than when it is dry. The increase was substantial at approximately 50% more with 14.9 ± 0.2 L/s total air flow rate passing through the wet planted module versus 10 ± 0.2 L/s when dry. Reducing the 15.5 ± 0.75% of airflow passing through the module's open top face was found to be essential to maximize the bio-filtration capacity. Adding a top cover to the module having six 10 mm holes for irrigation decreased the airflow through the top by 6 ± 0.75%, and directed it through the filter increasing the percentage of air flow passing through the front openings from 79 ± 4% to 85 ± 4%.

Abidi, IH, Mendelson, N, Tran, TT, Tyagi, A, Zhuang, M, Weng, L, Özyilmaz, B, Aharonovich, I, Toth, M & Luo, Z 2019, 'Selective Defect Formation in Hexagonal Boron Nitride', Advanced Optical Materials, vol. 7, no. 13, pp. 1900397-1900397.
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AbstractLuminescent defects in hexagonal boron nitride (hBN) have emerged as promising single photon emitters (SPEs) due to their high brightness and robust operation at room temperature. The ability to create such emitters with well‐defined optical properties is a cornerstone toward their integration into on‐chip photonic architectures. Here, an effective approach is reported to fabricate hBN SPEs with desired emission properties in distinct spectral regions via the manipulation of boron diffusion through copper during atmospheric pressure chemical vapor deposition (CVD)—a process termed gettering. Using the gettering technique the resulting zero‐phonon line is deterministically placed between the regions 550 and 600 nm or from 600 to 650 nm, paving the way for hBN SPEs with tailored emission properties. Additionally, rational control over the observed SPE density in the resulting films is demonstrated. The ability to control defect formation during hBN growth provides a cost effective means to improve the crystallinity of CVD hBN films, and lower defect density making it applicable to hBN growth for a wide‐range of applications. The results are important to understand defect formation of quantum emitters in hBN and deploy them for scalable photonic technologies.

Achlatis, M, Pernice, M, Green, K, de Goeij, JM, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2019, 'Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter', Proceedings of the Royal Society B: Biological Sciences, vol. 286, no. 1916, pp. 20192153-20192153.
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Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15 N- and 13 C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.

Aftab, W, Mahmood, A, Guo, W, Yousaf, M, Tabassum, H, Huang, X, Liang, Z, Cao, A & Zou, R 2019, 'Polyurethane-based flexible and conductive phase change composites for energy conversion and storage', Energy Storage Materials, vol. 20, pp. 401-409.
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Agbowuro, AA, Hwang, J, Peel, E, Mazraani, R, Springwald, A, Marsh, JW, McCaughey, L, Gamble, AB, Huston, WM & Tyndall, JDA 2019, 'Structure-activity analysis of peptidic Chlamydia HtrA inhibitors', Bioorganic & Medicinal Chemistry, vol. 27, no. 18, pp. 4185-4199.
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Chlamydia trachomatis high temperature requirement A (CtHtrA) is a serine protease that performs proteolytic and chaperone functions in pathogenic Chlamydiae; and is seen as a prospective drug target. This study details the strategies employed in optimizing the irreversible CtHtrA inhibitor JO146 [Boc-Val-Pro-ValP(OPh)2] for potency and selectivity. A series of adaptations both at the warhead and specificity residues P1 and P3 yielded 23 analogues, which were tested in human neutrophil elastase (HNE) and CtHtrA enzyme assays as well as Chlamydia cell culture assays. Trypsin and chymotrypsin inhibition assays were also conducted to measure off-target selectivity. Replacing the phosphonate moiety with α-ketobenzothiazole produced a reversible analogue with considerable CtHtrA inhibition and cell culture activity. Tertiary leucine at P3 (8a) yielded approximately 33-fold increase in CtHtrA inhibitory activity, with an IC50 = 0.68 ± 0.02 µM against HNE, while valine at P1 retained the best anti-chlamydial activity. This study provides a pathway for obtaining clinically relevant inhibitors.

Aggarwal, T, Wadhwa, R, Thapliyal, N, Sharma, K, Rani, V & Maurya, PK 2019, 'Oxidative, inflammatory, genetic, and epigenetic biomarkers associated with chronic obstructive pulmonary disorder', Journal of Cellular Physiology, vol. 234, no. 3, pp. 2067-2082.
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AbstractA large body of evidence indicates that chronic obstructive pulmonary disorder (COPD) is accompanied by oxidative stress and inflammatory and genetic pathways. Epidemiological studies indicate that COPD is a major cause of mortality and morbidity in the world. Recent research development in COPD focuses on accelerated aging and various oxidative stress biomarkers. It involves the clinical manifestation of the disease process and may also contain biochemical, immunological, physiological, morphological, and genetic aspects that add to the progressiveness of the disease. Herein, we summarize findings that highlight the role of dimensions of COPD in the investigation of oxidative stress, inflammatory responses, genetic and epigenetic studies, and pharmacological and dietary antioxidant intervention.

Aguilar, C, Raina, J-B, Fôret, S, Hayward, DC, Lapeyre, B, Bourne, DG & Miller, DJ 2019, 'Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress', BMC Genomics, vol. 20, no. 1.
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Ahmad, M, Yousaf, M, Nasir, A, Bhatti, IA, Mahmood, A, Fang, X, Jian, X, Kalantar-Zadeh, K & Mahmood, N 2019, 'Porous Eleocharis@MnPE Layered Hybrid for Synergistic Adsorption and Catalytic Biodegradation of Toxic Azo Dyes from Industrial Wastewater', Environmental Science & Technology, vol. 53, no. 4, pp. 2161-2170.
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Ahmadimanesh, M, Abbaszadegan, MR, Morshedi Rad, D, Moallem, SA, Mohammadpour, AH, Ghahremani, MH, Farid Hosseini, F, Behdani, F, Akhondpour Manteghi, A, Jowsey, P, Shabani Behbahani, F, Moallem, SMH & Etemad, L 2019, 'Effects of selective serotonin reuptake inhibitors on DNA damage in patients with depression', Journal of Psychopharmacology, vol. 33, no. 11, pp. 1364-1376.
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Background: The relationship between depression and increased oxidative stress is well known. DNA damage by oxidation factors is an important cause of the aging process in psychiatric disorders. Aims: Owing to the scarcity of human studies and high inconsistencies in studies of the effects of antidepressants on DNA damage, the current study was undertaken to investigate the effects of depression and its treatment on DNA damage. Methods: In a 15-week open-label study of citalopram ( n = 25) and sertraline ( n = 20), levels of DNA damage were measured by comet assay, proinflammatory (Interlukin-6 (IL-6)) and oxidative DNA damage (8-hydroxy-2’-deoxyguanosine (8-OHdG)) markers by ELISA, and gene expression of base excision repair enzymes (8-oxoguanine glycosylase (OGG1) and poly (ADP)-ribose polymerase-1 (PARP1)) by quantitative real-time polymerase chain reaction in healthy control patients ( n = 14), with depression at the baseline and the same patients after week 15. Results: DNA damage, 8-OHdG, IL-6 and expression of PARP1 were elevated in patients with depression compared with the healthy controls ( p < 0.001). Selective serotonin reuptake inhibitor (SSRI) therapy could significantly reduce the depression score ( p < 0.01), DNA damage ( p < 0.001), as well as 8-OHdG and IL-6 ( p < 0.0001). Nevertheless, the expression of PARP1 and OGG1 showed no significant changes after treatment. Conclusions: This is the first study on the effect of SSRIs on the DNA damage and some of the repair enzymes in depression. Based on the results, depression can cause increased DNA damage. This damage is followed by activation of compensatory mechanisms whereby the expressi...

Akter, A, Takahashi, S, Deng, W, Shea, DJ, Itabashi, E, Shimizu, M, Miyaji, N, Osabe, K, Nishida, N, Suzuki, Y, Helliwell, CA, Seki, M, Peacock, WJ, Dennis, ES & Fujimoto, R 2019, 'The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.', DNA Research, vol. 26, no. 5, pp. 433-443.
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Abstract Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.

Akyol, S, Ben Nissan, B, Karacan, I, Yetmez, M, Gokce, H, Suggett, DJ & Oktar, FN 2019, 'Morphology, characterization, and conversion of the corals Goniopora spp. and Porites cylindrica to hydroxyapatite', Journal of the Australian Ceramic Society, vol. 55, no. 3, pp. 893-901.
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© 2019, Australian Ceramic Society. The aim of this study is to obtain pure natural hydroxyapatite (HAp) and tricalcium phosphate (TCP) from a Goniopora spp. and from hump coral (Porites cylindrica), both sourced from Australia. Due to the nature of the conversion process, commercial coralline HAp has retained coral or CaCO3, and the structure possesses both nano- and mesopores within the interpore trabeculae resulting in high dissolution rates. To overcome these limitations, a newly patented coral double-conversion technique has been developed. The current technique involves a two-stage application route where in the first-stage complete conversion of coral to pure HAp is achieved. In the second stage, a sol-gel-derived HAp nanocoating is directly applied to cover the meso- and nanopores within the intrapore material, while maintaining the large pores. Here, we specifically investigated the morphological changes and characterized these corals prior to and after conversion. For this purpose, four groups designated as C0, C1, C2, and C3 were used. C0 is Porites, Goniopora, and cylindrica; the original coral is calcium carbonate with aragonite structure that contains proteins and polysaccharides. C1 is coral cleaned under ultrasound in bleach diluted with water. C2 is coral converted to hydroxyapatite (HAp) by hydrothermal treatment method at 200 °C under pressure in the presence of ammonium biphosphate. C3 is obtained by coating C2 with sol-gel alkoxide-derived nanohydroxyapatite to obtain a more bioactive osteoconductive material and improve mechanical properties. All groups were characterized by XRD, EDAX, DTA/TGA, and SEM. The results showed that the biaxial strengths of the C2 and C3 were significantly higher than the original coral. The work also showed the advantages of the hydrothermal conversion method and the effect of the nanocoating which is expected to improve the final bioactivity through microstructural changes of the surfaces.

Al-Asadi, S, Malik, A, Bakiu, R, Santovito, G, Menz, I & Schuller, K 2019, 'Characterization of the peroxiredoxin 1 subfamily from Tetrahymena thermophila', Cellular and Molecular Life Sciences, vol. 76, no. 23, pp. 4745-4768.
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ALFEUS, M & SCHLÖGL, E 2019, 'ON SPREAD OPTION PRICING USING TWO-DIMENSIONAL FOURIER TRANSFORM', International Journal of Theoretical and Applied Finance, vol. 22, no. 05, pp. 1950023-1950023.
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Spread options are multi-asset options with payoffs dependent on the difference of two underlying financial variables. In most cases, analytically closed form solutions for pricing such payoffs are not available, and the application of numerical pricing methods turns out to be nontrivial. We consider several such nontrivial cases and explore the performance of the highly efficient numerical technique of Hurd & Zhou[(2010) A Fourier transform method for spread option pricing, SIAM J. Financial Math. 1(1), 142–157], comparing this with Monte Carlo simulation and the lower bound approximation formula of Caldana & Fusai[(2013) A general closed-form spread option pricing formula, Journal of Banking & Finance 37, 4893–4906]. We show that the former is in essence an application of the two-dimensional Parseval’s Identity. As application examples, we price spread options in a model where asset prices are driven by a multivariate normal inverse Gaussian (NIG) process, in a three-factor stochastic volatility model, as well as in examples of models driven by other popular multivariate Lévy processes such as the variance Gamma process, and discuss the price sensitivity with respect to volatility. We also consider examples in the fixed-income market, specifically, on cross-currency interest rate spreads and on LIBOR/OIS spreads.

Alfeus, M, Overbeck, L & Schlögl, E 2019, 'Regime switching rough Heston model', Journal of Futures Markets, vol. 39, no. 5, pp. 538-552.
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AbstractThis model combines two important stylized features of volatility, the rough behavior consistent with a Hurst parameter less than , and the regime switching property consistent with more long‐term economic considerations. It is nevertheless highly tractable in the sense of semianalytic formulae for European options, and permits a partial Monte Carlo method of similar computational speed as the semianalytic formula (at an appropriate number of Monte Carlo simulations). While option prices are relatively insensitive to the choice of Hurst parameter, introducing rough volatility allows for a better fit to the at‐the‐money skew.

Alghalayini, A, Garcia, A, Berry, T & Cranfield, C 2019, 'The Use of Tethered Bilayer Lipid Membranes to Identify the Mechanisms of Antimicrobial Peptide Interactions with Lipid Bilayers', Antibiotics, vol. 8, no. 1, pp. 12-12.
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This review identifies the ways in which tethered bilayer lipid membranes (tBLMs) can be used for the identification of the actions of antimicrobials against lipid bilayers. Much of the new research in this area has originated, or included researchers from, the southern hemisphere, Australia and New Zealand in particular. More and more, tBLMs are replacing liposome release assays, black lipid membranes and patch-clamp electrophysiological techniques because they use fewer reagents, are able to obtain results far more quickly and can provide a uniformity of responses with fewer artefacts. In this work, we describe how tBLM technology can and has been used to identify the actions of numerous antimicrobial agents.

Alijani, H, Çetin, B, Akkuş, Y & Dursunkaya, Z 2019, 'Experimental Thermal Performance Characterization of Flat Grooved Heat Pipes', Heat Transfer Engineering, vol. 40, no. 9-10, pp. 784-793.
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Almohaywi, B, Yu, TT, Iskander, G, Chan, DSH, Ho, KKK, Rice, S, Black, DS, Griffith, R & Kumar, N 2019, 'Dihydropyrrolones as bacterial quorum sensing inhibitors', Bioorganic & Medicinal Chemistry Letters, vol. 29, no. 9, pp. 1054-1059.
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© 2019 Elsevier Ltd Bacteria regulate their pathogenicity and biofilm formation through quorum sensing (QS), which is an intercellular communication system mediated by the binding of signaling molecules to QS receptors such as LasR. In this study, a range of dihydropyrrolone (DHP) analogues were synthesized via the lactone-lactam conversion of lactone intermediates. The synthesized compounds were tested for their ability to inhibit QS, biofilm formation and bacterial growth of Pseudomonas aeruginosa. The compounds were also docked into a LasR crystal structure to rationalize the observed structure-activity relationships. The most active compound identified in this study was compound 9i, which showed 63.1% QS inhibition of at 31.25 µM and 60% biofilm reduction at 250 µM with only moderate toxicity towards bacterial cell growth.

Anand, A, Khurana, R, Wahal, N, Mahajan, S, Mehta, M, Satija, S, Sharma, N, Vyas, M & Khurana, N 2019, 'Vanillin: A comprehensive review of pharmacological activities', Plant Archives, vol. 19, pp. 1000-1004.
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Vanillin is the chief constituent of the vanilla bean extract obtained from the seed pods of Vanillus planifolia belonging to the family Orchidaceae. Nowadays, synthetic vanillin is being preferred as a flavouring agent in foods, beverages and pharmaceuticals. Chemically, it is a phenolic aldehyde with the molecular formula C8H8O3. Over years it has been used as a flavor in sweet foods like chocolates & ice creams, in cosmetics like perfumes, and in pharmaceuticals to mask the unpleasant odor and tastes in medicines. Also, vanillin-HCl is extensively used a visualizing agent in Thin Layer Chromatography. Quite recently, vanillin has been studied by researchers all over the world for its pharmacological effects. The compound has exhibited remarkable effects in treatment and management of several pathological conditions. This review focuses on the different reported pharmacological activities of vanillin.

Anantanawat, K, Pitsch, N, Fromont, C & Janitz, C 2019, 'High-throughput Quant-iT PicoGreen assay using an automated liquid handling system', BioTechniques, vol. 66, no. 6, pp. 290-294.
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Workflows in NGS facilities require high-standard practices and high-throughput pipelines to process the large number of samples received in a timely manner. Downstream protocols such as NGS library preparation require accurate estimation of nucleic acid concentrations, which can be achieved using fluorescent dye-based nucleic acid measurement. Here, we report a protocol for preparing a 384-well Quant-iT PicoGreen assay. The protocol allows the concentrations of 184 DNA samples to be measured simultaneously in duplicate in only 1 h using an Eppendorf epMotion 5075 liquid handling system. The advantages of this high-throughput approach include a reduction in both reagents (10x less reagents compared to a standard protocol) and time (3 h for 384 samples compared with 3 days).

Anderson, C, Hafen, R, Sofrygin, O & Ryan, L 2019, 'Comparing predictive abilities of longitudinal child growth models', Statistics in Medicine, vol. 38, no. 19, pp. 3555-3570.
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The Bill and Melinda Gates Foundation's Healthy Birth, Growth and Development knowledge integration project aims to improve the overall health and well‐being of children across the world. The project aims to integrate information from multiple child growth studies to allow health professionals and policy makers to make informed decisions about interventions in lower and middle income countries. To achieve this goal, we must first understand the conditions that impact on the growth and development of children, and this requires sensible models for characterising different growth patterns. The contribution of this paper is to provide a quantitative comparison of the predictive abilities of various statistical growth modelling techniques based on a novel leave‐one‐out validation approach. The majority of existing studies have used raw growth data for modelling, but we show that fitting models to standardised data provide more accurate estimation and prediction. Our work is illustrated with an example from a study into child development in a middle income country in South America.

Andersson, AJ, Venn, AA, Pendleton, L, Brathwaite, A, Camp, EF, Cooley, S, Gledhill, D, Koch, M, Maliki, S & Manfrino, C 2019, 'Ecological and socioeconomic strategies to sustain Caribbean coral reefs in a high-CO2 world', Regional Studies in Marine Science, vol. 29, pp. 100677-100677.
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© 2019 The Authors The Caribbean and Western Atlantic region hosts one of the world's most diverse geopolitical regions and a unique marine biota distinct from tropical seas in the Pacific and Indian Oceans. While this region varies in human population density, GDP and wealth, coral reefs, and their associated ecosystem services, are central to people's livelihoods. Unfortunately, the region's reefs have experienced extensive degradation over the last several decades. This degradation has been attributed to a combination of disease, overfishing, and multiple pressures from other human activities. Furthermore, the Caribbean region has experienced rapid ocean warming and acidification as a result of climate change that will continue and accelerate throughout the 21st century. It is evident that these changes will pose increasing threats to Caribbean reefs unless imminent actions are taken at the local, regional and global scale. Active management is required to sustain Caribbean reefs and increase their resilience to recover from acute stress events. Here, we propose local and regional solutions to halt and reverse Caribbean coral reef degradation under ongoing ocean warming and acidification. Because the Caribbean has already experienced high coral reef degradation, we suggest that this region may be suitable for more aggressive interventions that might not be suitable for other regions. Solutions with direct ecological benefits highlighted here build on existing knowledge of factors that can contribute to reef restoration and increased resilience in the Caribbean: (1)management of water quality, (2)reduction of unsustainable fishing practices, (3)application of ecological engineering, and (4)implementing marine spatial planning. Complementary socioeconomic and governance solutions include: (1)increasing communication and leveraging resources through the establishment of a regional reef secretariat, (2)incorporating reef health and sustainability goals into the bl...

Andrejic, OM, Vucic, RM, Pavlovic, M, McClements, L, Stokanovic, D, Jevtovic–Stoimenov, T & Nikolic, VN 2019, 'Association between Galectin-3 levels within central and peripheral venous blood, and adverse left ventricular remodelling after first acute myocardial infarction', Scientific Reports, vol. 9, no. 1, p. 13145.
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AbstractOur study investigates association between Galectin-3 levels and adverse left ventricular remodelling (LVR) at six months. Fifty-seven patients following first acute myocardial infarction (AMI) were enrolled in this study and blood samples collected on day 1 from the femoral vein and artery, the right atrium near the coronary sinus and the aortic root, and on day 30, from the cubital vein. Patients with LVESV ≥20% at six months, were included in the LVR group. On day 1, Galectin-3 plasma levels in the femoral vein (10.34 ng/ml ± 3.81 vs 8.22 ng/ml ± 2.34, p = 0.01), and near coronary sinus (10.7 ng/ml ± 3.97 vs 8.41 ng/ml ± 2.56, p = 0.007) were higher in the LVR group. Positive correlations between Galectin-3 levels from aortic root and coronary sinus, aortic root and femoral vein, and coronary sinus and femoral vein, were observed in both groups. On day 30, Galectin-3 concentration in the cubital vein was an independent risk factor of LVR six months post-AMI, demonstrating 1.5-fold increased risk. Day-30 Galectin-3 also showed positive correlations with echocardiography parameters indicative of diastolic and systolic dysfunction. Determining Galectin-3 plasma concentration on day 30 following AMI could have beneficial prognostic value in predicting LVR.

Angeloski, A, Cortie, MB, Scott, JA, Bordin, DM & McDonagh, AM 2019, 'Conversion of single crystals of a nickel(II) dithiocarbamate complex to nickel sulfide crystals', Inorganica Chimica Acta, vol. 487, pp. 228-233.
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© 2018 Elsevier B.V. Single crystals of bis(κ2S,S′-di(isopropyl)dithiocarbamato) nickel(II) were utilized as a single source precursor for the formation of NiS via thermolysis. The complex decomposed at ∼250 °C to form α-NiS exclusively with no β-NiS detected. Analysis of the thermolysis regime using in situ techniques showed that the thermolysis occurs in a single step with the major volatile side-products being isopropyl-isothiocyanate and carbon disulfide. The resultant NiS was examined using SEM and TEM to reveal a retention of precursor crystal edge-length and angle relationships.

Angeloski, A, Rawal, A, Bhadbhade, M, Hook, JM, Schurko, RW & McDonagh, AM 2019, 'An Unusual Mercury(II) Diisopropyldithiocarbamate Coordination Polymer', Crystal Growth & Design, vol. 19, no. 2, pp. 1125-1133.
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Copyright © 2019 American Chemical Society. A new polymeric mercury(II) diisopropyldithiocarbamate complex was synthesized by the reaction of sodium diisopropyldithiocarbamate with excess HgCl 2 in water. The precise structure of the new compound was determined by single-crystal X-ray diffraction. A similar reaction, using a stoichiometric excess of the ligand, yielded the known monomeric bis(diisopropyldithiocarbamato)mercury(II) complex. The complexes could not be distinguished from each other by their solution-phase NMR spectra or their FTIR spectra. Solid-state NMR spectroscopy ( 199 Hg and 13 C) provided unambiguous data and showed that the monomeric complex and polymeric complex do not interconvert in solution or during crystal growth. Thermogravimetric experiments revealed quite different thermal decomposition behavior between the two compounds.

Arhin, SK, Zhao, J, Ji, X, Shi, C, Tang, J, Gu, Y, Xi, H, Cheng, J, Qu, X, Shi, H, Jin, XL & Lv, JQ 2019, 'Multiple facilitated glucose transporters SLC2As are required for normal mouse preimplantation embryo development', American Journal of Translational Research, vol. 11, no. 6, pp. 3412-3425.
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Background: Glucose metabolism is an essential energy source for mammalian preimplantation embryonic development. Therefore, we aimed to analyze the expression of all 12 known glucose transporters (facilitated solute carrier family 2, Slc2a) during early mouse embryo development. Methods: Gene and protein expression of Slc2a transporters in oocytes and embryos were assessed by the TaqMan gene expression assay and confocal immunofluorescence, respectively. Results: Except for Slc2a2, the other 11 Slc2a transcripts were detected in oocytes. Transcripts of Slc2a1, Slc2a3, Slc2a4, and Slc2a8 were the most enriched and detected in preimplantation embryos. The transcription of other Slc2a isoforms was barely detectable or absent after fertilization; however, they were detected in blastocysts, except for Slc2a10 and Slc2a13. Embryo culture in the simple defined medium caused a reduction in transcription of Slc2a1, Slc2a3, Slc2a4, and Slc2a8 in blastocyst; yet, amino acids partially reversed this impaired transcription of Slc2a1 and Slc2a4. SLC2A1 and SLC2A4 proteins were detected at all embryonic stages with nuclear accumulation in the embryos at the early cleavage stage. SLC2A3 and SLC2A8 were not detected in embryos until the eight-cell stage. The cellular membrane localization of SLC2A1, SLC2A3, and SLC2A8 occurred after compaction and was characterized in blastocysts. SLC2A4 was evenly distributed in the cytoplasm and nuclei without its characteristic membrane localization. Indinavir sulfate (a SLC2A4 inhibitor) decreased the rate of development and prevented glucose utilization in embryos after compaction. These inhibitory activities were partially reversed by exogenous insulin. Conclusion: The results unveil distinct expression patterns of individual Slc2a glucose transporters during early embryo development. Taken together, they provide novel insights into the understanding and management of glucose metabolic infertility in assisted-reproductive technologies (ART).

Armbrecht, LH, Coolen, MJL, Lejzerowicz, F, George, SC, Negandhi, K, Suzuki, Y, Young, J, Foster, NR, Armand, LK, Cooper, A, Ostrowski, M, Focardi, A, Stat, M, Moreau, JW & Weyrich, LS 2019, 'Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation', Earth-Science Reviews, vol. 196, pp. 102887-102887.
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© 2019 Elsevier B.V. The study of ancient DNA (aDNA) from sediments (sedaDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sedaDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sedaDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

Arnold, MD 2019, 'Effective transport properties of conformal Voronoi-bounded columns via recurrent boundary element expansions', Journal of Applied Physics, vol. 126, no. 16, pp. 164307-164307.
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Effective transport properties of heterogeneous structures are predicted bygeometric microstructural parameters, but these can be difficult to calculate.Here, a boundary element code with a recurrent series method accurately andefficiently determines the high order parameters of polygonal and conformalprisms in regular two-dimensional lattices and Voronoi tessellations (VT). Thisreveals that proximity to simpler estimates is associated with: centroidal VT(cf random VT), compactness, and VT structures (cf similarly compactsemi-regular lattices). An error in previously reported values for triangularlattices is noted.

Arti, Kaur, A, Singh, M, Arora, S, Dhiman, S, Satija, S & Singh, TG 2019, 'Pharmacotherapy of amyotrophic lateral sclerosis: An insight', Plant Archives, vol. 19, pp. 1385-1397.
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Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease of motor neurons resulting in worsening of voluntary muscles and degeneration of motor neurons in the motor cortex brainstem and spinal cord. Pathogenetic mechanism of ALS includes involvement of mitochondrial dysfunction, glutamate excitotoxicity, oxidative stress and apoptosis showing that ALS is a multifactorial disease. Major symptoms include spasticity, cognitive impairment, malnutrition and muscle cramps. As ALS still remains fatal due to several complications involved, various advances have been made in modifying the disease course. Symptomatic treatment, due to complicated symptoms, and nutrition assessment and intervention, due to the involvement of malnutrition in patients has an important role in controlling the distress caused by the disease. This article reviews the current therapeutic approaches including recent advances in pharmacological treatment strategies along with nutrition and dietary supplements based on the potential to delay onset of disease, retard the progression of disease, extend the lifespan and improve the quality of life of patients.

Atto, B, Eapen, MS, Sharma, P, Frey, U, Ammit, AJ, Markos, J, Chia, C, Larby, J, Haug, G, Weber, HC, Mabeza, G, Tristram, S, Myers, S, Geraghty, DP, Flanagan, KL, Hansbro, PM & Sohal, SS 2019, 'New therapeutic targets for the prevention of infectious acute exacerbations of COPD: role of epithelial adhesion molecules and inflammatory pathways', Clinical Science, vol. 133, no. 14, pp. 1663-1703.
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AbstractChronic respiratory diseases are among the leading causes of mortality worldwide, with the major contributor, chronic obstructive pulmonary disease (COPD) accounting for approximately 3 million deaths annually. Frequent acute exacerbations (AEs) of COPD (AECOPD) drive clinical and functional decline in COPD and are associated with accelerated loss of lung function, increased mortality, decreased health-related quality of life and significant economic costs. Infections with a small subgroup of pathogens precipitate the majority of AEs and consequently constitute a significant comorbidity in COPD. However, current pharmacological interventions are ineffective in preventing infectious exacerbations and their treatment is compromised by the rapid development of antibiotic resistance. Thus, alternative preventative therapies need to be considered. Pathogen adherence to the pulmonary epithelium through host receptors is the prerequisite step for invasion and subsequent infection of surrounding structures. Thus, disruption of bacterial–host cell interactions with receptor antagonists or modulation of the ensuing inflammatory profile present attractive avenues for therapeutic development. This review explores key mediators of pathogen–host interactions that may offer new therapeutic targets with the potential to prevent viral/bacterial-mediated AECOPD. There are several conceptual and methodological hurdles hampering the development of new therapies that require further research and resolution.

Ayres, DL, Cummings, MP, Baele, G, Darling, AE, Lewis, PO, Swofford, DL, Huelsenbeck, JP, Lemey, P, Rambaut, A & Suchard, MA 2019, 'BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics', Systematic Biology, vol. 68, no. 6, pp. 1052-1061.
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Abstract BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.

Backwell, A, Macrina, A, Schlögl, E & Skovmand, D 2019, 'Term Rates, Multicurve Term Structures and Overnight Rate Benchmarks: a Roll-Over Risk Approach'.

Bailey, RL, Dodd, KW, Gahche, JJ, Dwyer, JT, Cowan, AE, Jun, S, Eicher-Miller, HA, Guenther, PM, Bhadra, A, Thomas, PR, Potischman, N, Carroll, RJ & Tooze, JA 2019, 'Best Practices for Dietary Supplement Assessment and Estimation of Total Usual Nutrient Intakes in Population-Level Research and Monitoring', The Journal of Nutrition, vol. 149, no. 2, pp. 181-197.
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© 2019 American Society for Nutrition. All rights reserved. The use of dietary supplements (DS) is pervasive and can provide substantial amounts of micronutrients to those who use them. Therefore when characterizing dietary intakes, describing the prevalence of inadequacy or excess, or assessing relations between nutrients and health outcomes, it is critical to incorporate DS intakes to improve exposure estimates. Unfortunately, little is known about the best methods to assess DS, and the structure of measurement error in DS reporting. Several characteristics of nutrients from DS are salient to understand when comparing to those in foods. First, DS can be consumed daily or episodically, in bolus form and can deliver discrete and often very high doses of nutrients that are not limited by energy intakes. These characteristics contribute to bimodal distributions and distributions severely skewed to the right. Labels on DS often provide nutrient forms that differ from those found in conventional foods, and underestimate analytically derived values. Finally, the bioavailability of many nutrient-containing DS is not known and it may not be the same as the nutrients in a food matrix. Current methods to estimate usual intakes are not designed specifically to handle DS. Two temporal procedures are described to refer to the order that nutrient intakes are combined relative to usual intake procedures, referred to as a shrinking the distribution to remove random error. The shrink then add approach is preferable to the add then shrink approach when users and nonusers are combined for most research questions. Stratifying by DS before usual intake methods is another defensible option. This review describes how to incorporate nutrient intakes from DS to usual intakes from foods, and describes the available methods and fit-for-purpose of different analytical strategies to address research questions where total usual intakes are of interest at the group level for use in ...

Bakshi, HA, Mishra, V, Satija, S, Mehta, M, Hakkim, FL, Kesharwani, P, Dua, K, Chellappan, DK, Charbe, NB, Shrivastava, G, Rajeshkumar, S, Aljabali, AA, Al-Trad, B, Pabreja, K & Tambuwala, MM 2019, 'Dynamics of Prolyl Hydroxylases Levels During Disease Progression in Experimental Colitis', Inflammation, vol. 42, no. 6, pp. 2032-2036.
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Bannwarth, A, Morelato, M, Benaglia, L, Been, F, Esseiva, P, Delemont, O & Roux, C 2019, 'The use of wastewater analysis in forensic intelligence: drug consumption comparison between Sydney and different European cities', Forensic Sciences Research, vol. 4, no. 2, pp. 141-151.
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© 2019, © 2019 The Author(s). Published by Taylor & Francis Group on behalf of the Academy of Forensic Science. Wastewater analysis offers objective and complementary information to illicit drug agencies by monitoring patterns of illicit drug consumption. In this study, wastewater samples from three different wastewater treatment plants in Sydney, Australia were collected in March 2016. Ten targeted drugs were analysed and temporal and geographical analyses were performed to obtain a better understanding of the type and amount of illicit drugs consumed in Sydney in comparison with similar studies conducted around Australia and in Europe. Among the targeted drugs, methamphetamine was consumed the most, followed by cocaine and 3,4-methylenedioxymethamphetamine (MDMA). Weekly patterns were observed where a peak during the weekend was present. The geographical analysis showed differences between the regions targeted. This observation may be related to socio-demographic aspects. The comparison of our study to other data sources from Australia showed a high consumption of methamphetamine in Sydney and Western Australia. The comparison between Sydney and different European cities revealed a difference in consumption, which is in line with traditional market indicators. The information obtained through wastewater analysis provides complementary information regarding illicit drug consumption, the size, and the evolution of the illicit drug market. This, ultimately, will assist authorities in making informed decisions.

Bansal, R, Care, A, Lord, MS, Walsh, TR & Sunna, A 2019, 'Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides', New Biotechnology, vol. 52, pp. 9-18.
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Bao, G & Jin, D 2019, 'Nanoparticles give mice infrared vision', Nature Photonics, vol. 13, no. 5, pp. 304-305.
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© 2019, Springer Nature Limited. The injection of rare-earth-doped upconversion nanoparticles into the eyes of mice allows them to visualize near-infrared light with a wavelength of ~1 μm.

Bao, G, Liu, Z, Luo, Y, Wong, K-L & Tanner, PA 2019, 'Effects of europium spectral probe interchange in Ln-dyads with cyclen and phen moieties', Dalton Transactions, vol. 48, no. 13, pp. 4314-4323.
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Antenna-lanthanide energy transfer is investigated via a bimetallic complex with one silent and one probe lanthanide ion, when their positions are interchanged in the complex.

Bao, G, Wong, K & Tanner, PA 2019, 'A Reversible Rhodamine B Based pH Probe with Large Pseudo‐Stokes Shift', ChemPlusChem, vol. 84, no. 7, pp. 816-820.
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AbstractA reversible and sensitive pH probe DPE−Rh operates by Förster resonance energy transfer from 1,2‐diphenylethyne (DPE) to Rhodamine B (Rh). In the presence of H+, the spirolactam ring of the Rhodamine B unit was opened and this resulted in ca. 1000‐fold enhancement of fluorescence intensity with linear change over the pH range of 2.0 to 5.5. The Förster resonance energy transfer offered this probe an effective excitation–emission wavelength shift of around 240 nm with about 100 % quenching of the donor emission. The response of the sensor is tolerant towards a wide range of metal ions and the sensing mechanism was deduced by 1H NMR spectrometry. This FRET‐based molecule not only provides a sensitive pH probe, but also suggests an effective strategy to eliminate the interference of excitation light.

Bao, W, Shuck, CE, Zhang, W, Guo, X, Gogotsi, Y & Wang, G 2019, 'Boosting Performance of Na–S Batteries Using Sulfur-Doped Ti₃C₂T_x MXene Nanosheets with a Strong Affinity to Sodium Polysulfides', ACS Nano, vol. 13, no. 10, pp. 11500-11509.
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Copyright © 2019 American Chemical Society. Sodium-sulfur batteries using abundant elements offer an attractive alternative to currently used batteries, but they need better sulfur host materials to compete with lithium-ion batteries in capacity and cyclability. We report an in situ sulfur-doping strategy to functionalize MXene nanosheets by introducing heteroatomic sulfur into the MXene structure form the MAX phase precursor. By employing the vacuum freeze-drying method, a three-dimensional (3D) wrinkled MXene nanoarchitecture with the high specific surface area was prepared. The tailor-made wrinkled sulfur-doped MXene (S-Ti3C2Tx) nanosheets were applied as an electrode host material in room temperature sodium-sulfur batteries. The S-Ti3C2Tx matrix shows high polarity with sodium polysulfides, restricting the diffusion of sodium polysulfides. The MXene/sulfur electrode can achieve high areal sulfur loading up to 4.5 mg cm-2 as well as good electrochemical performance (reversible capacity of 577 mAh g-1 at 2 C after 500 cycles).

Barratt, JLN & Ellis, J 2019, 'Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen – CORRIGENDUM', Parasitology, vol. 146, no. 10, pp. 1360-1360.
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© Cambridge University Press 2019. The authors apologise for an error in the manuscript: on page 1096, it was stated that most cases of angiostrongyliasis reported by Hochberg and colleagues (Hochberg et al., 2007, 2011) occurred in Honolulu, on the main island of Hawaii (Barratt et al., 2016). This is incorrect. The sentence should state that the highest incidence of cases reported by Hochberg and colleagues occurred on the island of Hawaii, which is the largest of the Hawaiian Islands. The Hawaii state capital of Honolulu is located on the island of Oahu, which is the most populous and third largest Hawaiian Island. We gratefully acknowledge Kirsten Snook (University of Hawaii at Hilo) and Dr Sarah Park (Hawaii Department of Health) who notified us independently of this error.

Barraza, V, Grings, F, Franco, M, Douna, V, Entekhabi, D, Restrepo-Coupe, N, Huete, A, Gassmann, M & Roitberg, E 2019, 'Estimation of latent heat flux using satellite land surface temperature and a variational data assimilation scheme over a eucalypt forest savanna in Northern Australia', Agricultural and Forest Meteorology, vol. 268, pp. 341-353.
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© 2019 Elsevier B.V. In this study, the performance of the combined-source variational data assimilation scheme (CS-VDA) is assessed in detail using in situ heat fluxes (i.e. sensible heat (H) and latent heat (LE)) collected at a Eucalypt forest savanna of Northern Australia (Howard Springs). The CS VDA scheme estimates surface turbulent heat fluxes via assimilation of sequences of land surface temperature (LST) and meteorological data into a surface energy balance model and a dynamic model. The main objectives of this paper were to extend previous studies to a semi-arid ecosystem and to evaluate the potential of using global meteorological forcing data (GMD) to drive the CS VDA model (rather than in-situ meteorological observations). In order to study the new errors associated with the use of GMD, the effects on LE of the uncertainty in air temperature and wind speed (the two key meteorological factors that controls the total estimation error) was quantitatively characterized. Using hourly in-situ measurements as inputs, the daily-averaged LE RMSE daily was 54 W/m 2 , which agrees with the errors previously reported in the literature. As expected, replacing local meteorological data with GMD reduces the performance of the LE estimation (GMA: RMSE daily = 82 W/m 2 , GLDAS: RMSE daily = 151 W/m 2 ). However, LE RMSE values at 8-day temporal scale for GMA are RMSE 8-days = 32 W/m 2 , similar to those reported in this area for other models (MODIS (MOD16A2) and Breathing Earth System Simulator (BESS)). The error propagation analysis indicate that the CS VDA model is very sensitive to uncertainties in wind speed measurements. Moreover, there are large discrepancies between in situ and GMD wind speed. These two factors combined can explain the degradation in LE estimations. In this context, our study is a first step towards the characterization of an operational daily LE estimation scheme using hourly LST observations.

Bartlett, M, Wang, J, Hay, L & Pang, G 2019, 'Health service use in the older person with complex health needs', Australian Health Review, vol. 43, no. 1, pp. 62-62.
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Objective Effective health care for older people with complex health needs requires a diverse range of healthcare professionals working together. The Building Partnerships Framework of the New South Wales Agency for Clinical Innovation seeks to promote collaboration and integration among service providers. The aim of the present study was to inform implementation and evaluation of the Framework. Methods Data from the 45 and Up Study was linked with deaths and service data from hospitalisations and the Medicare Benefits Schedule (MBS). Participants with a hospitalisation for conditions representing ‘geriatric syndrome’ were allocated to a complex needs group; the remainder were allocated to a comparison group. Hospital admissions and MBS services use were modelled using log-linear Poisson regression. Results Multivariate analysis showed that the rate of hospitalisation in the 2 years following index admission for the complex needs group was 18% (95% confidence interval (CI) 1.12–1.24) greater than the comparison group and specialist physician attendance was 13% (95% CI 1.06 – 1.21) greater. The rate of general practitioner (GP) attendances was 2% (95% CI 0.97–1.07) greater in the complex needs group, but this was not statistically significant. Discussion The greater rates of hospitalisation and specialist service use, the absence of a similar finding for GP services and the prominence of the role of primary care in service integration literature, policy and strategy underscore the importance of careful planning, consultation and inclusiveness in the development and implementation of integrated care policy. What is known about the topic? Older people with complex health needs are significant consumers of primary and secondary health services and benefit from well-planned and coordinated care. What does this paper add? The findings presented here indicate that although hospitals and specialist physicians provide a significantly greater volume of se...

Batmunkh, M, Vimalanathan, K, Wu, C, Bati, ASR, Yu, L, Tawfik, SA, Ford, MJ, Macdonald, TJ, Raston, CL, Priya, S, Gibson, CT & Shapter, JG 2019, 'Efficient Production of Phosphorene Nanosheets via Shear Stress Mediated Exfoliation for Low‐Temperature Perovskite Solar Cells', Small Methods, vol. 3, no. 5, pp. 1800521-1800521.
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AbstractA simple and fast “top‐down” protocol is introduced herein to prepare solution processable few‐layer phosphorene nanosheets using vortex fluidic mediated exfoliation under near‐infrared (NIR) pulsed laser irradiation. This novel shear‐exfoliation method requires short processing times and produces highly crystalline, atomically thin phosphorene nanosheets (4.3 ± 0.4 nm). The as‐prepared phosphorene nanosheets are used as an effective electron transporting material (ETM) for low‐temperature processed, planar n‐i‐p perovskite solar cells (PSCs). With the addition of phosphorene, the average power conversion efficiency (PCE) increases from 14.32% to 16.53% with a maximum PCE of 17.85% observed for the phosphorene incorporated PSCs which is comparable to the devices made using the traditional high‐temperature protocol. Experimental and theoretical (density‐functional theory) investigations reveal the PCE improvements are due to the high carrier mobility and suitable band energy alignment of the phosphorene. The work not only paves the way for novel synthesis of 2D materials, but also opens a new avenue in using phosphorene as an efficient ETM in photovoltaic devices.

Bawa, G, Mahajan, R, Mehta, M, Satija, S, Vyas, M, Sharma, N & Khurana, N 2019, 'Herbal drugs for the treatment of opioid withdrawal syndrome: A mini review', Plant Archives, vol. 19, pp. 1005-1011.
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Addiction to opioid drugs is the extensive medical and social burden of human life. Chronic usage of morphine in the severe pain has also been associated with its major drawback for development of dependence and tolerance. In different brain regions, there are various receptors which play important role in opioid withdrawal syndrome. The herbal drugs; like Nigella sativa, Withania somnifera, Aloe vera, Matricaria recutita, venlafaxine, curucumin play vital role to treat the abstinence syndrome. Most of the above mentioned drugs are related with some adverse effects. So there is need to develop some novel agents targeting the various mechanism underlying the opioid withdrawal, thereby providing significant relief from opioid withdrawal syndrome. In this review, we discussed the usefulness and limitations of various drug treatments for opioid withdrawal syndrome.

Bedward, TM, Xiao, L & Fu, S 2019, 'Application of Raman spectroscopy in the detection of cocaine in food matrices', Australian Journal of Forensic Sciences, vol. 51, no. 2, pp. 209-219.
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© 2017 Australian Academy of Forensic Sciences While modern methodologies for the smuggling of illicit substances often tend towards more elaborate inventions, the simple practice of concealing cocaine hydrochloride within food matrices is becoming increasingly popular. This study was conducted to develop and optimize a Raman spectroscopic method capable of identifying and quantifying cocaine hydrochloride concealed within food matrices. Samples of cocaine hydrochloride were concealed within baking powder, cake mix and white rum, with identification of the drug achieved through a combination of manual and automated detection methods and comparison with a digital spectral library. Principal component analysis (PCA) and partial least squares regression (PLSR) were employed to qualitatively and quantitatively examine the collected spectra, allowing for traces of cocaine hydrochloride found within each matrix to be identified and quantified. For each of the solid matrices, Raman spectroscopy enabled rapid, non-invasive, and unambiguous identification of the concealed drug. For the white rum samples, due to strong matrix interference, full spectrum matching was not possible, but presumptive identification of cocaine in the samples was achieved at 100%. No false positives or miss-identified samples were recorded, Results of the PLSR analysis showed potential, however difficulties in obtaining accurate concentrations served to limit the method’s use in quantitative analysis.

Belay, Y, Coetzee, L-C, Williams, DBG & Muller, A 2019, 'Synthesis of novel 1,2,3-triazole based polycarboxylic acid functionalised ligands for MOF systems', Tetrahedron Letters, vol. 60, no. 6, pp. 501-503.
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© 2019 Copper catalysed click reactions are excellent tools to generate various 1,2,3-triazole linked polytopic aromatic carboxylates. The general reaction route involves protection of the carboxylates before proceeding with the click reaction. These polycarboxylate azoles are conveniently prepared for potential utility as novel key building blocks for metal organic frameworks. In one case, the ligand crystallises into a solid structure containing 1D, 2D and 3D features, based on a zigzag 1D structure, a ‘chicken mesh’-like 2D structure and a 3D structure with very well-defined channels.

Bennett, N, Woodcock, S, Pluss, MA, Bennett, KJM, Deprez, D, Vaeyens, R, Lenoir, M & Fransen, J 2019, 'Forecasting the development of explosive leg power in youth soccer players', Science and Medicine in Football, vol. 3, no. 2, pp. 131-137.
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© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group. Purpose: Monitoring athletic development in youth soccer can help sporting professionals monitor athletic development and evaluate the effectiveness of training interventions. However, long-term follow up in talent development programmes in youth soccer is complicated. Therefore, the aim of this study was to forecast the developmental trajectories of explosive leg power in youth soccer players. Methods: Mixed effects regression models were used to forecast explosive leg power (countermovement (CMJ) and standing broad jump (SBJ)) in a longitudinal sample of 2201 youth soccer players from two high level Belgian acedemies and the Belgian National teams. Players were aged between 6 and 20 years (mean age = 13.04 ± 3.18 y) and were subdivided into three age cohorts (6–10, 11–15, and 16–20 y) for CMJ and two age cohorts (6–16, and 17–20 y) for SBJ. Results: This study was able to accurately forecast explosive leg power using different regression equations in each age cohort. Conclusions: Researchers, coaches, and sporting professionals can use these methods to either predict future explosive leg power from current performance measures, monitor the development of explosive leg power, or assess the effectiveness of training interactions aimed at altering predicted developmental trajectories.

Bharatula, LD, Rice, S, Marsili, E & Kwan, JJ 2019, 'Acoustically stressing biofilms formed by Pseudomonas aeruginosa', The Journal of the Acoustical Society of America, vol. 146, no. 4_Supplement, pp. 3031-3031.
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Bacterial biofilms, the complex and dynamic assemblages of bacterial cells, have shown increased tolerance to antimicrobials compared to their planktonic counterparts. Altered metabolism and micro-environments, in addition to the self-generated extracellular polymeric substances (EPS), collectively help to protect the bacteria from the effect of antimicrobials, thereby increasing the necessity for novel treatment methods that are effective against biofilms. To address this, we have investigated the effect of high intensity focused ultrasound (HIFU) in killing or dispersing biofilms. HIFU reduces the total biofilm biomass without significant cell killing. To investigate the molecular mechanism of action of HIFU, we quantified the intracellular concentrations of cyclic di-GMP, which regulates the switch between biofilm and planktonic life-styles. Biofilms grown on polymeric sheets were exposed to HIFU at 0.5 MHz frequency and the c di-GMP concentration was characterized using confocal microscopy. Changes in the c di-GMP activity localized at the acoustic focus were observed as the biomass decreased. The mechanisms promoting these changes were further investigated by examining the shape of individual bacterial colony grown on agar plates. The observed effects were compared to sham (negative control) and c di-GMP overproducing mutant (positive control).

Bharatula, LD, Rice, S, Marsili, E & Kwan, JJ 2019, 'Sounding out bacteria: Microstructural effects of therapeutic ultrasound on bacterial biofilms', The Journal of the Acoustical Society of America, vol. 145, no. 3_Supplement, pp. 1894-1894.
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Treatment of chronic infections due to formation of bacterial biofilms are a huge risk due to the growing concerns with antimicrobial resistance. Biofilms grow in a complex and dynamic environment that weaken the effect of antimicrobials. Yet, the current strategy to tackle the problem is the development of novel drugs. However, the increasing prevalence of antimicrobial resistance suggests that an alternative treatment strategy without, or in synergy with, antibiotics is necessary to combat the biofilm infections. We and others have proposed high intensity focused ultrasound (HIFU) as a means to disrupt the biofilm matrix and improve therapy. Yet to date, there is limited knowledge on the cellular activity triggered by the biofilm-acoustic interactions. Here, we report the effect of HIFU at 500 kHz center frequency in absence of antibiotics or microbubbles on the microstructure of biofilms formed by Pseudomonas aeruginosa. Changes to the biofilm after acoustic exposure were characterized by confocal microscopy and electrochemical impedance spectroscopy. We observed a drop in the biomass at pressures where non-linear acoustics were dominant, and an increase in cellular activity. Our results suggest that there are acoustic bio-effects present in these bacteria that have not yet been reported.

Bharill, N, Patel, OP, Tiwari, A, Mu, L, Li, D-L, Mohanty, M, Kaiwartya, O & Prasad, M 2019, 'A Generalized Enhanced Quantum Fuzzy Approach for Efficient Data Clustering', IEEE Access, vol. 7, pp. 50347-50361.
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© 2013 IEEE. Data clustering is a challenging task to gain insights into data in various fields. In this paper, an Enhanced Quantum-Inspired Evolutionary Fuzzy C-Means (EQIE-FCM) algorithm is proposed for data clustering. In the EQIE-FCM, quantum computing concept is utilized in combination with the FCM algorithm to improve the clustering process by evolving the clustering parameters. The improvement in the clustering process leads to improvement in the quality of clustering results. To validate the quality of clustering results achieved by the proposed EQIE-FCM approach, its performance is compared with the other quantum-based fuzzy clustering approaches and also with other evolutionary clustering approaches. To evaluate the performance of these approaches, extensive experiments are being carried out on various benchmark datasets and on the protein database that comprises of four superfamilies. The results indicate that the proposed EQIE-FCM approach finds the optimal value of fitness function and the fuzzifier parameter for the reported datasets. In addition to this, the proposed EQIE-FCM approach also finds the optimal number of clusters and more accurate location of initial cluster centers for these benchmark datasets. Thus, it can be regarded as a more efficient approach for data clustering.

Billings, JL, Gordon, SL, Rawling, T, Doble, PA, Bush, AI, Adlard, PA, Finkelstein, DI & Hare, DJ 2019, 'l‐3,4‐dihydroxyphenylalanine (l‐DOPA) modulates brain iron, dopaminergic neurodegeneration and motor dysfunction in iron overload and mutant alpha‐synuclein mouse models of Parkinson's disease', Journal of Neurochemistry, vol. 150, no. 1, pp. 88-106.
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AbstractTreatment with the dopamine (DA) precursor l‐3,4‐dihydroxyphenylalanine (l‐DOPA) provides symptomatic relief arising from DA denervation in Parkinson's disease. Mounting evidence that DA autooxidation to neurotoxic quinones is involved in Parkinson's disease pathogenesis has raised concern about potentiation of oxidative stress by l‐DOPA. The rate of DA quinone formation increases in the presence of excess redox‐active iron (Fe), which is a pathological hallmark of Parkinson's disease. Conversely, l‐DOPA has pH‐dependent Fe‐chelating properties, and may act to ‘redox silence’ Fe and partially allay DA autoxidation. We examined the effects of l‐DOPA in three murine models of parkinsonian neurodegeneration: early‐life Fe overexposure in wild‐type mice, transgenic human (h)A53T mutant α‐synuclein (α‐syn) over‐expression, and a combined ‘multi‐hit’ model of Fe‐overload in hA53T mice. We found that l‐DOPA was neuroprotective and prevented age‐related Fe accumulation in the substantia nigra pars compacta (SN

Bilokur, M, Gentle, AR, Arnold, MD, Cortie, MB & Smith, GB 2019, 'High temperature optically stable spectrally-selective Ti1xAlxN-based multilayer coating for concentrated solar thermal applications', Solar Energy Materials and Solar Cells, vol. 200, pp. 109964-109964.
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© 2019 Elsevier B.V. Spectrally-selective solar absorbing coatings based on the Ti1-xAlxN system were deposited using DC magnetron sputtering. Due to their refractory nature and very suitable optical properties, these were considered for high temperature solar thermal energy conversion. The composition of Ti1-xAlxN, (effectively, the Ti/Al ratio) was optimized to achieve a maximized solar absorptance. The optimum composition was then tested in a tandem absorber which included anti-reflective layers. A stainless steel substrate was used in order to simulate service in parabolic trough-based power plants that use stainless steel pipe to carry the heat-transfer fluid. High temperature annealing of the stack caused structural modifications but the solar absorptance of 92% was retained even after annealing at 900 °C.

Biswal, JK, Ranjan, R, Subramaniam, S, Mohapatra, JK, Patidar, S, Sharma, MK, Bertram, MR, Brito, B, Rodriguez, LL, Pattnaik, B & Arzt, J 2019, 'Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India', PLOS ONE, vol. 14, no. 6, pp. e0214832-e0214832.
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Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The role of foot-and-mouth disease virus (FMDV) persistently infected ruminants in initiating new outbreaks remains controversial, and the perceived threat posed by such animals hinders international trade in FMD-endemic countries. In this study we report longitudinal analyses of genetic and antigenic variations of FMDV serotype O/ME-SA/Ind2001d sublineage during naturally occurring, persistent infection in cattle and buffalo at an organised dairy farm in India. The proportion of animals from which FMDV RNA was recovered was not significantly different between convalescent (post-clinical) and sub-clinically infected animals or between cattle and buffalo across the sampling period. However, infectious virus was isolated from a higher proportion of buffalo samples and for a longer duration compared to cattle. Analysis of the P1 sequences from recovered viruses indicated fixation of mutations at the rate of 1.816 x 10-2substitution/site/year (s/s/y) (95% CI 1.362–2.31 x 10−2 s/s/y). However, the majority of point mutations were transitional substitutions. Within individual animals, the mean dN/dS (ω) value for the P1 region varied from 0.076 to 0.357, suggesting the selection pressure acting on viral genomes differed substantially across individual animals. Statistical parsimony analysis indicated that all of the virus isolates from carrier animals originated from the outbreak virus. The antigenic relationship value as determined by 2D-VNT assay revealed fluctuation of antigenic variants within and between carrier animals during the carrier state which suggested that some carrier viruses had diverged substantially from the protection provided by the vaccine strain. This study contr...

Black, HD, Xu, W, Hortle, E, Robertson, SI, Britton, WJ, Kaur, A, New, EJ, Witting, PK, Chami, B & Oehlers, SH 2019, 'The cyclic nitroxide antioxidant 4-methoxy-TEMPO decreases mycobacterial burden in vivo through host and bacterial targets', Free Radical Biology and Medicine, vol. 135, pp. 157-166.
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Bodachivskyi, I, Kuzhiumparambil, U & Bradley G. Williams, D 2019, 'High Yielding Acid‐Catalysed Hydrolysis of Cellulosic Polysaccharides and Native Biomass into Low Molecular Weight Sugars in Mixed Ionic Liquid Systems', ChemistryOpen, vol. 8, no. 10, pp. 1316-1324.
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AbstractIonic media comprising 1‐butyl‐3‐methylimidazolium chloride and the acidic deep eutectic solvent choline chloride/oxalic acid as co‐solvent‐catalyst, very efficiently convert various cellulosic substrates, including native cellulosic biomass, into water‐soluble carbohydrates. The optimum reaction systems yield a narrow range of low molecular weight carbohydrates directly from cellulose, lignocellulose, or algal saccharides, in high yields and selectivities up to 98 %. Cellulose possesses significant potential as a renewable platform from which to generate large volumes of green replacements to many petrochemical products. Within this goal, the production of low molecular weight saccharides from cellulosic substances is the key to success. Native cellulose and lignocellulosic feedstocks are less accessible for such transformations and depolymerisation of polysaccharides remains a primary challenge to be overcome. In this study, we identify the catalytic activity associated with selected deep eutectic solvents that favours the hydrolysis of polysaccharides and develop reaction conditions to improve the outcomes of desirable low molecular weight sugars. We successfully apply the chemistry to raw bulk, non‐pretreated cellulosic substances.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3208-3208.
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AbstractInvited for this month′s cover is the group of Prof. Bradley Williams at the University of Technology Sydney. The image depicts the manifold products that can be selected in transformations of glucose through manipulation of the Brønsted or Lewis acidity of the catalyst. The Full Paper itself is available at 10.1002/cssc.201900292.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3263-3270.
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AbstractThe specific type of acidity associated with the given metal trifloromethanesulfonates (Brønsted or Lewis acidity) dramatically influences the course of reactions, and it is possible to select for disaccharides, fructose, methyl glucosides, or methyl levulinate. Glucose is transformed into a range of value‐added molecules in water and methanol under the action of acidic metal triflates as catalysts, including their analogous Brønsted acid‐assisted or Brønsted base‐modified systems. A systematic study is presented of a range of metal triflates in methanol and water, pinning down the preferred conditions to select for each product.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Acid‐Catalysed Conversion of Carbohydrates into Furan‐Type Molecules in Zinc Chloride Hydrate', ChemPlusChem, vol. 84, no. 4, pp. 352-357.
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AbstractAcid‐catalysed conversion of biomass, specifically cellulose, holds promise to create value‐added, renewable replacements for many petrochemical products. We investigated an unusual acid‐catalysed transformation of cellulose and cellobiose in the biphasic solvent system zinc chloride hydrate (ionic liquid)/anisole. Here, furyl hydroxymethyl ketone and furfural are obtained as major products, which are valuable but less commonly formed in high yields in transformations of cellulosic substrates. We explored this chemistry in small‐scale model reactions and applied the optimised methods to the conversion of cellulose in bench‐scale processes. The optimum reaction system and preferred reaction conditions are defined to select for highly desirable furanoid products in the highest known yields (up to 46 %) directly from cellulose or cellobiose. The method avoids the use of added catalysts: the ionic solvent zinc chloride hydrate possesses the intrinsic acidity required for the hydrolysis and chemical transformation steps. The process involves inexpensive media for the catalytic conversion of cellulose into high‐value products under mild processing conditions.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Metal triflates are tunable acidic catalysts for high yielding conversion of cellulosic biomass into ethyl levulinate', Fuel Processing Technology, vol. 195, pp. 106159-106159.
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© 2019 Metal triflates and their mixtures with Brønsted acids are excellent catalysts for the selective and high yielding transformation of microcrystalline cellulose into ethyl levulinate, in ethanol, producing synergistic catalyst effects in some instances. The pretreatment of raw and unrefined cellulosic materials with a deep eutectic solvent enables similarly excellent catalysed conversion thereof into ethyl levulinate in superb yield (up to 75%) and selectivity (up to 88%). When using fermentation-derived ethanol, the product possesses 100% renewable content.

Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'The role of the molecular formula of ZnCl₂·nH₂O on its catalyst activity: a systematic study of zinc chloride hydrates in the catalytic valorisation of cellulosic biomass', Catalysis Science & Technology, vol. 9, no. 17, pp. 4693-4701.
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We show the efficient and direct transformation of a range of low value cellulosic substrates such as lignocellulose and algal biomass, into higher value chemicals, including low molecular weight reducing saccharides and furanoid products.

Bojer, MS, Wacnik, K, Kjelgaard, P, Gallay, C, Bottomley, AL, Cohn, MT, Lindahl, G, Frees, D, Veening, J, Foster, SJ & Ingmer, H 2019, 'SosA inhibits cell division in Staphylococcus aureus in response to DNA damage', Molecular Microbiology, vol. 112, no. 4, pp. 1116-1130.
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SummaryInhibition of cell division is critical for viability under DNA‐damaging conditions. DNA damage induces the SOS response that in bacteria inhibits cell division while repairs are being made. In coccoids, such as the human pathogen, Staphylococcus aureus, this process remains poorly studied. Here, we identify SosA as the staphylococcal SOS‐induced cell division inhibitor. Overproduction of SosA inhibits cell division, while sosA inactivation sensitizes cells to genotoxic stress. SosA is a small, predicted membrane protein with an extracellular C‐terminal domain in which point mutation of residues that are conserved in staphylococci and major truncations abolished the inhibitory activity. In contrast, a minor truncation led to SosA accumulation and a strong cell division inhibitory activity, phenotypically similar to expression of wild‐type SosA in a CtpA membrane protease mutant. This suggests that the extracellular C‐terminus of SosA is required both for cell division inhibition and for turnover of the protein. Microscopy analysis revealed that SosA halts cell division and synchronizes the cell population at a point where division proteins such as FtsZ and EzrA are localized at midcell, and the septum formation is initiated but unable to progress to closure. Thus, our findings show that SosA is central in cell division regulation in staphylococci.

Bonou, SAS, Sagbo, E, Aubry, C, Charvillat, C, Ben-Nissan, B & Cazalbou, S 2019, 'Conversion of snail shells (Achatina achatina) acclimatized in Benin to calcium phosphate for medical and engineering use', Journal of the Australian Ceramic Society, vol. 55, no. 4, pp. 1177-1186.
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Botté, ES, Nielsen, S, Abdul Wahab, MA, Webster, J, Robbins, S, Thomas, T & Webster, NS 2019, 'Changes in the metabolic potential of the sponge microbiome under ocean acidification', Nature Communications, vol. 10, no. 1, p. 4134.
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AbstractAnthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of marine organisms. Here we assess the possible effects of ocean acidification on the metabolic potential of sponge symbionts, inferred by metagenomic analyses of the microbiomes of two sponge species sampled at a shallow volcanic CO2 seep and a nearby control reef. When comparing microbial functions between the seep and control sites, the microbiome of the sponge Stylissa flabelliformis (which is more abundant at the control site) exhibits at the seep reduced potential for uptake of exogenous carbohydrates and amino acids, and for degradation of host-derived creatine, creatinine and taurine. The microbiome of Coelocarteria singaporensis (which is more abundant at the seep) exhibits reduced potential for carbohydrate import at the seep, but greater capacity for archaeal carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate pathway, as well as archaeal and bacterial urea production and ammonia assimilation from arginine and creatine catabolism. Together these metabolic features might contribute to enhanced tolerance of the sponge symbionts, and possibly their host, to ocean acidification.

Bouckaert, R, Vaughan, TG, Barido-Sottani, J, Duchêne, S, Fourment, M, Gavryushkina, A, Heled, J, Jones, G, Kühnert, D, De Maio, N, Matschiner, M, Mendes, FK, Müller, NF, Ogilvie, HA, du Plessis, L, Popinga, A, Rambaut, A, Rasmussen, D, Siveroni, I, Suchard, MA, Wu, C-H, Xie, D, Zhang, C, Stadler, T & Drummond, AJ 2019, 'BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis', PLOS Computational Biology, vol. 15, no. 4, pp. e1006650-e1006650.
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© 2019 Bouckaert 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. Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

Bozier, J, Rutting, S, Xenaki, D, Peters, M, Adcock, I & Oliver, BG 2019, 'Heightened response to e-cigarettes in COPD', ERJ Open Research, vol. 5, no. 1, pp. 00192-2018.
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E-cigarettes induce greater inflammatory mediators from COPD lung cells; therefore, the risks of e-cigarette use in COPD might be greater than in people without COPD http://ow.ly/xmnN30nzDhX.

Bradac, C, Gao, W, Forneris, J, Trusheim, ME & Aharonovich, I 2019, 'Quantum nanophotonics with group IV defects in diamond', Nature Communications, vol. 10, no. 1.
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AbstractDiamond photonics is an ever-growing field of research driven by the prospects of harnessing diamond and its colour centres as suitable hardware for solid-state quantum applications. The last two decades have seen the field shaped by the nitrogen-vacancy (NV) centre with both breakthrough fundamental physics demonstrations and practical realizations. Recently however, an entire suite of other diamond defects has emerged—group IV colour centres—namely the Si-, Ge-, Sn- and Pb-vacancies. In this perspective, we highlight the leading techniques for engineering and characterizing these diamond defects, discuss the current state-of-the-art group IV-based devices and provide an outlook of the future directions the field is taking towards the realisation of solid-state quantum photonics with diamond.

Bradbury, P, Patel, BS, Cidem, A, Nader, CP, Oliver, BG & Ammit, AJ 2019, 'Prostaglandin E2, but not cAMP nor β2-agonists, induce tristetraprolin (TTP) in human airway smooth muscle cells', Inflammation Research, vol. 68, no. 5, pp. 369-377.
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© 2019, Springer Nature Switzerland AG. Tristetraprolin (TTP) is an anti-inflammatory molecule known to post-transcriptionally regulate cytokine production and is, therefore, an attractive drug target for chronic respiratory diseases driven by inflammation, such as asthma and chronic obstructive pulmonary disease. Our recent in vitro studies in primary human airway smooth (ASM) cells have confirmed the essential anti-inflammatory role played by TTP as a critical partner in a cytokine regulatory network. However, several unanswered questions remain. While prior in vitro studies have suggested that TTP is regulated in a cAMP-mediated manner, raising the possibility that this may be one of the ways in which β2-agonists achieve beneficial effects beyond bronchodilation, the impact of β2-agonists on ASM cells is unknown. Furthermore, the effect of prostaglandin E2 (PGE2) on TTP expression in ASM cells has not been reported. We address this herein and reveal, for the first time, that TTP is not regulated by cAMP-activating agents nor following treatment with long-acting β2-agonists. However, PGE2 does induce TTP mRNA expression and protein upregulation in ASM cells. Although the underlying mechanism of action remains undefined, we can confirm that PGE2-induced TTP upregulation is not mediated via cAMP, or EP2/EP4 receptor activation, and occurred in a manner independent of the p38 MAPK-mediated pathway. Taken together, these data confirm that β2-agonists do not upregulate TTP in human ASM cells and indicate that another way in which PGE2 may achieve beneficial effects in asthma and COPD may be via upregulation of the master controller of inflammation—TTP.

Bradbury, P, Rumzhum, NN & Ammit, AJ 2019, 'EP₂ and EP₄ receptor antagonists: Impact on cytokine production and β₂‐adrenergic receptor desensitization in human airway smooth muscle', Journal of Cellular Physiology, vol. 234, no. 7, pp. 11070-11077.
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AbstractProstaglandin E2 (PGE2) is a key prostanoid known to have both proinflammatory and anti‐inflammatory impact in the context of chronic respiratory diseases. We hypothesize that these opposing effects may be the result of different prostanoid E (EP) receptor‐mediated signaling pathways. In this study, we focus on two of the four EP receptors, EP2 and EP4, as they are known to induce cyclic adenosine monophosphate (cAMP)‐dependent signaling pathways. Using primary human airway smooth muscle (ASM) cells, we first focussed on the PGE2‐induced production of two cAMP‐dependent proinflammatory mediators: interleukin 6 (IL‐6) and cyclo‐oxygenase 2 production. We show that PGE2‐induced IL‐6 protein secretion occurs via an EP2‐mediated pathway, in a manner independent of receptor‐mediated effects on messenger RNA (mRNA) expression and temporal activation kinetics of the transcription factor cAMP response element binding. Moreover, stimulation of ASM with PGE2 did not establish a positive, receptor‐mediated, feedback loop, as mRNA expression for EP2 and EP4 receptors were not upregulated and receptor antagonists were without effect. Our studies revealed that the EP2, but not the EP4, receptor is responsible for β2‐adrenergic desensitization induced by PGE2. We demonstrate that PGE2‐induced heterologous receptor desensitization responsible for tachyphylaxis to short‐ (salbutamol) or long‐ (formoterol) β2‐agonists (measured by cAMP release) can be reversed by the EP2 receptor antagonist PF‐04418948. Importantly, this study highlights that inhibiting the EP2

Bretherton, L, Poulton, AJ, Lawson, T, Rukminasari, N, Balestreri, C, Schroeder, D, Mark Moore, C & Suggett, DJ 2019, 'Day length as a key factor moderating the response of coccolithophore growth to elevated pCO₂', Limnology and Oceanography, vol. 64, no. 3, pp. 1284-1296.
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AbstractThe fate of coccolithophores in the future oceans remains uncertain, in part due to key factors having not been standardized across experiments. A potentially moderating role for differences in day length (photoperiod) remains largely unexplored. We therefore cultured four different geographical isolates of the species Emiliania huxleyi, as well as two additional species, Gephyrocapsa oceanica (tropical) and Coccolithus braarudii (temperate), to test for interactive effects of pCO2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO2 under 14 : 10 h L : D, but these reductions were dampened under continuous (24 h) light. The dynamics underpinning this pattern generally differed for the temperate vs. tropical isolates. Reductions in PIC : POC with elevated pCO2 for tropical taxa were largely through reduced calcification and enhanced photosynthesis under 14 : 10 h L : D, with differences dampened under continuous light. In contrast, reduced PIC : POC for temperate strains reflected increases of photosynthesis that outpaced increases in calcification rates under 14 : 10 h L : D, with both responses again dampened under continuous light. A multivariate analysis of 35 past studies of E. huxleyi further demonstrated that differences in photoperiod account for as much as 40% (strain B11/92) to 55% (strain NZEH) of ...

Brodersen, KE, Trevathan-Tackett, SM, Nielsen, DA, Connolly, RM, Lovelock, CE, Atwood, TB & Macreadie, PI 2019, 'Oxygen Consumption and Sulfate Reduction in Vegetated Coastal Habitats: Effects of Physical Disturbance', Frontiers in Marine Science, vol. 6, no. FEB.
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© 2019 Brodersen, Trevathan-Tackett, Nielsen, Connolly, Lovelock, Atwood and Macreadie. Vegetated coastal habitats (VCHs), such as mangrove forests, salt marshes and seagrass meadows, have the ability to capture and store carbon in the sediment for millennia, and thus have high potential for mitigating global carbon emissions. Carbon sequestration and storage is inherently linked to the geochemical conditions created by a variety of microbial metabolisms, where physical disturbance of sediments may expose previously anoxic sediment layers to oxygen (O 2 ), which could turn them into carbon sources instead of carbon sinks. Here, we used O 2 , hydrogen sulfide (H 2 S) and pH microsensors to determine how biogeochemical conditions, and thus aerobic and anaerobic metabolic pathways, vary across mangrove, salt marsh and seagrass sediments (case study from the Sydney area, Australia). We measured the biogeochemical conditions in the top 2.5 cm of surface (0-10 cm depth) and experimentally exposed deep sediments (> 50 cm depth) to simulate undisturbed and physically exposed sediments, respectively, and how these conditions may affect carbon cycling processes. Mangrove surface sediment exhibited the highest rates of O 2 consumption and sulfate (SO 42- ) reduction based on detailed microsensor measurements, with a diffusive O 2 uptake rate of 102 mmol O 2 m -2 d -1 and estimated sulfate reduction rate of 57 mmol S tot2- m -2 d -1 . Surface sediments (0-10 cm) across all the VCHs generally had higher O 2 consumption and estimated sulfate reduction rates than deeper layers (> 50 cm depth). O 2 penetration was < 4 mm for most sediments and only down to 1 mm depth in mangrove surface sediments, which correlated with a significantly higher percent organic carbon content (%C org ) within sediments originating from mangrove forests as compared to those from seagrass and salt marsh ecosystems. Additionally, pH dropped from 8.2 at the sediment/water interface to < 7-7.5 ...

Brown, P, Tan, A-C, El-Esawi, MA, Liehr, T, Blanck, O, Gladue, DP, Almeida, GMF, Cernava, T, Sorzano, CO, Yeung, AWK, Engel, MS, Chandrasekaran, AR, Muth, T, Staege, MS, Daulatabad, SV, Widera, D, Zhang, J, Meule, A, Honjo, K, Pourret, O, Yin, C-C, Zhang, Z, Cascella, M, Flegel, WA, Goodyear, CS, van Raaij, MJ, Bukowy-Bieryllo, Z, Campana, LG, Kurniawan, NA, Lalaouna, D, Hüttner, FJ, Ammerman, BA, Ehret, F, Cobine, PA, Tan, E-C, Han, H, Xia, W, McCrum, C, Dings, RPM, Marinello, F, Nilsson, H, Nixon, B, Voskarides, K, Yang, L, Costa, VD, Bengtsson-Palme, J, Bradshaw, W, Grimm, DG, Kumar, N, Martis, E, Prieto, D, Sabnis, SC, Amer, SEDR, Liew, AWC, Perco, P, Rahimi, F, Riva, G, Zhang, C, Devkota, HP, Ogami, K, Basharat, Z, Fierz, W, Siebers, R, Tan, K-H, Boehme, KA, Brenneisen, P, Brown, JAL, Dalrymple, BP, Harvey, DJ, Ng, G, Werten, S, Bleackley, M, Dai, Z, Dhariwal, R, Gelfer, Y, Hartmann, MD, Miotla, P, Tamaian, R, Govender, P, Gurney-Champion, OJ, Kauppila, JH, Zhang, X, Echeverría, N, Subhash, S, Sallmon, H, Tofani, M, Bae, T, Bosch, O, Cuív, PO, Danchin, A, Diouf, B, Eerola, T, Evangelou, E, Filipp, FV, Klump, H, Kurgan, L, Smith, SS, Terrier, O, Tuttle, N, Ascher, DB, Janga, SC, Schulte, LN, Becker, D, Browngardt, C, Bush, SJ, Gaullier, G, Ide, K, Meseko, C, Werner, GDA, Zaucha, J, Al-Farha, AA, Greenwald, NF, Popoola, SI, Rahman, MS, Xu, J, Yang, SY, Hiroi, N, Alper, OM, Baker, CI, Bitzer, M, Chacko, G, Debrabant, B, Dixon, R, Forano, E, Gilliham, M, Kelly, S, Klempnauer, K-H, Lidbury, BA, Lin, MZ, Lynch, I, Ma, W, Maibach, EW, Mather, DE, Nandakumar, KS, Ohgami, RS, Parchi, P, Tressoldi, P, Xue, Y, Armitage, C, Barraud, P, Chatzitheochari, S, Coelho, LP, Diao, J, Doxey, AC, Gobet, A, Hu, P, Kaiser, S, Mitchell, KM, Salama, MF, Shabalin, IG, Song, H, Stevanovic, D, Yadollahpour, A, Zeng, E, Zinke, K, Alimba, CG, Beyene, TJ, Cao, Z, Chan, SS, Gatchell, M, Kleppe, A, Piotrowski, M, Torga, G, Woldesemayat, AA, Cosacak, MI, Haston, S, Ross, SA, Williams, R, Wong, A, Abramowitz, MK, Effiong, A, Lee, S, Abid, MB, Agarabi, C, Alaux, C, Albrecht, DR, Atkins, GJ, Beck, CR, Bonvin, AMJJ, Bourke, E, Brand, T, Braun, RJ, Bull, JA, Cardoso, P, Carter, D, Delahay, RM, Ducommun, B, Duijf, PHG, Epp, T, Eskelinen, E-L, Fallah, M, Farber, DB, Fernandez-Triana, J, Feyerabend, F, Florio, T, Friebe, M, Furuta, S, Gabrielsen, M, Gruber, J, Grybos, M, Han, Q & et al. 2019, 'Large expert-curated database for benchmarking document similarity detection in biomedical literature search', Database, vol. 2019, pp. 1-66.
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Abstract Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

Bryant, C, Aleks Lau, KH, Vuckovic, S, Marsh-Wakefield, F, Kruzins, A, McGuire, H, Yang, S, Fazekas de St. Groth, B, Nassif, N, Byrne, SN, Gibson, J, Brown, C, Larsen, S, McCulloch, D, Boyle, R, Joshua, D & Ho, PJ 2019, 'Accumulation of CD69+ Terminal Effector CD8+ T cells occurs in the bone marrow of newly diagnosed Myeloma patients who lack protective clonal Vb expanded cytotoxic T cells', Clinical Lymphoma Myeloma and Leukemia, vol. 19, no. 10, pp. e29-e29.
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Buapet, P, Mohammadi, NS, Pernice, M, Kumar, M, Kuzhiumparambil, U & Ralph, PJ 2019, 'Excess copper promotes photoinhibition and modulates the expression of antioxidant-related genes in Zostera muelleri', Aquatic Toxicology, vol. 207, pp. 91-100.
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© 2018 Elsevier B.V. Copper (Cu) is an essential micronutrient for plants and as such is vital to many metabolic processes. Nevertheless, when present at elevated concentrations, Cu can exert toxic effects on plants by disrupting protein functions and promoting oxidative stress. Due to their proximity to the urbanised estuaries, seagrasses are vulnerable to chemical contamination via industrial runoff, waste discharges and leachates. Zostera muelleri is a common seagrass species that forms habitats in the intertidal areas along the temperate coast of Australia. Previous studies have shown the detrimental effects of Cu exposure on photosynthetic efficiency of Z. muelleri. The present study focuses on the impacts of sublethal Cu exposure on the physiological and molecular responses. By means of a single addition, plants were exposed to 250 and 500 μg Cu L−1 (corresponding to 3.9 and 7.8 μM, respectively) as well as uncontaminated artificial seawater (control) for 7 days. Chlorophyll fluorescence parameters, measured as the effective quantum yield (ϕPSII), the maximum quantum yield (Fv/Fm) and non-photochemical quenching (NPQ) were assessed daily, while Cu accumulation in leaf tissue, total reactive oxygen species (ROS) and the expression of genes involved in antioxidant activities and trace metal binding were determined after 1, 3 and 7 days of exposure. Z. muelleri accumulated Cu in the leaf tissue in a concentration-dependent manner and the bioaccumulation was saturated by day 3. Cu exposure resulted in an acute suppression of ϕPSII and Fv/Fm. These two parameters also showed a concentration- and time-dependent decline. NPQ increased sharply during the first few days before subsequently decreasing towards the end of the experiment. Cu accumulation induced oxidative stress in Z. muelleri as an elevated level of ROS was detected on day 7. Lower Cu concentration promoted an up-regulation of genes encoding Cu/Zn-superoxide dismutase (Cu/Zn-sod), ascorbate p...

Budden, KF, Shukla, SD, Rehman, SF, Bowerman, KL, Keely, S, Hugenholtz, P, Armstrong-James, DPH, Adcock, IM, Chotirmall, SH, Chung, KF & Hansbro, PM 2019, 'Functional effects of the microbiota in chronic respiratory disease', The Lancet Respiratory Medicine, vol. 7, no. 10, pp. 907-920.
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© 2019 Elsevier Ltd The composition of the lung microbiome is increasingly well characterised, with changes in microbial diversity or abundance observed in association with several chronic respiratory diseases such as asthma, cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease. However, the precise effects of the microbiome on pulmonary health and the functional mechanisms by which it regulates host immunity are only now beginning to be elucidated. Bacteria, viruses, and fungi from both the upper and lower respiratory tract produce structural ligands and metabolites that interact with the host and alter the development and progression of chronic respiratory diseases. Here, we review recent advances in our understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases. We also describe the present understanding of how respiratory microbiota can influence the efficacy of common therapies for chronic respiratory disease, and the potential of manipulation of the microbiome as a therapeutic strategy. Finally, we highlight some of the limitations in the field and propose how these could be addressed in future research.

Buis, R, Rust, L, Nizio, KD, Rai, T, Stuart, BH & Forbes, SL 2019, 'Investigating the Sensitivity of Cadaver- Detection Dogs to Aged, Diluted Decomposition Fluid', Journal of Forensic Identification, vol. 69, no. 3, pp. 367-377.
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Cadaver-detection dogs (also known as human remains detection dogs) are used worldwide to locate deceased victims and human remains. Ethical restrictions often prevent the dog handlers from using cadavers as training aids, resulting in a reliance on pseudo-scents or human tissues, such as blood, bone, and decomposition fluid. Often these aids must be re-used many times because of the difficulty in obtaining new materials. The aim of this study was to investigate the dogs' sensitivity to aged human decomposition fluid samples that are used as a training aid. Human decomposition fluid was collected and serially diluted to 1 part-per-trillion (10u) and aged up to two years. The samples were presented throughout the aging process to three police accredited cadaver-detectior. dog teams under standard indoor training conditions. The dogs were capable of detecting the oldest and lowest dilution levels of decomposition fluid samples. Ongoing training to retain this level of sensitivity is recommended. The results of these trials indicate human decomposition fluid is a valid training aid for cadaver-detection dogs.

Burke, C 2019, 'Designing for “touch”, “reach” and “movement” in postwar (1946–1972) English primary and infant school environments', The Senses and Society, vol. 14, no. 2, pp. 207-220.
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Butcher, EV, van Oorschot, RAH, Morgan, RM & Meakin, GE 2019, 'Opportunistic crimes: Evaluation of DNA from regularly-used knives after a brief use by a different person', Forensic Science International: Genetics, vol. 42, pp. 135-140.
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© 2019 Elsevier B.V. When evaluating trace DNA recovered from evidential items in forensic casework, it is crucial to consider how the DNA got there, and such evaluative interpretations should ideally be informed by published experimental data. A key activity-level question is whether the DNA obtained comes from the regular user, the last user (ostensibly the user at the time of the crime) or from indirect transfer events. The aim of this experiment was to provide data to contribute to answering this question, particularly when considering opportunistic crimes, in which an offender might grab the nearest item at hand required for their purpose, e.g. a weapon or tool, and therefore only handle it very briefly. Volunteers (‘regular users’) used knives in a prescribed manner to simulate regular use (one user per knife); DNA recovery by mini-tapes from these knives gave ˜1–10 ng DNA, with <16% non-donor DNA from indirect transfer events. Different volunteers (‘second users’) then stabbed replicate sets of regularly-used knives into a foam block for either 2, 30 or 60 s (on different occasions), with each timeframe in triplicate, and DNA was recovered from the knife handles using mini-tapes. For knives regularly-used by three of the four volunteers, the ratios of regular user to second user DNA were approximately 4:1, 2:1 and 1:1 for durations of use by the second user of 2, 30 and 60 s, respectively. Analysis of the respective quantities of DNA showed that this trend resulted from a decrease in regular user DNA via transfer to the second user's hands, rather than an increase in DNA deposition from the second user. However, for knives regularly-used by the fourth volunteer, DNA from the regular user remained at significantly higher quantities than DNA from the second user and unknown sources, irrespective of duration of use by the second user. Furthermore, one volunteer deposited a similar amount of DNA through regular use as the amount of indirectly-transfe...

Calarco, L & Ellis, J 2019, 'Annotating the ‘hypothetical’ in hypothetical proteins: In-silico analysis of uncharacterised proteins for the Apicomplexan parasite, Neospora caninum', Veterinary Parasitology, vol. 265, pp. 29-37.
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Neospora caninum is a parasite of veterinary and economic importance, affecting beef and dairy cattle industries globally. While this species has been recognised as a serious cause of disease in cattle and dogs for over 30 years, treatment and control options are still not available. Furthermore, whilst vaccination was identified as the most economic control strategy, vaccine discovery programs require new leads to investigate as vaccines. The current lack of gene annotation available for N. caninum, especially compared to the closely related model organism, Toxoplasma gondii, considerably hinders vaccine related research. Moreover, due to the high degree of similarity between the two organisms, a significant amount of gene annotation available for N. caninum stems from sequence homology between the species. However, there is a plethora of literature identifying conserved virulence factors between members of the Apicomplexa, which suggests that key players are contributing to successful parasite invasion, motility, and host cell attachment. In this study, bioinformatic approaches classified 125 uncharacterised proteins within the N. caninum genome, as transmembrane proteins with signal peptide sequences. Functional annotation assigned enriched gene ontologies for cell-adhesion, ATP binding, protein serine/threonine phosphatase complex, immune system process, antigen binding, and proteolysis. Additionally, 32 of these proteins were also identified as adhesins, or having adhesin-like properties, which were further characterised through the discovery of domains and gene ontology, to reveal their potential functional significance as virulence factors for N. caninum. This study identifies a new, small subset of proteins within N. caninum, that may be involved in host-cell interaction, parasite adhesion, and invasion, thereby implicating them as potential targets to exploit in the development of control options against the disease.

CAMERON, G, Loering, S, Deshpande, A, Jiang, S, Molofsky, A, McKenzie, A, Hansbro, P & Starkey, M 2019, 'SAT-129 GROUP 2 INNATE LYMPHOID CELLS ARE REDUNDANT IN EXPERIMENTAL RENAL ISCHEMIA-REPERFUSION INJURY', Kidney International Reports, vol. 4, no. 7, pp. S59-S59.
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Cameron, GJM, Cautivo, KM, Loering, S, Jiang, SH, Deshpande, AV, Foster, PS, McKenzie, ANJ, Molofsky, AB, Hansbro, PM & Starkey, MR 2019, 'Group 2 Innate Lymphoid Cells Are Redundant in Experimental Renal Ischemia-Reperfusion Injury', Frontiers in Immunology, vol. 10, no. MAR.
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© 2019 Cameron, Cautivo, Loering, Jiang, Deshpande, Foster, McKenzie, Molofsky, Hansbro and Starkey. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Acute kidney injury (AKI) can be fatal and is a well-defined risk factor for the development of chronic kidney disease. Group 2 innate lymphoid cells (ILC2s) are innate producers of type-2 cytokines and are critical regulators of homeostasis in peripheral organs. However, our knowledge of their function in the kidney is relatively limited. Recent evidence suggests that increasing ILC2 numbers by systemic administration of recombinant interleukin (IL)-25 or IL-33 protects against renal injury. Whilst ILC2s can be induced to protect against ischemic- or chemical-induced AKI, the impact of ILC2 deficiency or depletion on the severity of renal injury is unknown. Firstly, the phenotype and location of ILC2s in the kidney was assessed under homeostatic conditions. Kidney ILC2s constitutively expressed high levels of IL-5 and were located in close proximity to the renal vasculature. To test the functional role of ILC2s in the kidney, an experimental model of renal ischemia-reperfusion injury (IRI) was used and the severity of injury was assessed in wild-type, ILC2-reduced, ILC2-deficient, and ILC2-depleted mice. Surprisingly, there were no differences in histopathology, collagen deposition or mRNA expression of injury-associated (Lcn2), inflammatory (Cxcl1, Cxcl2, and Tnf) or extracellular matrix (Col1a1, Fn1) factors following IRI in the absence of ILC2s. These data suggest the absence of ILC2s does not alter the severi...

Cameron, GJM, Jiang, SH, Loering, S, Deshpande, AV, Hansbro, PM & Starkey, MR 2019, 'Emerging therapeutic potential of group 2 innate lymphoid cells in acute kidney injury', The Journal of Pathology, vol. 248, no. 1, pp. 9-15.
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AbstractAcute kidney injury (AKI) remains a global challenge and, despite the availability of dialysis and transplantation, can be fatal. Those that survive an AKI are at increased risk of developing chronic kidney disease and end stage renal failure. Understanding the fundamental mechanisms underpinning the pathophysiology of AKI is critical for developing novel strategies for diagnosis and treatment. A growing body of evidence indicates that amplifying type 2 immunity may have therapeutic potential in kidney injury and disease. Of particular interest are the recently described subset of innate immune cells, termed group 2 innate lymphoid cells (ILCs). Group 2 ILCs are crucial tissue‐resident immune cells that maintain homeostasis and regulate tissue repair at multiple organ sites, including the kidney. They are critical mediators of type 2 immune responses following infection and injury. The existing literature suggests that activation of group 2 ILCs and production of a local type 2 immune milieu is protective against renal injury and associated pathology. In this review, we describe the emerging role for group 2 ILCs in renal homeostasis and repair. We provide an in‐depth discussion of the most recent literature that use preclinical models of AKI and assess the therapeutic effect of modulating group 2 ILC function. We debate the potential for targeting these cells as novel cellular therapies in AKI and discuss the implications for future studies and translation. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Camp, EF, Edmondson, J, Doheny, A, Rumney, J, Grima, AJ, Huete, A & Suggett, DJ 2019, 'Mangrove lagoons of the Great Barrier Reef support coral populations persisting under extreme environmental conditions', Marine Ecology Progress Series, vol. 625, pp. 1-14.
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© The authors 2019. Global degradation of coral reefs has increased the urgency of identifying stress-tolerant coral populations, to enhance understanding of the biology driving stress tolerance, as well as identifying stocks of stress-hardened populations to aid reef rehabilitation. Surprisingly, scientists are continually discovering that naturally extreme environments house established coral populations adapted to grow within extreme abiotic conditions comparable to seawater conditions predicted over the coming century. Such environments include inshore mangrove lagoons that carry previously unrecognised ecosystem service value for corals, spanning from refuge to stress preconditioning. However, the existence of such hot-spots of resilience on the Great Barrier Reef (GBR) remains entirely unknown. Here we describe, for the first time, 2 extreme GBR mangrove lagoons (Woody Isles and Howick Island), exposing taxonomically diverse coral communities (34 species, 7 growth morphologies) to regular extreme low pH (<7.6), low oxygen (<1 mg l−1) and highly variable temperature range (>7°C) conditions. Coral cover was typically low (<5%), but highly patchy and included established colonies (>0.5 m diameter), with net photosynthesis and calcification rates of 2 dominant coral species (Acropora millepora, Porites lutea) reduced (20−30%), and respiration enhanced (11−35%), in the mangrove lagoon relative to adjacent reefs. Further analysis revealed that physiological plasticity (photosynthetic ‘strategy’) and flexibility of Symbiodiniaceae taxa associations appear crucial in supporting coral capacity to thrive from reef to lagoon. Prevalence of corals within these extreme conditions on the GBR (and elsewhere) increasingly challenge our understanding of coral resilience to stressors, and highlight the need to study unfavourable coral environments to better resolve mechanisms of stress tolerance.

Canonico, G, Buttigieg, PL, Montes, E, Muller-Karger, FE, Stepien, C, Wright, D, Benson, A, Helmuth, B, Costello, M, Sousa-Pinto, I, Saeedi, H, Newton, J, Appeltans, W, Bednaršek, N, Bodrossy, L, Best, BD, Brandt, A, Goodwin, KD, Iken, K, Marques, AC, Miloslavich, P, Ostrowski, M, Turner, W, Achterberg, EP, Barry, T, Defeo, O, Bigatti, G, Henry, L-A, Ramiro-Sánchez, B, Durán, P, Morato, T, Roberts, JM, García-Alegre, A, Cuadrado, MS & Murton, B 2019, 'Global Observational Needs and Resources for Marine Biodiversity', Frontiers in Marine Science, vol. 6, no. JUL.
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© 2019 Canonico, Buttigieg, Montes, Muller-Karger, Stepien, Wright, Benson, Helmuth, Costello, Sousa-Pinto, Saeedi, Newton, Appeltans, Bednaršek, Bodrossy, Best, Brandt, Goodwin, Iken, Marques, Miloslavich, Ostrowski, Turner, Achterberg, Barry, Defeo, Bigatti, Henry, Ramiro-Sánchez, Durán, Morato, Roberts, García-Alegre, Cuadrado and Murton. The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models.

Cao, J, Soiaporn, K, Carroll, RJ & Ruppert, D 2019, 'Modeling and Prediction of Multiple Correlated Functional Outcomes', Journal of Agricultural, Biological and Environmental Statistics, vol. 24, no. 1, pp. 112-129.
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© 2018, International Biometric Society. We propose a copula-based approach for analyzing functional data with correlated multiple functional outcomes exhibiting heterogeneous shape characteristics. To accommodate the possibly large number of parameters due to having several functional outcomes, parameter estimation is performed in two steps: first, the parameters for the marginal distributions are estimated using the skew t family, and then the dependence structure both within and across outcomes is estimated using a Gaussian copula. We develop an estimation algorithm for the dependence parameters based on the Karhunen–Loève expansion and an EM algorithm that significantly reduces the dimension of the problem and is computationally efficient. We also demonstrate prediction of an unknown outcome when the other outcomes are known. We apply our methodology to diffusion tensor imaging data for multiple sclerosis (MS) patients with three outcomes and identify differences in both the marginal distributions and the dependence structure between the MS and control groups. Our proposed methodology is quite general and can be applied to other functional data with multiple outcomes in biology and other fields. Supplementary materials accompanying this paper appear online.

Cao, M, Ellis, JT, Marriott, D, Harkness, J & Stark, D 2019, 'Evaluation of the EasyScreen Protozoan Detection Kit for the diagnosis of Entamoeba histolytica', Pathology, vol. 51, no. 4, pp. 426-428.
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Cao, Y, Wang, L, Wang, C, Su, D, Liu, Y & Hu, X 2019, 'Photoelectrochemical determination of malathion by using CuO modified with a metal-organic framework of type Cu-BTC', Microchimica Acta, vol. 186, no. 7.
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© 2019, Springer-Verlag GmbH Austria, part of Springer Nature. A photoelectrochemical (PEC) sensor was constructed for the detection of non-electroactive malathion. It is based on the use of a hierarchical CuO material derived from a Cu-BTC metal-organic framework (where BTC stands for benzene-1,3,5-tricarboxylic acid). The modified CuO was obtained by calcination of Cu-BTC at a high temperature (300 °C) and possesses a high photocurrent conversion efficiency. Under irradiation with visible light and in the presence of malathion, the formation of the CuO-malathion complex on the CuO gave rise to an increase in steric hindrance. This results in a decrease in photocurrent. This novel PEC detection method has a lower detection limit of 8.6 × 10−11 mol L−1 and a wide linear range (1.0 × 10−10 ~ 1.0 × 10−5 mol L−1). [Figure not available: see fulltext.]

Caramori, G, Ruggeri, P, Mumby, S, Ieni, A, Lo Bello, F, Chimankar, V, Donovan, C, Andò, F, Nucera, F, Coppolino, I, Tuccari, G, Hansbro, PM & Adcock, IM 2019, 'Molecular links between COPD and lung cancer: new targets for drug discovery?', Expert Opinion on Therapeutic Targets, vol. 23, no. 6, pp. 539-553.
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© 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group. Introduction: COPD and lung cancer are leading causes of morbidity and mortality worldwide, and they share a common environmental risk factor in cigarette smoke exposure and a genetic predisposition represented by their incidence in only a fraction of smokers. This reflects the ability of cigarette smoke to induce an inflammatory response in the airways of susceptible smokers. Moreover, COPD could be a driving factor in lung cancer, by increasing oxidative stress and the resulting DNA damage and repression of the DNA repair mechanisms, chronic exposure to pro-inflammatory cytokines, repression of innate immunity and increased cellular proliferation. Areas covered: We have focused our review on the potential pathogenic molecular links between tobacco smoking-related COPD and lung cancer and the potential molecular targets for new drug development by understanding the common signaling pathways involved in COPD and lung cancer. Expert commentary: Research in this field is mostly limited to animal models or small clinical trials. Large clinical trials are needed but mostly combined models of COPD and lung cancer are necessary to investigate the processes caused by chronic inflammation, including genetic and epigenetic alteration, and the expression of inflammatory mediators that link COPD and lung cancer, to identify new molecular therapeutic targets.

Cardona, T, Sánchez‐Baracaldo, P, Rutherford, AW & Larkum, AW 2019, 'Early Archean origin of Photosystem II', Geobiology, vol. 17, no. 2, pp. 127-150.
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AbstractPhotosystem II is a photochemical reaction center that catalyzes the light‐driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

Cardoso, BR, Roberts, BR, Malpas, CB, Vivash, L, Genc, S, Saling, MM, Desmond, P, Steward, C, Hicks, RJ, Callahan, J, Brodtmann, A, Collins, S, Macfarlane, S, Corcoran, NM, Hovens, CM, Velakoulis, D, O'Brien, TJ, Hare, DJ & Bush, AI 2019, 'Supranutritional Sodium Selenate Supplementation Delivers Selenium to the Central Nervous System: Results from a Randomized Controlled Pilot Trial in Alzheimer's Disease', Neurotherapeutics, vol. 16, no. 1, pp. 192-202.
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© 2018, The American Society for Experimental NeuroTherapeutics, Inc. Insufficient supply of selenium to antioxidant enzymes in the brain may contribute to Alzheimer’s disease (AD) pathophysiology; therefore, oral supplementation may potentially slow neurodegeneration. We examined selenium and selenoproteins in serum and cerebrospinal fluid (CSF) from a dual-dose 24-week randomized controlled trial of sodium selenate in AD patients, to assess tolerability, and efficacy of selenate in modulating selenium concentration in the central nervous system (CNS). A pilot study of 40 AD cases was randomized to placebo, nutritional (0.32 mg sodium selenate, 3 times daily), or supranutritional (10 mg, 3 times daily) groups. We measured total selenium, selenoproteins, and inorganic selenium levels, in serum and CSF, and compared against cognitive outcomes. Supranutritional selenium supplementation was well tolerated and yielded a significant (p < 0.001) but variable (95% CI = 13.4–24.8 μg/L) increase in CSF selenium, distributed across selenoproteins and inorganic species. Reclassifying subjects as either responsive or non-responsive based on elevation in CSF selenium concentrations revealed that responsive group did not deteriorate in Mini-Mental Status Examination (MMSE) as non-responsive group (p = 0.03). Pooled analysis of all samples revealed that CSF selenium could predict change in MMSE performance (Spearman’s rho = 0.403; p = 0.023). High-dose sodium selenate supplementation is well tolerated and can modulate CNS selenium concentration, although individual variation in selenium metabolism must be considered to optimize potential benefits in AD. The Vel002 study is listed on the Australian and New Zealand Clinical Trials Registry (http://www.anzctr.org.au/), ID: ACTRN12611001200976.

Carney, RL, Labbate, M, Siboni, N, Tagg, KA, Mitrovic, SM & Seymour, JR 2019, 'Urban beaches are environmental hotspots for antibiotic resistance following rainfall', Water Research, vol. 167, pp. 115081-115081.
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© 2019 Elsevier Ltd To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.

Carter, A, Richards, LJ, Apthorp, D, Azghadi, MR, Badcock, DR, Balleine, B, Bekkers, JM, Berk, M, Bourne, JA, Bradley, AP, Breakspear, M, Brichta, A, Carter, O, Castles, A, Chakli, K, Cohen-Woods, S, Conn, SJ, Cornish, J, Cornish, K, de Zubicaray, G, Egan, GF, Enticott, PG, Fitzgibbon, BM, Forlini, C, Fornito, A, Griffiths, L, Gullifer, J, Hall, W, Halliday, G, Hannan, AJ, Harrer, S, Harvey, A, Hatherly, C, Hickie, IB, Kennett, J, Kiernan, M, Kilpatrick, T, Kiral-Kornek, I, Korgaonkar, MS, Lawrence, AJ, Leventer, R, Levy, N, Licinio, J, Lovell, N, Mackellar, G, Malcolm, L, Mason, A, Mattingley, JB, Medland, SE, Michie, PT, Nithianantharajah, J, Parker, J, Payne, JM, Poole-Warren, L, Sah, P, Sarnyai, Z, Schofield, PR, Shimoni, O, Shum, DHK, Silk, T, Slee, M, Smith, AE, Soulis, T, Sriram, S, Stuart, GJ, Tapson, J, Thompson, MB, van Schaik, A, Vincent, NA, Vissel, B & Waters, A 2019, 'A Neuroethics Framework for the Australian Brain Initiative', Neuron, vol. 101, no. 3, pp. 365-369.
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© 2019 Elsevier Inc. Neuroethics is central to the Australian Brain Initiative's aim to sustain a thriving and responsible neurotechnology industry. Diverse and inclusive community and stakeholder engagement and a trans-disciplinary approach to neuroethics will be key to the success of the Australian Brain Initiative.

Casey, E, Ribaux, O & Roux, C 2019, 'The Kodak Syndrome: Risks and Opportunities Created by Decentralization of Forensic Capabilities', Journal of Forensic Sciences, vol. 64, no. 1, pp. 127-136.
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AbstractForensic science laboratories are being challenged by the expanding decentralization of forensic capabilities, particularly for digital traces. This study recommends laboratories undertake digital transformations to capitalize on the decentralization movement, develop a more comprehensive understanding of crime and security‐relevant problems, and play a more central role in problem‐solving collaboratively with law enforcement organizations and other stakeholders. A framework for the bilateral transfer of information and knowledge is proposed to magnify the impact of forensic science laboratories on abating crime, strengthening security, and reinforcing the criminal justice system. To accomplish digital transformations, laboratories require personnel with different expertise, including investigative reasoning, knowledge codification, data analytics, and forensic intelligence. Ultimately, this study encourages managers, educators, researchers, and policymakers to look beyond the usefulness of forensic results for solving individual investigations, and to realize the value of combined forensic knowledge and intelligence for developing broader strategies to deal with crime in digitalized society.

Castorina, A, Vogiatzis, M, Kang, JWM & Keay, KA 2019, 'PACAP and VIP expression in the periaqueductal grey of the rat following sciatic nerve constriction injury', Neuropeptides, vol. 74, pp. 60-69.
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© 2018 Nerve injuries often result in neuropathic pain with co-morbid changes in social behaviours, motivation, sleep-wake cycles and neuroendocrine function. In an animal model of neuropathic injury (CCI) similar co-morbid changes are evoked in a subpopulation (~30%) of injured rats. In addition to anatomical evidence of altered neuronal and glial function, the periaqueductal grey (PAG) of these rats shows evidence of cell death. These changes in the PAG may play a role in the disruption of the normal emotional coping responses triggered by nerve injury. Cell death can occur via a number of mechanisms, including the disruption of neuroprotective mechanisms. Pituitary adenylate cyclase activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are two endogenous neuropeptides whose activities are tightly regulated by two receptors subtypes, namely the PAC1 and VPAC receptors. These peptides and their receptors exert robust neuroprotective roles. In these studies, we hypothesized that rats expressing disabilities following CCI showed altered expression of PACAP and VIP in the PAG. Rats were categorized as having either Pain alone, Transient or Persistent disability, based on changes in social behaviours pre- and post-CCI. Social interaction behavioural tested (BT), sham-injured and naïve untested rats were also included. For measurements of mRNA and protein expression we utilised micro-dissected PAGs blocks taken from each group. At the mRNA level, VIP was downregulated and PAC1 was upregulated in BT animals, whilst VPAC1 mRNA was specifically increased in the Pain alone group. Interestingly, protein levels of both PACAP and VIP were remarkably increased in the Persistent Disability group. Taken together, sciatic nerve CCI that triggers neuropathic pain and persistent disability results in abnormally increased VIP and PACAP expression in the PAG. Our data also suggest that these effects are likely to be governed by post-transcriptional mechanisms.

Castrogiovanni, P, Di Rosa, M, Ravalli, S, Castorina, A, Guglielmino, C, Imbesi, R, Vecchio, M, Drago, F, Szychlinska, M & Musumeci, G 2019, 'Moderate Physical Activity as a Prevention Method for Knee Osteoarthritis and the Role of Synoviocytes as Biological Key', International Journal of Molecular Sciences, vol. 20, no. 3, pp. 511-511.
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The purpose of this study was to investigate the influence of moderate physical activity (MPA) on the expression of osteoarthritis (OA)-related (IL-1β, IL-6, TNF-α, MMP-13) and anti-inflammatory and chondroprotective (IL-4, IL-10, lubricin) biomarkers in the synovium of an OA-induced rat model. A total of 32 rats were divided into four groups: Control rats (Group 1); rats performing MPA (Group 2); anterior cruciate ligament transection (ACLT)-rats with OA (Group 3); and, ACLT-rats performing MPA (Group 4). Analyses were performed using Hematoxylin & Eosin (H&E) staining, histomorphometry and immunohistochemistry. In Group 3, OA biomarkers were significantly increased, whereas, IL-4, IL-10, and lubricin were significantly lower than in the other experimental groups. We hypothesize that MPA might partake in rescuing type B synoviocyte dysfunction at the early stages of OA, delaying the progression of the disease.

Chahwan, B, Kwan, S, Isik, A, van Hemert, S, Burke, C & Roberts, L 2019, 'Gut feelings: A randomised, triple-blind, placebo-controlled trial of probiotics for depressive symptoms', Journal of Affective Disorders, vol. 253, pp. 317-326.
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© 2019 Background: Depression is the leading cause of disability worldwide; with evidence suggesting that decreased gut barrier function and inflammation are correlated with depressive symptoms. We conducted a clinical trial to determine the effect of consumption of probiotic supplements (Winclove's Ecologic® Barrier) on depressive symptoms in a sample of participants with mild to severe depression. Method: 71 participants were randomly allocated to either probiotic or placebo, which was, consumed daily over eight weeks. Pre- and post-intervention measures of symptoms and vulnerability markers of depression as well as gut microbiota composition were compared. Clinical trial participants were also compared on psychological variables and gut microbiota composition to a non-depressed group (n = 20). Results: All clinical trial participants demonstrated improvement in symptoms, suggesting non-specific therapeutic effects associated with weekly monitoring visits. Participants in the probiotic group demonstrated a significantly greater reduction in cognitive reactivity compared with the placebo group, particularly in the mild/moderate subgroup. Probiotics did not significantly alter the microbiota of depressed individuals, however, a significant correlation was found between Ruminococcus gnavus and one depression metric. Limitations: There was a high attrition rate, which may be attributed to weekly monitoring visits. Additionally, modulation of the gut microbiota may need more specific testing to distinguish subtle changes. Conclusions: While microbiota composition was similar between all groups, probiotics did affect a psychological variable associated with susceptibility to depression. Further research is needed to investigate how probiotics can be utilised to modify mental wellbeing, and whether they can act as an adjunct to existing treatments.

Chan, DKY, Zhang, S, Liu, Y, Upton, C, Kurien, PE, Li, R, Hohenberg, MI & Hung, WT 2019, 'Effectiveness and analysis of factors predictive of discharge to home in a 4‐year cohort in a residential transitional care unit', AGING MEDICINE, vol. 2, no. 3, pp. 162-167.
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AbstractObjectiveThe aim of this study was to evaluate the effectiveness and identify factors predictive of home discharge in a cohort of patients admitted to the residential Transitional Aged Care Program (r‐TACP) after a stay in an acute hospital.MethodsA retrospective observational cohort study of patients admitted to a single r‐TACP unit between 1 January 2014 and 31 December 2017 was carried out. Baseline patient characteristics and discharge outcomes were analyzed.ResultsThree hundred sixty‐nine patients were admitted during the study period. The discharge outcomes were as follows: 68% returned home, 17% went onto residential care, 14% were readmitted to hospital, and 1% died. Factors associated with not returning home were increased age, increased comorbidities, and lower Barthel Index on admission to the r‐TACP.ConclusionOur r‐TACP is an effective program that successfully returns the majority (67.8%) of older patients home after an acute hospital admission. Older patients with greater comorbidities and poorer baseline functional status in our program were less likely to return home.

Chan, YL, Wang, B, Chen, H, Ho, KF, Cao, J, Hai, G, Jalaludin, B, Herbert, C, Thomas, PS, Saad, S & Oliver, BGG 2019, 'Pulmonary inflammation induced by low-dose particulate matter exposure in mice', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 317, no. 3, pp. L424-L430.
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Air pollution is a ubiquitous problem and comprises gaseous and particulate matter (PM). Epidemiological studies have clearly shown that exposure to PM is associated with impaired lung function and the development of lung diseases, such as chronic obstructive pulmonary disease and asthma. To understand the mechanisms involved, animal models are often used. However, the majority of such models represent high levels of exposure and are not representative of the exposure levels in less polluted countries, such as Australia. Therefore, in this study, we aimed to determine whether low dose PM10 exposure has any detrimental effect on the lungs. Mice were intranasally exposed to saline or traffic-related PM10 (1μg or 5μg/day) for 3 wk. Bronchoalveolar lavage (BAL) and lung tissue were analyzed. PM10 at 1 μg did not significantly affect inflammatory and mitochondrial markers. At 5 μg, PM10 exposure increased lymphocytes and macrophages in BAL fluid. Increased NACHT, LRR and PYD domains-containing protein 3 (NLRP3) and IL-1β production occurred following PM10 exposure. PM10 (5 μg) exposure reduced mitochondrial antioxidant manganese superoxide (antioxidant defense system) and mitochondrial fusion marker (OPA-1), while it increased fission marker (Drp-1). Autophagy marker light-chain 3 microtubule-associated protein (LC3)-II and phosphorylated-AMPK were reduced, and apoptosis marker (caspase 3) was increased. No significant change of remodeling markers was observed. In conclusion, a subchronic low-level exposure to PM can have an adverse effect on lung health, which should be taken into consideration for the planning of roads and residential buildings.

Chellappan, DK, Sze Ning, QL, Su Min, SK, Bin, SY, Chern, PJ, Shi, TP, Ee Mei, SW, Yee, TH, Qi, OJ, Thangavelu, L, Rajeshkumar, S, Negi, P, Chellian, J, Wadhwa, R, Gupta, G, Collet, T, Hansbro, PM & Dua, K 2019, 'Interactions between microbiome and lungs: Paving new paths for microbiome based bio-engineered drug delivery systems in chronic respiratory diseases', Chemico-Biological Interactions, vol. 310, pp. 108732-108732.
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© 2019 Elsevier B.V. Background: The human body is a home to thousands of microbiotas. It is defined as a community of symbiotic, commensal and pathogenic microorganisms that have existed in all exposed sites of the body, which have co-evolved with diet, lifestyle, genetic factors and immune factors. Human microbiotas have been studied for years on their effects with relation to health and diseases. Methods: Relevant published studies, literature and reports were searched from accessible electronic databases and related institutional databases. We used keywords, viz; microbiome, microbiota, microbiome drug delivery and respiratory disease. Selected articles were carefully read through, clustered, segregated into subtopics and reviewed. Findings: The traditional belief of sterile lungs was challenged by the emergence of culture-independent molecular techniques and the recently introduced invasive broncho-alveolar lavage (BAL) sampling method. The constitution of a lung microbiome mainly depends on three main ecological factors, which include; firstly, the immigration of microbes into airways, secondly, the removal of microbes from airways and lastly, the regional growth conditions. In healthy conditions, the microbial communities that co-exist in our lungs can build significant pulmonary immunity and could act as a barrier against diseases, whereas, in an adverse way, microbiomes may interact with other pathogenic bacteriomes and viromes, acting as a cofactor in inflammation and host immune responses, which may lead to the progression of a disease. Thus, the use of microbiota as a target, and as a drug delivery system in the possible modification of a disease state, has started to gain massive attention in recent years. Microbiota, owing to its unique characteristics, could serve as a potential drug delivery system, that could be bioengineered to suit the interest. The engineered microbiome-derived therapeutics can be delivered through BC, bacteriophage,...

Chellappan, DK, Yee, NJ, Kaur Ambar Jeet Singh, BJ, Panneerselvam, J, Madheswaran, T, Chellian, J, Satija, S, Mehta, M, Gulati, M, Gupta, G & Dua, K 2019, 'Formulation and characterization of glibenclamide and quercetin-loaded chitosan nanogels targeting skin permeation', Therapeutic Delivery, vol. 10, no. 5, pp. 281-293.
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Aim: Our aim was to develop and characterize a nanogel formulation containing both glibenclamide and quercetin and to explore the permeation profile of this combination. Methods: Drug-loaded nanogel was prepared by ionic gelation. In addition, optimum encapsulation efficiencies of glibenclamide and quercetin were also obtained. The average nanoparticle size at optimum conditions was determined by Zetasizer. Results: The particle size of the nanogel was found to be 370.4 ± 4.78 nm with a polydispersity index of 0.528 ± 0.04, while the λ potential was positive in a range of 17.6 to 24.8 mV. The percentage cumulative drug release also showed favorable findings. Conclusion: The chitosan nanogel could be a potential alternative for delivering glibenclamide and quercetin through skin.

Chen, C, liu, Z & Jin, D 2019, 'Bypassing the limit in volumetric imaging of mesoscale specimens', Advanced Photonics, vol. 1, no. 02, pp. 1-1.
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Chen, C, Pistono, A, Ryan, S, Szkuta, B & Meakin, GE 2019, 'The effect of climatic simulations on DNA persistence on glass, cotton and polyester', Forensic Science International: Genetics Supplement Series, vol. 7, no. 1, pp. 274-276.
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© 2019 Elsevier B.V. It is important to understand the variables impacting DNA persistence when considering the recovery, and evaluative interpretation, of DNA evidence from crime scenes. Whilst it is known that temperature, humidity and UV affect DNA persistence, little research has been conducted to explore these effects in a combined and controlled manner. This study includes two experiments in which a climate chamber was used to simulate climatic conditions over a repeating 24-h period. Aliquots of ∼50 ng DNA were added to each substrate and DNA recovered at 0, 1, 3 and 7 days after deposition. Samples were run in triplicate, extracted and quantified. The first experiment investigated the effect of typical Southern English winter and summer days on DNA persistence on glass and cotton, with DNA being recovered by wet and dry swabs from glass and mini-tapes from cotton. The second experiment investigated the effect of typical Northern Italian winter and summer days on DNA persistence on cotton and polyester, with DNA being recovered by wet and moist swabs from both fabrics. Quantities of DNA on all substrates significantly declined over 7 days under summer conditions (p < 0.05), and more DNA tended to persist on the fabric substrates in both studies under conditions of winter than summer. These results contribute to our understanding of DNA persistence under different climatic conditions and will help inform investigators’ DNA recovery strategies.

Chen, H & Lim, CED 2019, 'The efficacy of using acupuncture in managing polycystic ovarian syndrome', Current Opinion in Obstetrics & Gynecology, vol. 31, no. 6, pp. 428-432.
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Purpose of review Polycystic ovarian syndrome (PCOS) is a common reproductive disorder, which significantly impairs the fertility of 3–10% of women at reproductive age. It is getting very popular for women with PCOS to seek alternative therapies to treat PCOS, for example, acupuncture. This review examines the currently available evidence from the randomized controlled trial to guide future recommendation on using acupuncture to assist the treatment of PCOS. Recent findings PCOS is manifested by oligo-amenorrhoea, infertility, and hirsutism. The standard treatment of PCOS includes oral pharmacological agents, lifestyle changes, and surgical modalities. Pharmacologically based therapies are only effective in 60% of the patients, which are also associated with different side-effects. As such, acupuncture offered an alternative option. Acupuncture can affect β-endorphin production, which may, in turn, affect gonadotropin-releasing hormone secretion and affecting ovulation and menstrual cycle. Therefore, it is postulated that acupuncture may induce ovulation and restore menstrual cycle via increasing β-endorphin production. Summary Although modern medical science has discovered the action mechanisms underlying how acupuncture may manage the symptoms of PCOS, majority of the trials are small in sample size and lack of consistency in the choice of acupoints. Larger scale trials are needed to provide standardized protocols.

Chen, H, Li, Y, Chen, Y, Li, Y, McGowan, E & Lin, Y 2019, 'Serglycin level in peripheral circulating blood cells has prognostic significance in patients with hepatocellular carcinoma', Annals of Oncology, vol. 30, pp. iv8-iv9.
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Chen, H, Steele, J, Li, G, Chan, Y, Oliver, B, Saad, S & Machaalani, R 2019, 'E-vapour inhalation – How does it affect memory?', IBRO Reports, vol. 6, pp. S208-S209.
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Chen, T, Liu, AB, Sun, S, Ajami, NJ, Ross, MC, Wang, H, Zhang, L, Reuhl, K, Kobayashi, K, Onishi, JC, Zhao, L & Yang, CS 2019, 'Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐Abundance Groups Correlating with the Blood Glucose Lowering Effect', Molecular Nutrition & Food Research, vol. 63, no. 8, pp. e1801064-1801064.
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ScopeThe effects of green tea polyphenols, Polyphenon E (PPE), and black tea polyphenols, theaflavins (TFs), on gut microbiota and development of diabetes in db/db mice are investigated and compared.Methods and resultsSupplementation of PPE (0.1%) in the diet of female db/db mice for 7 weeks decreases fasting blood glucose levels and mesenteric fat while increasing the serum level of insulin, possibly through protection against β‐cell damage. However, TFs are less or not effective. Microbiome analysis through 16S rRNA gene sequencing shows that PPE and TFs treatments significantly alter the bacterial community structure in the cecum and colon, but not in the ileum. The key bacterial phylotypes responding to the treatments are then clustered into 11 co‐abundance groups (CAGs). CAGs 6 and 7, significantly increased by PPE but not by TFs, are negatively associated with blood glucose levels. The operational taxonomic units in these CAGs are from two different phyla, Firmicutes and Bacteroidetes. CAG 10, decreased by PPE and TFs, is positively associated with blood glucose levels.ConclusionGut microbiota respond to tea polyphenol treatments as CAGs instead of taxa. Some of the CAGs associated with the blood glucose lowering effect are enriched by PPE, but not TFs.

Chen, X-X, Lin, X-Y, Wu, X, Gale, PA, Anslyn, EV & Jiang, Y-B 2019, 'Design of Chiral Supramolecular Polymers Exhibiting a Negative Nonlinear Response', The Journal of Organic Chemistry, vol. 84, no. 22, pp. 14587-14592.
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Chen, Y, Ju, LA, Zhou, F, Liao, J, Xue, L, Su, QP, Jin, D, Yuan, Y, Lu, H, Jackson, SP & Zhu, C 2019, 'An integrin αIIbβ3 intermediate affinity state mediates biomechanical platelet aggregation', Nature Materials, vol. 18, no. 7, pp. 760-769.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Integrins are membrane receptors that mediate cell adhesion and mechanosensing. The structure–function relationship of integrins remains incompletely understood, despite the extensive studies carried out because of its importance to basic cell biology and translational medicine. Using a fluorescence dual biomembrane force probe, microfluidics and cone-and-plate rheometry, we applied precisely controlled mechanical stimulations to platelets and identified an intermediate state of integrin αIIbβ3 that is characterized by an ectodomain conformation, ligand affinity and bond lifetimes that are all intermediate between the well-known inactive and active states. This intermediate state is induced by ligand engagement of glycoprotein (GP) Ibα via a mechanosignalling pathway and potentiates the outside-in mechanosignalling of αIIbβ3 for further transition to the active state during integrin mechanical affinity maturation. Our work reveals distinct αIIbβ3 state transitions in response to biomechanical and biochemical stimuli, and identifies a role for the αIIbβ3 intermediate state in promoting biomechanical platelet aggregation.

Chen, Y, Toth, M & He, C 2019, 'Facile and fast fabrication of high structure-stable thin film nanocomposite membrane for potential application in solvent resistance nanofiltration', Applied Surface Science, vol. 496, pp. 143483-143483.
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© 2019 Elsevier B.V. We propose an interfacial design strategy to prepare novel, highly structure-stable thin film nanocomposite (TFN) nanofiltration (NF) membranes. It employs NMG-assisted dopamine modification on nanoparticles and a substrate, followed by interfacial polymerization. Our approach overcomes two problems that are typical of composite membranes – a weak interlayer interactive force, and poor compatibility between inorganic nanoparticles and a polymer matrix in nanocomposite membranes. The TFN membrane presented here has a high methanol permeance (2.18 L·m−2 ·h−1·bar−1) and a high rejection (99.1%) to acid red 18 (MW = 509 g·mol−1), which is superior to commercial solvent resistant NF (SRNF) membranes and most literature on SRNF membranes. More importantly, our TFN membranes exhibit a high degree of structural stability, demonstrated by immersion in three organic solvents for 15 days and a two day continuous filtration test. Our strategy is facile and highly flexible, has high potential for deployment in SRNF, and may stimulate the development of practical SRNF applications in the near future.

Chen, Y, Zhang, W, Zhou, D, Tian, H, Su, D, Wang, C, Stockdale, D, Kang, F, Li, B & Wang, G 2019, 'Co–Fe Mixed Metal Phosphide Nanocubes with Highly Interconnected-Pore Architecture as an Efficient Polysulfide Mediator for Lithium–Sulfur Batteries', ACS Nano, vol. 13, no. 4, pp. 4731-4741.
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Copyright © 2019 American Chemical Society. Lithium-sulfur (Li-S) batteries have been regarded as one of the most promising candidates for next-generation energy storage owing to their high energy density and low cost. However, the practical deployment of Li-S batteries has been largely impeded by the low conductivity of sulfur, the shuttle effect of polysulfides, and the low areal sulfur loading. Herein, we report the synthesis of uniform Co-Fe mixed metal phosphide (Co-Fe-P) nanocubes with highly interconnected-pore architecture to overcome the main bottlenecks of Li-S batteries. With the highly interconnected-pore architecture, inherently metallic conductivity, and polar characteristic, the Co-Fe-P nanocubes not only offer sufficient electrical contact to the insulating sulfur for high sulfur utilization and fast redox reaction kinetics but also provide abundant adsorption sites for trapping and catalyzing the conversion of lithium polysulfides to suppress the shuttle effect, which is verified by both the comprehensive experiments and density functional theory calculations. As a result, the sulfur-loaded Co-Fe-P (S@Co-Fe-P) nanocubes delivered a high discharge capacity of 1243 mAh g -1 at 0.1 C and excellent cycling stability for 500 cycles with an average capacity decay rate of only 0.043% per cycle at 1 C. Furthermore, the S@Co-Fe-P electrode showed a high areal capacity of 4.6 mAh cm -2 with superior stability when the sulfur loading was increased to 5.5 mg cm -2 . More impressively, the prototype soft-package Li-S batteries based on S@Co-Fe-P cathodes also exhibited superior cycling stability with great flexibility, demonstrating their great potential for practical applications.

Cheng, B, Nikitopoulos, CS & Schlögl, E 2019, 'Interest rate risk in long‐dated commodity options positions: To hedge or not to hedge?', Journal of Futures Markets, vol. 39, no. 1, pp. 109-127.
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AbstractWe empirically assess hedging interest rate risk beyond the conventional delta, gamma, and vega hedges in long‐dated crude oil options positions. Using factor hedging in a model featuring stochastic interest rates and stochastic volatility, interest rate hedges consistently provide an improvement beyond delta, gamma, and vega hedges. Under high interest rate volatility and/or when a rolling hedge is used, combining interest rate and delta hedging improves performance by up to four percentage points over the common hedges of gamma and/or vega. Thus, contrary to common practice, hedging interest rate risk should have priority over these “second‐order” hedges.

Cheng, H, Yang, S, Cai, S, Ma, X, Qin, H, Zhang, W, Fu, L, Zeng, Q, Wen, M, Peng, X & Wang, H 2019, 'Clinical and Prognostic Characteristics of 53 Cases of Extracranial Malignant Rhabdoid Tumor in Children. A Single-Institute Experience from 2007 to 2017', The Oncologist, vol. 24, no. 7, pp. e551-e558.
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Abstract Background The aim of this study is to add to the current knowledge regarding extracranial malignant rhabdoid tumor (MRT), a rare and highly aggressive tumor that occurs most commonly in infants and young children. Patients and Methods A retrospective medical record review was conducted on 53 patients with pathologically confirmed MRT in Beijing Children's Hospital between January 2007 and October 2017. Results Fifty-three patients were diagnosed with MRT at a median age of 16 months, including 32 cases of malignant rhabdoid tumor of the kidney (MRTK) and 21 cases of extrarenal extracranial rhabdoid tumor (EERT). Fourteen (14/32, 43.75%) patients with MRTK and five (5/21, 23.81%) patients with EERT had metastases at diagnosis, and quite a few number of cases occurred tumor rupture (26.42%). Among the 53 patients, 40 (75.47%) patients died, 10 (18.87%) patients survived, and 3 patients (5.66%) were lost to follow-up. Among the 40 dead patients, 38 patients died from rapid progression of the disease or tumor recurrence, and 2 patients died of severe postoperative complications. Most of the recurrent or relapsed cases (94.11%) occurred within 8 months, with a median time of 76 days after diagnosis. The overall survival rates of 3 years and 5 years for the entire cohort were 23.71% and 18.44%, respectively. After survival analysis, it was clear that a younger age at diagnosis and distant stage patients had relatively poor outcomes. The effect of treatment was the most difficult to analyze because patients were not treated uniformly. Statistically significant differences in ...

Cherk Yong, DO, Saker, SR, Wadhwa, R, Chellappan, DK, Madheswaran, T, Panneerselvam, J, Tambuwala, MM, Bakshi, HA, Kumar, P, Pillay, V, Gupta, G, Oliver, BG, Wark, P, Hsu, A, Hansbro, PM, Dua, K & Zeeshan, F 2019, 'Preparation, characterization and in-vitro efficacy of quercetin loaded liquid crystalline nanoparticles for the treatment of asthma', Journal of Drug Delivery Science and Technology, vol. 54, pp. 101297-101297.
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© 2019 Elsevier B.V. The present study aims to formulate quercetin loaded liquid crystalline nanoparticles (LCN) and surface modified liquid crystalline nanoparticles (sm-LCN) as well as investigate their anti-inflammatory activity in human primary bronchial epithelial cell line (BCi-NS1.1) induced with lipopolysaccharide (LPS). Quercetin LCN were prepared using ultrasonication method. The formulated LCNs and sm-LCNs were characterised in terms of particle size, zeta potential as well as the drug encapsulation efficiency. Furthermore, their morphology and in vitro release profile were also studied. In addition, the anti-inflammatory activity of quercetin LCN and sm-LCNs were evaluated by measuring the concentration of pro-inflammatory markers namely interleukin (IL)-1β, IL-6 and IL-8 in BCI-NS1.1 cell lines via cytometric bead array. The molecular mechanism inherent to the inclusion of quercetin into monoolein nanosystem and surface modification of the nanosystem with chitosan was elucidated via molecular mechanics simulations. Quercetin LCN and sm-LCN significantly (p < 0.05) decreased the production of IL-1β, IL-6 and IL-8 compared to LPS only group. Encapsulation of quercetin into LCN and sm-LCN further enhanced its anti-inflammatory activity compared to quercetin in dimethyl sulfoxide (DMSO). In addition to that, quercetin LCN and sm-LCN also exhibited comparable activity to fluticasone in terms of significantly (p < 0.05) reducing the production of IL-1β and IL-6. Quercetin loaded LCN and sm-LCN could be a potential therapeutic intervention for asthma as they are efficacious in suppressing the production of key pro-inflammatory cytokines associated with the development of asthma.

Cheung, EYY, Phillips, C, Eduardoff, M, Lareu, MV & McNevin, D 2019, 'Performance of ancestry-informative SNP and microhaplotype markers', Forensic Science International: Genetics, vol. 43, pp. 102141-102141.
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The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.

Chikoidze, E, Rogers, DJ, Teherani, FH, Rubio, C, Sauthier, G, Von Bardeleben, HJ, Tchelidze, T, Ton-That, C, Fellous, A, Bove, P, Sandana, EV, Dumont, Y & Perez-Tomas, A 2019, 'Puzzling robust 2D metallic conductivity in undoped β-Ga2O3 thin films', Materials Today Physics, vol. 8, pp. 10-17.
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© 2018 Elsevier Ltd Here, we report the analogy of an extremely stable topological-like ultra-wide bandgap insulator, a solid that is a pure insulator in its bulk but has a metallic conductive surface, presenting a two-dimensional conductive channel at its surface that challenges our current thinking about semiconductor conductivity engineering. Nominally undoped epitaxial β-Ga 2 O 3 thin films without any detectable defect (after a range of state-of-the-art techniques) showed the unexpectedly low resistivity of 3 × 10 −2 Ωcm which was found to be also resistant to high dose proton irradiation (2 MeV, 5 × 10 15 cm −2 dose) and was largely invariant (metallic) over the phenomenal temperature range of 2 K up to 850 K. The unique resilience and stability of the electrical properties under thermal and highly ionizing radiation stressing, combined with the extended transparency range (thanks to the ultra-wide bandgap) and the already known toughness under high electrical field could open up new perspectives for use as expanded spectral range transparent electrodes (e.g., for UV harvesting solar cells or UV LEDs/lasers) and robust Ohmic contacts for use in extreme environments/applications and for novel optoelectronic and power device concepts.

Chmelík, D, Hrouzek, P, Fedorko, J, Vu, DL, Urajová, P, Mareš, J & Červený, J 2019, 'Accumulation of cyanobacterial oxadiazine nocuolin A is enhanced by temperature shift during cultivation and is promoted by bacterial co-habitants in the culture', Algal Research, vol. 44, pp. 101673-101673.
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© 2019 Elsevier B.V. Proper setting of cultivation conditions is essential for production of high-value compounds in microbial biotechnology. The present study characterizes photoautotrophic growth and capacity to accumulate the antiproliferative secondary metabolite Nocuolin A (NoA) in cyanobacterium Nostoc sp. CCAP 1453/38. As the cyanobacterial culture was found to be non-axenic, the bacteria accompanying the culture were characterized, then the growth demands and NoA production in the Nostoc-bacterial consortium were determined, and finally an axenic strain was prepared. For the purposes of growth characterization, the culture was maintained in a quasi-continuous regime under various light intensities, temperatures, and inorganic carbon concentrations in a small-scale laboratory photobioreactor. The maximum biomass growth rate obtained was 0.10 h−1 (doubling time Dt = 6.93 h). Following optimal growth conditions were identified: temperature of 35 °C, light intensity 600 μmol(photons) m−2 s−1, and 2500 ppm CO2 in the sparging gas. As the temperature optima for the biomass production and for NoA accumulation differed, biphasic cultivation for maximal NoA yield was designed, leading to a three times more effective cultivation procedure compared to batch culture maintained at a temperature optimal for NoA production. The increased NoA accumulation at reduced temperature that correlated with enhanced expression of NoA biosynthetic genes after the temperature shift suggested its regulation occurs at the expression level. It has further been shown that NoA production is reduced in axenic culture, which indicates that it is also triggered by presence of bacteria. This study shows an example of how a biphasic cultivation mode with different temperatures can be used in high-value compound production processes. It also brings direct evidence that cyanobacterial strain axenization can lead to a rapid decrease in production of valuable compounds and that non-axenic strain...

Choi, S, Seo, DH, Kaiser, MR, Zhang, C, van der laan, T, Han, ZJ, Bendavid, A, Guo, X, Yick, S, Murdock, AT, Su, D, Lee, BR, Du, A, Dou, SX & Wang, G 2019, 'WO₃ nanolayer coated 3D-graphene/sulfur composites for high performance lithium/sulfur batteries', Journal of Materials Chemistry A, vol. 7, no. 9, pp. 4596-4603.
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WO₃/graphene composite minimizes the polysulfide dissolution problem in the lithium–sulfur (Li–S) battery systems while exhibiting an excellent battery performance.

Christensen, S, Halili, MA, Strange, N, Petit, GA, Huston, WM, Martin, JL & McMahon, RM 2019, 'Oxidoreductase disulfide bond proteins DsbA and DsbB form an active redox pair in Chlamydia trachomatis, a bacterium with disulfide dependent infection and development', PLOS ONE, vol. 14, no. 9, pp. e0222595-e0222595.
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© 2019 Christensen 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 is an obligate intracellular bacterium with a distinctive biphasic developmental cycle that alternates between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body (RB). Members of the genus Chlamydia are dependent on the formation and degradation of protein disulfide bonds. Moreover, disulfide cross-linking of EB envelope proteins is critical for the infection phase of the developmental cycle. We have identified in C. trachomatis a homologue of the Disulfide Bond forming membrane protein Escherichia coli (E. coli) DsbB (hereafter named CtDsbB) and—using recombinant purified proteins—demonstrated that it is the redox partner of the previously characterised periplasmic oxidase C. trachomatis Disulfide Bond protein A (CtDsbA). CtDsbA protein was detected in C. trachomatis inclusion vacuoles at 20 h post infection, with more detected at 32 and similar levels at 44 h post infection as the developmental cycle proceeds. As a redox pair, CtDsbA and CtDsbB largely resemble their homologous counterparts in E. coli; CtDsbA is directly oxidised by CtDsbB, in a reaction in which both periplasmic cysteine pairs of CtDsbB are required for complete activity. In our hands, this reaction is slow relative to that observed for E. coli equivalents, although this may reflect a non-native expression system and use of a surrogate quinone cofactor. CtDsbA has a second non-catalytic disulfide bond, which has a small stabilising effect on the protein’s thermal stability, but which does not appear to influence the interaction of CtDsbA with its partner protein CtDsbB. Expression of CtDsbA during the RB replicative phase and during...

Christensen, S, McMahon, RM, Martin, JL & Huston, WM 2019, 'Life inside and out: making and breaking protein disulfide bonds inChlamydia', Critical Reviews in Microbiology, vol. 45, no. 1, pp. 33-50.
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© 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Disulphide bonds are widely used among all domains of life to provide structural stability to proteins and to regulate enzyme activity. Chlamydia spp. are obligate intracellular bacteria that are especially dependent on the formation and degradation of protein disulphide bonds. Members of the genus Chlamydia have a unique biphasic developmental cycle alternating between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body. The proteins in the envelope of the EB are heavily cross-linked with disulphides and this is known to be critical for this infectious phase. In this review, we provide a comprehensive summary of what is known about the redox state of chlamydial envelope proteins throughout the developmental cycle. We focus especially on the factors responsible for degradation and formation of disulphide bonds in Chlamydia and how this system compares with redox regulation in other organisms. Focussing on the unique biology of Chlamydia enables us to provide important insights into how specialized suites of disulphide bond (Dsb) proteins cater for specific bacterial environments and lifecycles.

Chughtai, AA, Stelzer-Braid, S, Rawlinson, W, Pontivivo, G, Wang, Q, Pan, Y, Zhang, D, Zhang, Y, Li, L & MacIntyre, CR 2019, 'Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers', BMC Infectious Diseases, vol. 19, no. 1.
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BACKGROUND:Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Airborne respiratory pathogens may settle on the surface of used masks layers, resulting in contamination. The main aim of this study was to study the presence of viruses on the surface of medical masks. METHODS:Two pilot studies in laboratory and clinical settings were carried out to determine the areas of masks likely to contain maximum viral particles. A laboratory study using a mannequin and fluorescent spray showed maximum particles concentrated on upper right, middle and left sections of the medical masks. These findings were confirmed through a small clinical study. The main study was then conducted in high-risk wards of three selected hospitals in Beijing China. Participants (n = 148) were asked to wear medical masks for a shift (6-8 h) or as long as they could tolerate. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. RESULTS:Overall virus positivity rate was 10.1% (15/148). Commonly isolated viruses from masks samples were adenovirus (n = 7), bocavirus (n = 2), respiratory syncytial virus (n = 2) and influenza virus (n = 2). Virus positivity was significantly higher in masks samples worn for > 6 h (14.1%, 14/99 versus 1.2%, 1/49, OR 7.9, 95% CI 1.01-61.99) and in samples used by participants who examined > 25 patients per day (16.9%, 12/71 versus 3.9%, 3/77, OR 5.02, 95% CI 1.35-18.60). Most of the participants (83.8%, 124/148) reported at least one problem associated with mask use. Commonly reported problems were pressure on face (16.9%, 25/148), breathing difficulty (12.2%, 18/148), discomfort (9.5% 14/148), trouble communicating with the patient (7.4%, 11/148) and headache (6.1%, 9/148). CONCLUSION:Respiratory pathogens on the outer surface of the used medical masks may result in self-contamination. The risk is...

Chumnumwat, S, Lu, ZH, Sukasem, C, Winther, MD, Capule, FR, Abdul Hamid, AAAT, Bhandari, B, Chaikledkaew, U, Chanhom, N, Chantarangsu, S, Charoenyingwattana, A, Hang, TT, Hlaing, TM, Htun, KS, Jittikoon, J, Le, L, Mahasirimongkol, S, Mohamed Noor, DA, Shrestha, J, Suwannoi, L, Tragulpiankit, P, Turongkaravee, S, Wattanapokayakit, S, Xangsayarath, P, Yuliwulandari, R, Zain, SM & Chantratita, W 2019, 'Southeast Asian Pharmacogenomics Research Network (SEAPharm): Current Status and Perspectives', Public Health Genomics, vol. 22, no. 3-4, pp. 132-139.
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Pharmacogenomics (PGx) is increasingly being recognized as a potential tool for improving the efficacy and safety of drug therapy. Therefore, several efforts have been undertaken globally to facilitate the implementation process of PGx into routine clinical practice. Part of these efforts include the formation of PGx working groups working on PGx research, synthesis, and dissemination of PGx data and creation of PGx implementation strategies. In Asia, the Southeast Asian Pharmacogenomics Research Network (SEAPharm) is established to enable and strengthen PGx research among the various PGx communities within but not limited to countries in SEA; with the ultimate goal to support PGx implementation in the region. From the perspective of SEAPharm member countries, there are several key elements essential for PGx implementation at the national level. They include pharmacovigilance database, PGx research, health economics research, dedicated laboratory to support PGx testing for both research and clinical use, structured PGx education, and supportive national health policy. The status of these essential elements is presented here to provide a broad picture of the readiness for PGx implementation among the SEAPharm member countries, and to strengthen the PGx research network and practice in this region.

Chung, H-P, Lee, C-H, Huang, K-H, Yang, S-L, Wang, K, Solntsev, AS, Sukhorukov, AA, Setzpfandt, F & Chen, Y-H 2019, 'Broadband on-chip polarization mode splitters in lithium niobate integrated adiabatic couplers', Optics Express, vol. 27, no. 2, pp. 1632-1632.
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© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement. We report, to the best of our knowledge, the first broadband polarization mode splitter (PMS) based on the adiabatic light passage mechanism in the lithium niobate (LiNbO3) waveguide platform. A broad bandwidth of ~140 nm spanning telecom S, C, and L bands at polarization-extinction ratios (PER) of >20 dB and >18 dB for the TE and TM polarization modes, respectively, is found in a five-waveguide adiabatic coupler scheme whose structure is optimized by an adiabaticity engineering process in titanium-diffused LiNbO3 waveguides. When the five-waveguide PMS is integrated with a three-waveguide “shortcut to adiabaticity” structure, we realize a broadband, high splitting-ratio (ηc) mode splitter for spatial separation of TE- (H-) polarized pump (700-850 nm for ηc>99%), TM- (V-) polarized signal (1510-1630 nm for ηc>97%), and TE- (H-) polarized idler (1480-1650 nm for ηc>97%) modes. Such a unique integrated-optical device is of potential for facilitating the on-chip implementation of a pump-filtered, broadband tunable entangled quantum-state generator.

Clases, D, Fingerhut, S, Jeibmann, A, Sperling, M, Doble, P & Karst, U 2019, 'LA-ICP-MS/MS improves limits of detection in elemental bioimaging of gadolinium deposition originating from MRI contrast agents in skin and brain tissues', Journal of Trace Elements in Medicine and Biology, vol. 51, pp. 212-218.
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© 2018 Elsevier GmbH A novel analytical method to detect the retention of gadolinium from contrast agents for magnetic resonance imaging (MRI) in tissue samples of patients is presented. It is based on laser ablation - inductively coupled plasma - triple quadrupole - mass spectrometry (LA-ICP-MS/MS). Both Gd and P were monitored with a mass shift of +16, corresponding to mono-oxygenated species, as well as Zn, Ca, and Fe on-mass. This method resulted in a significantly reduced background and improved limits of detection not only for phosphorus, but also for gadolinium. These improvements were essential to perform elemental bioimaging with improved resolution of 5 μm x 5 μm, allowing the detection of small Gd deposits in fibrotic skin and brain tumour tissue with diameters of approximately 50 μm. Detailed analyses of these regions revealed that most Gd was accompanied with P and Ca, indicating co-precipitation.

Clases, D, Gonzalez de Vega, R, Adlard, PA & Doble, PA 2019, 'On-line reverse isotope dilution analysis for spatial quantification of elemental labels used in immunohistochemical assisted imaging mass spectrometry via LA-ICP-MS', Journal of Analytical Atomic Spectrometry, vol. 34, no. 2, pp. 407-412.
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We present a novel on-line isotope dilution analysis (IDA) approach for the quantification of isotopically enriched metal labels used in immunohistochemical assisted imaging mass spectrometry.

Clases, D, Gonzalez de Vega, R, Bishop, D & Doble, P 2019, 'SEC-ICP-MS and on-line isotope dilution analysis for characterisation and quantification of immunochemical assays', Analytical and Bioanalytical Chemistry, vol. 411, no. 16, pp. 3553-3560.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. This study presents a novel size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) method for the characterisation and quantification of immunoassays with lanthanide-labelled antibodies. SEC-ICP-MS in combination with a double isotope dilution approach enabled facile validation of the antibodies’ integrity, the determination of the batch to batch labelling efficiency, monitoring of each labelling step, and quantification of the immunocomplexes after incubation with the target protein. The addition of oxygen into the dynamic reaction cell improved the detection of sulphur as a marker for the antibodies and target protein via mass-shifting (LOD = 3.7 ng/mL), whilst maintaining sufficient sensitivity for the analysis of the lanthanides. Ultra-high performance liquid chromatography (UHPLC) SEC ensured a rapid chromatographic method with separation times under 7 min of the labelled and unlabelled antibodies, the immunocomplexes, and the unconjugated polymer used to lanthanide-label the antibodies. SEC calibration estimated the molecular weights of all peaks and provided valuable insights in immunochemical reactions and the stoichiometry of the reactants and products. A novel on-line isotope dilution analysis (IDA) enabled absolute quantification of sulphur and lanthanide signals and the protein of interest. The chromatographic separation of immunocomplexes and labelled antibodies allowed the simultaneous determination of the antibody/metal stoichiometry and target protein concentration from a single mass flow chromatogram. An immunoglobulin protein was quantified after incubation with an 153Eu-labelled primary polyclonal antibody. The procedure was validated with direct labelling of the target protein with 156Gd for parallel, simultaneous quantification. The concentration determined via direct labelling of the protein deviated 1.9% from the immunochemical approach...

Cleverly, J, Eamus, D, Edwards, W, Grant, M, Grundy, MJ, Held, A, Karan, M, Lowe, AJ, Prober, SM, Sparrow, B & Morris, B 2019, 'TERN, Australia’s land observatory: addressing the global challenge of forecasting ecosystem responses to climate variability and change', Environmental Research Letters, vol. 14, no. 9, pp. 095004-095004.
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The global challenge of understanding and forecasting ecosystem responses to climate extremes and climate change is addressed in this review of research enabled through environmental research infrastructure (RI) provided by Australia's Terrestrial Ecosystem Research Network (TERN). Two primary climatic drivers of ecosystem structure and function in Australia are fire and aridity, to which Australian flora and fauna has shown marked adaptability. Australian vegetation shows resilience to climate extremes of flooding rains, droughts and heatwaves such that variability in primary productivity of Australian vegetation has a tangible effect on the global carbon cycle. Nonetheless, Australian flora and ecosystems could be vulnerable to projected climate change (e.g., to increasing vapour pressure deficit). Refugia are also vulnerable to climate change, with conditions in these areas already near the tipping point for a change in community composition. Ensuring genetic diversity during directional change in climate (e.g., increasing aridity) requires proactive approaches to conservation and restoration projects. To address these challenges, TERN provides environmental research infrastructure (RI) at three scales of observation: i) environmental monitoring using remote sensing techniques at a landscape and continental scale; ii) a spatially extensive network of ecosystem monitoring plots; and iii) intensely measured sites collecting detailed data on ecosystem processes. Through partnerships with international environmental RIs, TERN enables research that addresses global challenges, on the first steps toward the forecasting of ecosystem–climate interactions.

Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2019, 'WITHDRAWN: Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, pp. 103650-103650.
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Coil, DA, Jospin, G, Darling, AE, Wallis, C, Davis, IJ, Harris, S, Eisen, JA, Holcombe, LJ & O’Flynn, C 2019, 'Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment', PLOS ONE, vol. 14, no. 6, pp. e0214354-e0214354.
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Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach required fewer subjective decisions, and required far less labor. The primary differences in the non-identical taxonomic assignments involved cases where GTDB has proposed taxonomic revisions.

Coleman, MA, Clark, JS, Doblin, MA, Bishop, MJ & Kelaher, BP 2019, 'Genetic differentiation between estuarine and open coast ecotypes of a dominant ecosystem engineer', Marine and Freshwater Research, vol. 70, no. 7, pp. 977-977.
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Temperate intertidal shores globally are often dominated by habitat-forming seaweeds, but our knowledge of these systems is heavily biased towards northern hemisphere species. Rocky intertidal shores throughout Australia and New Zealand are dominated by a single monotypic species, Hormosira banksii. This species plays a key role in facilitating biodiversity on both rocky shores and estuarine habitats, yet we know little about the processes that structure populations. Herein we characterise the genetic diversity and structure of Hormosira and demonstrate strong restrictions to gene flow over small spatial scales, as well as between estuarine and open coast populations. Estuarine ecotypes were often genetically unique from nearby open coast populations, possibly due to extant reduced gene flow between habitats, founder effects and coastal geomorphology. Deviations from random mating in many locations suggest complex demographic processes are at play within shores, including clonality in estuarine populations. Strong isolation by distance in Hormosira suggests that spatial management of intertidal habitats will necessitate a network of broad-scale protection. Understanding patterns of genetic diversity and gene flow in this important ecosystem engineer will enhance the ability to manage, conserve and restore this key species into the future.

Collison, AM, Li, J, de Siqueira, AP, Lv, X, Toop, HD, Morris, JC, Starkey, MR, Hansbro, PM, Zhang, J & Mattes, J 2019, 'TRAIL signals through the ubiquitin ligase MID1 to promote pulmonary fibrosis', BMC Pulmonary Medicine, vol. 19, no. 1.
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© 2019 The Author(s). Background: Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) has previously been demonstrated to play a pro-inflammatory role in allergic airways disease and COPD through the upregulation of the E3 ubiquitin ligase MID1 and the subsequent deactivation of protein phosphatase 2A (PP2A). Methods: Biopsies were taken from eight IPF patients presenting to the Second Affiliated Hospital of Jilin University, China between January 2013 and February 2014 with control samples obtained from resected lung cancers. Serum TRAIL, MID1 protein and PP2A activity in biopsies, and patients' lung function were measured. Wild type and TRAIL deficient Tnfsf10 -/- BALB/c mice were administered bleomycin to induce fibrosis and some groups were treated with the FTY720 analogue AAL(s) to activate PP2A. Mouse fibroblasts were treated with recombinant TRAIL and fibrotic responses were assessed. Results: TRAIL in serum and MID1 protein levels in biopsies from IPF patients were increased compared to controls. MID1 levels were inversely associated while PP2A activity levels correlated with DLco. Tnfsf10 -/- and mice treated with the PP2A activator AAL(s) were largely protected against bleomycin-induced reductions in lung function and fibrotic changes. Addition of recombinant TRAIL to mouse fibroblasts in-vitro increased collagen production which was reversed by PP2A activation with AAL(s). Conclusion: TRAIL signalling through MID1 deactivates PP2A and promotes fibrosis with corresponding lung function decline. This may provide novel therapeutic targets for IPF.

Commault, AS, Fabris, M, Kuzhiumparambil, U, Adriaans, J, Pernice, M & Ralph, PJ 2019, 'Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii', Algal Research, vol. 39, pp. 101462-101462.
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© 2019 Elsevier B.V. Terpenoids are a large and diverse class of naturally occurring metabolites serving many industrial applications and natural roles. Economically important terpenoids are often produced in low abundance from their natural sources, making their industrial-scale production challenging or uneconomical, therefore engineered microorganisms are frequently used as heterologous production platforms. Photosynthetic microorganisms, such as the green alga Chlamydomonas reinhardtii, represent promising systems to produce terpenoids in a cost-effective and sustainable manner, but knowledge about the regulation of their terpenoid metabolism remains limited. Here we report on the investigation of the phytohormone methyl jasmonate (MeJA) as elicitor of algal terpenoid synthesis. We treated C. reinhardtii cells in mid-exponential growth phase with three different concentrations of MeJA (0.05, 0.5 and 1 mM). The highest concentration of MeJA affected the photosynthetic activity of the cells, arrested the growth and up-regulated key genes of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, leading to a significant increase in intermediates of this pathway, squalene and (S)-2,3-epoxysqualene, while the abundance of cycloartenol, and two main sterols (ergosterol and 7-dehydroporiferasterol) decreased. These data suggest the redirection of the carbon flux towards the synthesis of yet uncharacterised triterpenoid secondary metabolites upon MeJA treatment. Our results offer important new insights into the regulation of the triterpenoid metabolism in C. reinhardtii and raise important questions on hormonal signalling in microalgae. Phytohormone treatment is tested for the first time in algae, where it holds great potential for identifying key transcriptional regulators of the MEP pathway as targets for future metabolic engineering studies for improve production of high-value triterpenoids.

Cooke, I, Mead, O, Whalen, C, Boote, C, Moya, A, Ying, H, Robbins, S, Strugnell, JM, Darling, A, Miller, D, Voolstra, CR & Adamska, M 2019, 'Molecular techniques and their limitations shape our view of the holobiont', Zoology, vol. 137, pp. 125695-125695.
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It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.

Corbit, L, Kendig, M & Moul, C 2019, 'The role of serotonin 1B in the representation of outcomes', Scientific Reports, vol. 9, no. 1.
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AbstractDisrupted serotonin neurotransmission has been implicated in the etiology of psychopathic traits. Empirical research has found that people with high levels of psychopathic traits have a deficit in reinforcement learning that is thought to be linked with amygdala dysfunction. Altered serotonin neurotransmission provides a plausible explanation for amygdala dysfunction in psychopathic traits and recent research suggests that this may be associated with serotonin 1B (5-HT1B) receptor function. This research used an animal model to test the hypothesis that 5-HT1B receptors are involved in the encoding of the specific features of reinforcing outcomes. An outcome devaluation task was used to test the effect of the systemic administration of a selective 5-HT1B receptor agonist administered before encoding of “action-outcome” associations. Results showed that while administration of a 5-HT1B receptor agonist allowed rats to acquire instrumental responding for food, when the content of that learning was further probed using an outcome devaluation task, performance differed from controls. 5-HT1B agonism impaired learning about the specific sensory qualities of food rewards associated with distinct instrumental responses, required to direct choice performance when the value of one outcome changed. These findings suggest a role for 5-HT1B receptor function in the encoding of the specific features of reinforcing outcomes.

Cranfield, CG 2019, 'ABA/ASB Membrane Biophysics session II 2018', Biophysical Reviews, vol. 11, no. 3, pp. 281-282.
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Crispino, F, Roux, C, Delémont, O & Ribaux, O 2019, 'Is the (traditional) Galilean science paradigm well suited to forensic science?', WIREs Forensic Science, vol. 1, no. 6.
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AbstractFor more than 10 years, forensic science has been at best, criticized for its lack of scientific foundations and at worst, presented as an oxymoron. An exclusive focus on standard operating procedures and quality management could cause forensic science to fall short of addressing the epistemological issue initiated by judges. This is particularly so in rapidly changing times, including digital transformation of society and decentralization of forensic services. As a consequence, the present understanding of forensic science by both scientists and its stakeholders is questioned. It is argued that that forensic science fundamental principles and, more broadly, forensic science philosophy are pivotal to the reliable application of science to address security and justice questions.This article is categorized under:Forensic Science in Action/Crime Scene Investigation > Epistemology and MethodJurisprudence and Regulatory Oversight > Communication across Science and LawJurisprudence and Regulatory Oversight > Expert Evidence and Narrative

Cummins, ML, Reid, CJ, Roy Chowdhury, P, Bushell, RN, Esbert, N, Tivendale, KA, Noormohammadi, AH, Islam, S, Marenda, MS, Browning, GF, Markham, PF & Djordjevic, SP 2019, 'Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene', Microbial Genomics, vol. 5, no. 2.
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Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the...

Cummins, ML, Roy Chowdhury, P, Marenda, MS, Browning, GF & Djordjevic, SP 2019, 'Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate', mSphere, vol. 4, no. 3.
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SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii , and other members of the Enterobacteriaceae . SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE . For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

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 2019, 'Author Correction: DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton', Nature Microbiology, vol. 4, no. 3, pp. 540-542.
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In the version of this Letter originally published, the Methods incorrectly stated that all phytoplankton cultures were sampled in mid-exponential phase. The low-nitrogen cultures were sampled in early stationary phase and at the point at which Fv/Fm values decreased, to indicate that cultures were experiencing low-nitrogen conditions. All other phytoplankton cultures were sampled in exponential phase. Growth and Fv/Fm data are provided here on high- and low-nitrogen cultures (Figs 1, 2 and 3) to clarify and support this correction. The Methods also stated that cell counting was done using a Beckman Multisizer 3 Coulter Counter, but a CASY Model TT Cell Counter was used.

Curtis, EM, Knight, CA & Leigh, A 2019, 'Intracanopy adjustment of leaf-level thermal tolerance is associated with microclimatic variation across the canopy of a desert tree (Acacia papyrocarpa)', Oecologia, vol. 189, no. 1, pp. 37-46.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Tree crowns are spatially heterogeneous, sometimes resulting in significant variation in microclimate across the canopy, particularly with respect to temperature. Yet it is not known whether such localised temperature variation equates to intracanopy variation in leaf-level physiological thermal tolerance. Here, we studied whether microclimate variation across the canopy of a dominant desert tree equated to localised variation in leaf thermal thresholds (T 50 ) among four canopy positions: upper south, upper north, lower south, lower north. Principal component analysis was used to generate a composite climatic stress variable (C STRESS ) from canopy temperature, vapour pressure deficit, and relative humidity. We also determined the average number of days that maximum temperatures exceeded the air temperature equating to this species’ critical threshold of 49 °C (AT 49 ). To estimate how closely leaf temperatures track ambient temperature, we predicted the thermal time constant (τ) for leaves at each canopy position. We found that C STRESS and AT 49 were significantly greater in lower and north-facing positions in the canopy. Differences in wind speed with height resulted in significantly longer predicted τ for leaves positioned at lower, north-facing positions. Variation in these drivers was correlated with significantly higher T 50 for leaves in these more environmentally stressful canopy positions. Our findings suggest that this species may optimise resources to protect against thermal damage at a whole-plant level. They also indicate that, particularly in desert environments with steep intracanopy microclimatic gradients, whole-plant carbon models could substantially under- or overestimate productivity under heat stress, depending on where in the canopy T 50 is measured.

Cwiklinski, K, Donnelly, S, Drysdale, O, Jewhurst, H, Smith, D, De Marco Verissimo, C, Pritsch, IC, O'Neill, S, Dalton, JP & Robinson, MW 2019, 'The cathepsin-like cysteine peptidases of trematodes of the genus Fasciola', Advances in Parasitology, vol. 104, pp. 113-164.
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© 2019 Elsevier Ltd Fasciolosis caused by trematode parasites of the genus Fasciola is a global disease of livestock, particularly cattle, sheep, water buffalo and goats. It is also a major human zoonosis with reports suggesting that 2.4–17 million people are infected worldwide, and 91.1 million people currently living at risk of infection. A unique feature of these worms is their reliance on a family of developmentally-regulated papain-like cysteine peptidases, termed cathepsins. These proteolytic enzymes play central roles in virulence, infection, tissue migration and modulation of host innate and adaptive immune responses. The availability of a Fasciola hepatica genome, and the exploitation of transcriptomic and proteomic technologies to probe parasite growth and development, has enlightened our understanding of the cathepsin-like cysteine peptidases. Here, we clarify the structure of the cathepsin-like cysteine peptidase families and, in this context, review the phylogenetics, structure, biochemistry and function of these enzymes in the host-parasite relationship.

Dan, X, Wang, C, Xu, X, Liu, Y, Cheng, X, Fronzi, M, Bi, L & Zhao, XS 2019, 'Improving the sinterability of CeO2 by using plane-selective nanocubes', Journal of the European Ceramic Society, vol. 39, no. 14, pp. 4429-4434.
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© 2019 Elsevier Ltd CeO2 nanocubes with (100) surface orientation are successfully synthesized and found to facilitate the sinterability of CeO2 material. The CeO2 nanocubes show a much-improved sinterability relative to CeO2 nanoparticles prepared by the conventional citric-nitrate method. The nanocubes can be successfully sintered at a relatively low temperature of 1200 °C without using any sintering aids. In contrast, a pellet using conventional CeO2 nano-powder obtained from the conventional citric-nitrate method can be densified only after sintering at 1400 °C, which is 200 °C higher than that for the CeO2 nanocube sintering, although the starting particle size of both CeO2 samples is similar. Density functional theory indicates that the surface energy of the (100) plane is significantly higher than that of the (111) plane, which is the more typical surface presentation of conventional CeO2 particles. This high surface energy allows fast growth of the CeO2 nanocubes during sintering, contributing to their improved sinterability.

Danastas, K, Whittington, CM, Dowland, SN, Combes, V, Murphy, CR & Lindsay, LA 2019, 'Ovarian Hyperstimulation Reduces Vascular Endothelial Growth Factor-A During Uterine Receptivity', Reproductive Sciences, vol. 26, no. 2, pp. 259-268.
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The angiogenic factor vascular endothelial growth factor-A (VEGFA) plays a critical role during early pregnancy in many species including the rat, and any alterations in VEGFA levels can severely impact blastocyst implantation rates. The rat ovarian hyperstimulation (OH) model is useful in studying how the induction of superovulation affects VEGFA levels and endometrial receptivity to blastocyst implantation. The present study shows that the major isoform in the rat uterus, Vegf188, is reduced at the time of receptivity in OH compared to normal pregnancy, whereas there is no change in Vegf164 and Vegf120 messenger RNA (mRNA). The VEGFA receptor 2 (VEGFR2) protein levels are also reduced at the time of receptivity in OH. Our ovariectomy studies show that Vegf164, Vegf188, and Vegf120 are significantly decreased by estrogen, and, to a lesser extent progesterone, when compared to control animals. Although no change in the percentage of endometrial blood vessels was seen across all stages of pregnancy, at the time of receptivity in OH pregnancies, blood vessels were typically larger compared to other stages. The altered progesterone-estrogen ratio seen in OH, taken together with our ovariectomy studies, explains the changes to Vegfa mRNA in OH at the time of receptivity. Since VEGFA is important during implantation, the changes to Vegfa and VEGFR2 levels in the endometrium may help explain the observed lower endometrial receptivity following OH. This study aimed to analyse how ovarian hyperstimulation alters the levels of vascular endothleial growth factor and its major receptor, VEGFR2 in the uterus in a rat model.

Dang, KD, Quiroz, M, Kohn, R, Tran, MN & Villani, M 2019, 'Hamiltonian monte carlo with energy conserving subsampling', Journal of Machine Learning Research, vol. 20, pp. 1-31.
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Hamiltonian Monte Carlo (HMC) samples efficiently from high-dimensional posterior distributions with proposed parameter draws obtained by iterating on a discretized version of the Hamiltonian dynamics. The iterations make HMC computationally costly, especially in problems with large data sets, since it is necessary to compute posterior densities and their derivatives with respect to the parameters. Naively computing the Hamiltonian dynamics on a subset of the data causes HMC to lose its key ability to generate distant parameter proposals with high acceptance probability. The key insight in our article is that efficient subsampling HMC for the parameters is possible if both the dynamics and the acceptance probability are computed from the same data subsample in each complete HMC iteration. We show that this is possible to do in a principled way in a HMC-within-Gibbs framework where the subsample is updated using a pseudo marginal MH step and the parameters are then updated using an HMC step, based on the current subsample. We show that our subsampling methods are fast and compare favorably to two popular sampling algorithms that use gradient estimates from data subsampling. We also explore the current limitations of subsampling HMC algorithms by varying the quality of the variance reducing control variates used in the estimators of the posterior density and its gradients.

De Kauwe, MG, Medlyn, BE, Pitman, AJ, Drake, JE, Ukkola, A, Griebel, A, Pendall, E, Prober, S & Roderick, M 2019, 'Examining the evidence for decoupling between photosynthesis and transpiration during heat extremes', Biogeosciences, vol. 16, no. 4, pp. 903-916.
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Abstract. Recent experimental evidence suggests that during heat extremes, woodedecosystems may decouple photosynthesis and transpiration, reducingphotosynthesis to near zero but increasing transpiration into the boundarylayer. This feedback may act to dampen, rather than amplify, heat extremes inwooded ecosystems. We examined eddy covariance databases (OzFlux andFLUXNET2015) to identify whether there was field-based evidence to supportthese experimental findings. We focused on two types of heat extremes:(i) the 3 days leading up to a temperature extreme, defined as includinga daily maximum temperature >37 ∘C (similar to the widely usedTXx metric), and (ii) heatwaves, defined as 3 or more consecutive daysabove 35 ∘C. When focusing on (i), we found some evidence ofreduced photosynthesis and sustained or increased latent heat fluxes at sevenAustralian evergreen wooded flux sites. However, when considering the role ofvapour pressure deficit and focusing on (ii), we were unable to conclusivelydisentangle the decoupling between photosynthesis and latent heat flux fromthe effect of increasing the vapour pressure deficit. Outside of Australia, theTier-1 FLUXNET2015 database provided limited scope to tackle this issue as itdoes not sample sufficient high temperature events with which to probe thephysiological response of trees to extreme heat. Thus, further work isrequired to determine whether this photosynthetic decoupling occurs widely,ideally by matching experimental species with those found at eddy covariancetower sites. Such measurements would allow this decoupling mechanism to beprobed experimentally and at the ecosystem scale. Transpiration duringheatwaves remains a key issue to resolve, as no land surface model includes adecoupling mechanism, and any potential dampening of the land–atmosphereamplification is thus not included in climate model projections.

de las Peñas, MLAN, Verzosa, DMB, Aberin, MAQ, Garces, LPDM, Francisco, FF, Bautista, EP, Tolentino, MAC & Tabares, WC 2019, 'Digital simulations for grade 7 to 10 mathematics', Philippine Journal of Science, vol. 148, no. 4, pp. 735-749.
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This article describes a Department of Science and Technology – Philippine Council for Industry, Energy and Emerging Technology (DOST-PCIEERD) project aimed to facilitate the implementation of the mathematical objectives raised by the Department of Education’s (DepEd) K to 12 program in the Philippines through the use of innovative digital technologies. In particular, a selection of application software (“apps”) were created for Grade 7 to 10 mathematics that covered topics indicated in the five strands outlined in the K to 12 program – namely (1) number, (2) geometry, (3) measurement, (4) patterns and algebra, and (5) statistics and probability. The design of the apps was informed by an amalgamated framework of the Cognitive Theory of Multimedia Learning (Mayer 2005) and Mathematical Theories of Representation (Goldin 1998). The design was informed by how students learn and how students learn mathematics. The project also aimed to design manipulable software that allows learners to construct and grapple with their mental representations of mathematical concepts. This paper describes a selection of the apps designed by the project and how their features were informed by the theoretical framework. It also presents results from pilot studies that demonstrate the apps’ potential to increase performance, facilitate conceptual development, and increase learners’ engagement.

de Lima Ribeiro, A, Artlett, C, Ajani, PA, Derkenne, C & Pask, H 2019, 'Impact of fluorescence on Raman remote sensing of temperature in natural water samples', Optics Express, vol. 27, no. 16, pp. 22339-22339.
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© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement A comprehensive investigation into the impact of spectral baseline on temperature prediction in natural marine water samples by Raman spectroscopy is presented. The origin of baseline signals is investigated using principal component analysis and phytoplankton cultures in laboratory experiments. Results indicate that fluorescence from photosynthetic pigments and dissolved organic matter may overlap with the Raman peak for 532 nm excitation and compromise the accuracy of temperature predictions. Two methods of spectral baseline correction in natural waters are evaluated: a traditional tilted baseline correction and a new correction by temperature marker values, with accuracies as high as ± 0.2°C being achieved in both cases.

Deepika, Arora, S, Kaur, R, Singh, TG, Singh, M, Satija, S & Singh, R 2019, 'Prescribing pattern of antihypertensive drugs in a tertiary care hospital: A review', Plant Archives, vol. 19, pp. 1311-1316.
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Hypertension is one the leading cause of mortality in various developing countries like India. For the effective management of this lifestyle disorder a rational approach & measures are required to be taken by the health care professionals. In order to achieve this, prescription pattern analysis is a powerful tool which elaborated the trends of prescribing and their evaluation in reference to the standard treatment guidelines by the various health agencies. An ample of studies focusing on prescribing patterns of antihypertensive drugs was reviewed in this article. It has been concluded that most of the studies were showing that monotherapy including ACEIs (Angiotensin converting enzyme inhibitors) was first choice antihypertensive treatment. Additionally, ARBs (angiotensin receptor blockers) were the second most preferred class followed by CCBs (calcium channel blockers), Diuretics and BB (beta blockers). However, most of the studies have shown that the prescribing trends were according to the recommended guidelines but JNC 8 guidelines were not being completely followed. Due to persistent clinical challenges in the management of hypertension, we still require additional care & monitoring of the treatment patterns. So adoption of a rational approach aligned with standard treatment guidelines is essential which will not only fill the gaps in the clinical practice but also help in complete & effective management of this illness.

DeMaere, MZ & Darling, AE 2019, 'bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes', Genome Biology, vol. 20, no. 1, pp. 46-46.
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© 2019 The Author(s). Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C).

Dennis, L & Peacock, J 2019, 'Genes Directing Flower Development in Arabidopsis', The Plant Cell, vol. 31, no. 6, pp. 1192-1193.
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Deplazes, E, White, J, Murphy, C, Cranfield, CG & Garcia, A 2019, 'Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers', Biophysical Reviews, vol. 11, no. 3, pp. 483-490.
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© 2019, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature. Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water–lipid interface. In this short review, we discuss the similarities between the proton–membrane and alkali ion–membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid–ion and lipid–ion–water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water–phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.

Deschaseaux, E, O'Brien, J, Siboni, N, Petrou, K & Seymour, JR 2019, 'Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate &lt;i&gt;Alexandrium minutum&lt;/i&gt; during a simulated marine heatwave', Biogeosciences, vol. 16, no. 22, pp. 4377-4391.
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Abstract. The biogenic sulfur compounds dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) are produced andtransformed by diverse populations of marine microorganisms and havesubstantial physiological, ecological and biogeochemical importance spanningorganism to global scales. Understanding the production and transformationdynamics of these compounds under shifting environmental conditions isimportant for predicting their roles in a changing ocean. Here, we reportthe physiological and biochemical response of a robust strain ofAlexandrium minutum, a dinoflagellate with the highest reported intracellular DMSP content,exposed to a 6 d increase in temperature mimicking mild and extremecoastal marine heatwave conditions (+4 and +12 ∘C). Under mild temperature increases (+4 ∘C), A. minutum growth wasenhanced, with no measurable physiological stress response. However, under avery acute increase in temperature (+12 ∘C) triggering thermalstress, A. minutum growth declined, photosynthetic efficiency (FV∕FM) wasimpaired, and enhanced oxidative stress was observed. These physiologicalresponses indicative of thermal stress were accompanied by increased DMS andDMSO concentrations followed by decreased DMSP concentration. At thistemperature extreme, we observed a cascading stress response in A. minutum, which wasinitiated 6 h after the start of the experiment by a spike in DMS and DMSOconcentrations and a rapid decrease in FV∕FM. This was followed byan increase in reactive oxygen species (ROS) and an abrupt decline in DMSand DMSO on day 2 of the experiment. A subsequent decrease in DMSP coupledwith a decline in the growth rate of both A. minutum and its associated totalbacterial assemblage coincided with a shift in the composition of the A. minutummicrobiome. Specifically, an increase in the relative abundance of the operational taxonomic units (OTUs)matching Oceanicaulis (17.0 %), Phycisphaeraceae ...

Dietrich, A, Bürk, M, Steiger, ES, Antoniuk, L, Tran, TT, Nguyen, M, Aharonovich, I, Jelezko, F & Kubanek, A 2019, 'Reply to “Comment on ‘Observation of Fourier transform limited lines in hexagonal boron nitride’”', Physical Review B, vol. 100, no. 4.
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© 2019 American Physical Society. In this Reply, we answer to the comments by Langbein [Phys. Rev. B 100, 047401 (2019)10.1103/PhysRevB.100.047401]. We disagree with the argument that our measured spectral shapes and the extracted linewidths are caused by temporal blinking. We give detailed information on our evaluation process to exclude blinking events. Beyond the question raised in the Comment, we analyze the influence of spectral diffusion. Although spectral diffusion is an ongoing limitation for defect centers in hexagonal boron nitride, we prove that it is not influencing our extracted linewidths.

Ding, B, Shao, S, Jiang, F, Dang, P, Sun, C, Huang, S, Ma, P, Jin, D, Kheraif, AAA & Lin, J 2019, 'MnO₂-Disguised Upconversion Hybrid Nanocomposite: An Ideal Architecture for Tumor Microenvironment-Triggered UCL/MR Bioimaging and Enhanced Chemodynamic Therapy', Chemistry of Materials, vol. 31, no. 7, pp. 2651-2660.
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Copyright © 2019 American Chemical Society. Upconversion nanoparticles (UCNPs) and MnO 2 hybrid theranostic nanoplatform (UCMn) is highly desired; however, the rational design of such UCMn hybrid nanomaterials is still a great challenge. Herein, a simple and versatile strategy for the in situ growth of MnO 2 on the surfaces of UCNPs was reported using a sacrificial template method to construct an ideal MnO 2 -disguised and tumor microenvironment-triggered architecture. Such sophisticated architecture not only achieves activatable magnetic resonance imaging and restorable upconversion luminescence (UCL) imaging with over 100-fold enhancement of UCL in vivo but also significantly improves the efficiency of chemodynamic therapy (CDT) by glutathione depletion- and cisplatin-activation-enhanced • OH generation simultaneously. Additionally, the synergetic effect of CDT and chemotherapy presents excellent therapeutic effect in vivo as compared to either CDT or chemotherapy alone. We believe that the ideal design of the MnO 2 -disguised upconversion hybrid nanocomposite will provide more revelations on the future research on nanoscale theranostic systems.

Djordjevic, SP & Morgan, BS 2019, 'A One Health genomic approach to antimicrobial resistance is essential for generating relevant data for a holistic assessment of the biggest threat to public health', Microbiology Australia, vol. 40, no. 2, pp. 73-73.
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Antimicrobial resistance (AMR) threatens modern medicine as we know it. AMR infections may ultimately be untreatable and routine surgeries will become inherently risky1. By 2050 more people may die of drug-resistant infections (DRIs) every year than of cancer, which equates to more than 10 million annual deaths globally2 and the World Bank has estimated that AMR could cost the global economy $1 trillion every year after 2030. DRIs also lead to an increase in the length of hospital stays, the use of more toxic or costly antibiotics and an increased likelihood of death3. BRIC nations (Brazil, Russia, India, China) and socio-economically challenged countries and people who already have higher rates of infectious diseases will feel the greatest impact2. Indeed, AMR has been likened to the 2008 global financial crisis on an annual repeat cycle. That is because the effects of AMR are not just confined to the human medical sector. The veterinary sector is also reliant on the availability of antimicrobials to treat infectious diseases in companion and food-producing animals.

Djurichkovic, LD, Donelson, JM, Fowler, AM, Feary, DA & Booth, DJ 2019, 'The effects of water temperature on the juvenile performance of two tropical damselfishes expatriating to temperate reefs', Scientific Reports, vol. 9, no. 1.
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AbstractOcean warming associated with global climate change is already inducing geographic range shifts of marine species. Juvenile coral reef fishes transported into temperate latitudes (termed ‘vagrant’ fishes) can experience winter water temperatures below their normal thermal minimum. Such environmental extremes may increase energetic costs for such fishes, resulting in reduced performance, which may be the governing factor that limits the potential for poleward range expansion of such fishes. This study compared the juvenile physiological performance and behaviour of two congeneric tropical damselfishes which settle during austral summer months within temperate eastern Australia: Abudefduf vaigiensis have an extended southern range, and lower threshold survival temperature than the congeneric A. whitleyi. Physiological and behavioural performance parameters that may be affected by cooler temperature regimes at higher latitudes were measured in aquaria. Lower water temperature resulted in reduced growth rates, feeding rates, burst escape speed and metabolic rates of both species, with significantly reduced performance (up to six-fold reductions) for fishes reared at 18 °C relative to 22 °C and 26 °C. However, A. whitleyi exhibited lower growth rates than A. vaigiensis across all temperatures, and lower aerobic capacity at the lowest temperature (18 °C). This difference between species in growth and metabolic capacity suggests that the extended southern distribution and greater overwintering success of A. vaigiensis, in comparison to A. whitleyi is related to thermal performance parameters which are critical in maintaining individual health and survival. Our results support previous findings in the region that water temperature below 22 °C represents a critic...

Donelson, JM, Sunday, JM, Figueira, WF, Gaitán-Espitia, JD, Hobday, AJ, Johnson, CR, Leis, JM, Ling, SD, Marshall, D, Pandolfi, JM, Pecl, G, Rodgers, GG, Booth, DJ & Munday, PL 2019, 'Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 374, no. 1768, pp. 20180186-20180186.
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Climate change is leading to shifts in species geographical distributions, but populations are also probably adapting to environmental change at different rates across their range. Owing to a lack of natural and empirical data on the influence of phenotypic adaptation on range shifts of marine species, we provide a general conceptual model for understanding population responses to climate change that incorporates plasticity and adaptation to environmental change in marine ecosystems. We use this conceptual model to help inform where within the geographical range each mechanism will probably operate most strongly and explore the supporting evidence in species. We then expand the discussion from a single-species perspective to community-level responses and use the conceptual model to visualize and guide research into the important yet poorly understood processes of plasticity and adaptation.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.

Donnelly, S, Dean, S, Razavy, S & Levett-Jones, T 2019, 'Correction: Measuring the impact of an interdisciplinary learning project on nursing, architecture and landscape design students’ empathy', PLOS ONE, vol. 14, no. 11, pp. e0225719-e0225719.
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© 2019 The PLOS ONE Staff. 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. There are errors in the Author Contributions. The correct contributions are: Conceptualization: Samantha Donnelly, Suzanne Dean Data curation: Shohreh Razavy Formal analysis: Shohreh Razavy Investigation: Samantha Donnelly, Suzanne Dean Methodology: Tracy Levett-Jones Project administration: Suzanne Dean Supervision: Tracy Levett-Jones Writing–original draft: Samantha Donnelly Writing–review & editing: Shohreh Razavy, Suzanne Dean, Tracy Levett-Jones The second author, Suzanne Dean, is incorrectly noted as the corresponding author. The correct corresponding author is Samantha Donnelly. Dr. Donnelly’s email address is: samantha.donnelly@uts.edu.au. The publisher apologizes for these errors.

Donnelly, S, Dean, S, Razavy, S & Levett-Jones, T 2019, 'Measuring the impact of an interdisciplinary learning project on nursing, architecture and landscape design students’ empathy', PLOS ONE, vol. 14, no. 10, pp. e0215795-e0215795.
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© 2019 Donnelly 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. Domestic violence and refuge services in Australia In Australia and internationally, domestic violence is a major cause of homelessness for women and children and yet provision for accommodation for this user-group is not well documented or understood. When designing emergency accommodation, the concerns, preferences, and perspectives of individuals who access refuge services must be sought in order to create spaces that are conducive to the needs of this diverse and vulnerable group. An empathic 'lens' can provide meaningful insights that can inform the design of refuge services specifically targeted at addressing these needs. This paper describes an authentic interdisciplinary learning experience for nursing, architecture and landscape students at a university in Sydney, Australia, and presents the results of a study designed to measure the impact of this initiative on participants' empathy towards women and children who access refuge services as a result of homelessness and/or domestic violence. Empathy levels were measured using the Comprehensive State Empathy Scale, a validated measurement tool. An authentic interdisciplinary learning experience The learning experience consisted of collaborative meetings with stakeholders from the refuge sector, fieldwork, individual research, exchanging ideas and problem-solving in teams. Students then developed design guides for refuges that demonstrated their emerging understanding of the specific needs and perspectives of the issues faced by women and children who had experienced violence and found themselves homeless. Pre-post Comprehensive State Empathy Scale results indicated that the empathy levels of nursing and landscape students increased and those o...

Donovan, C & Hansbro, PM 2019, 'TRPA1: A potential target for cold‐induced airway disease?', Respirology, vol. 24, no. 3, pp. 193-194.
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Dörk, T, Peterlongo, P, Mannermaa, A, Bolla, MK, Wang, Q, Dennis, J, Ahearn, T, Andrulis, IL, Anton-Culver, H, Arndt, V, Aronson, KJ, Augustinsson, A, Freeman, LEB, Beckmann, MW, Beeghly-Fadiel, A, Behrens, S, Bermisheva, M, Blomqvist, C, Bogdanova, NV, Bojesen, SE, Brauch, H, Brenner, H, Burwinkel, B, Canzian, F, Chan, TL, Chang-Claude, J, Chanock, SJ, Choi, J-Y, Christiansen, H, Clarke, CL, Couch, FJ, Czene, K, Daly, MB, dos-Santos-Silva, I, Dwek, M, Eccles, DM, Ekici, AB, Eriksson, M, Evans, DG, Fasching, PA, Figueroa, J, Flyger, H, Fritschi, L, Gabrielson, M, Gago-Dominguez, M, Gao, C, Gapstur, SM, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Giles, GG, Goldberg, MS, Goldgar, DE, Guénel, P, Haeberle, L, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Hartman, M, Hauke, J, Hein, A, Hillemanns, P, Hogervorst, FBL, Hooning, MJ, Hopper, JL, Howell, T, Huo, D, Ito, H, Iwasaki, M, Jakubowska, A, Janni, W, John, EM, Jung, A, Kaaks, R, Kang, D, Kapoor, PM, Khusnutdinova, E, Kim, S-W, Kitahara, CM, Koutros, S, Kraft, P, Kristensen, VN, Kwong, A, Lambrechts, D, Marchand, LL, Li, J, Lindström, S, Linet, M, Lo, W-Y, Long, J, Lophatananon, A, Lubiński, J, Manoochehri, M, Manoukian, S, Margolin, S, Martinez, E, Matsuo, K, Mavroudis, D, Meindl, A, Menon, U, Milne, RL, Mohd Taib, NA, Muir, K, Mulligan, AM, Neuhausen, SL, Nevanlinna, H, Neven, P, Newman, WG, Offit, K, Olopade, OI, Olshan, AF, Olson, JE, Olsson, H, Park, SK, Park-Simon, T-W, Peto, J, Plaseska-Karanfilska, D, Pohl-Rescigno, E, Presneau, N, Rack, B, Radice, P, Rashid, MU, Rennert, G, Rennert, HS, Romero, A, Ruebner, M, Saloustros, E, Schmidt, MK, Schmutzler, RK, Schneider, MO, Schoemaker, MJ, Scott, C, Shen, C-Y, Shu, X-O, Simard, J, Slager, S, Smichkoska, S, Southey, MC, Spinelli, JJ, Stone, J, Surowy, H, Swerdlow, AJ, Tamimi, RM, Tapper, WJ, Teo, SH, Terry, MB, Toland, AE, Tollenaar, RAEM, Torres, D, Torres-Mejía, G, Troester, MA, Truong, T, Tsugane, S, Untch, M, Vachon, CM, Ouweland, AMWVD, Veen, EMV, Vijai, J, Wendt, C, Wolk, A, Yu, J-C, Zheng, W, Ziogas, A, Ziv, E, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, CS, Marsh, D, Morey, A, Pathmanathan, N, Scott, R, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Zeps, N, Børresen-Dale, A-L, Grenaker Alnæs, GI, Sahlberg, KK, Ottestad, L, Kåresen, R, Schlichting, E, Holmen, MM, Sauer, T & et al. 2019, 'Two truncating variants in FANCC and breast cancer risk', Scientific Reports, vol. 9, no. 1, p. 12524.
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AbstractFanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Douglas, ANJ, Irga, PJ & Torpy, FR 2019, 'Determining broad scale associations between air pollutants and urban forestry: A novel multifaceted methodological approach', Environmental Pollution, vol. 247, pp. 474-481.
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© 2019 Elsevier Ltd Global urbanisation has resulted in population densification, which is associated with increased air pollution, mainly from anthropogenic sources. One of the systems proposed to mitigate urban air pollution is urban forestry. This study quantified the spatial associations between concentrations of CO, NO₂ SO₂ and PM₁₀ and urban forestry, whilst correcting for anthropogenic sources and sinks, thus explicitly testing the hypothesis that urban forestry is spatially associated with reduced air pollution on a city scale. A Land Use Regression (LUR) model was constructed by combining air pollutant concentrations with environmental variables, such as land cover type and use, to develop predictive models for air pollutant concentrations. Traffic density and industrial air pollutant emissions were added to the model as covariables to permit testing of the main effects after correcting for these air pollutant sources. It was found that the concentrations of all air pollutants were negatively correlated with tree canopy cover and positively correlated with dwelling density, population density and traffic count. The LUR models enabled the establishment of a statistically significant spatial relationship between urban forestry and air pollution mitigation. These findings further demonstrate the spatial relationships between urban forestry and reduced air pollution on a city-wide scale, and could be of value in developing planning policies focused on urban greening.

Dua, K, Gupta, G, Chellappan, DK, Shukla, S & Hansbro, PM 2019, 'Targeting bacterial biofilms in pulmonary diseases in pediatric population', Minerva Pediatrica, vol. 71, no. 3, pp. 309-310.
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Dua, K, Malyla, V, Singhvi, G, Wadhwa, R, Krishna, RV, Shukla, SD, Shastri, MD, Chellappan, DK, Maurya, PK, Satija, S, Mehta, M, Gulati, M, Hansbro, N, Collet, T, Awasthi, R, Gupta, G, Hsu, A & Hansbro, PM 2019, 'Increasing complexity and interactions of oxidative stress in chronic respiratory diseases: An emerging need for novel drug delivery systems', Chemico-Biological Interactions, vol. 299, pp. 168-178.
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© 2018 Elsevier B.V. Oxidative stress is intensely involved in enhancing the severity of various chronic respiratory diseases (CRDs) including asthma, chronic obstructive pulmonary disease (COPD), infections and lung cancer. Even though there are various existing anti-inflammatory therapies, which are not enough to control the inflammation caused due to various contributing factors such as anti-inflammatory genes and antioxidant enzymes. This leads to an urgent need of novel drug delivery systems to combat the oxidative stress. This review gives a brief insight into the biological factors involved in causing oxidative stress, one of the emerging hallmark feature in CRDs and particularly, highlighting recent trends in various novel drug delivery carriers including microparticles, microemulsions, microspheres, nanoparticles, liposomes, dendrimers, solid lipid nanocarriers etc which can help in combating the oxidative stress in CRDs and ultimately reducing the disease burden and improving the quality of life with CRDs patients. These carriers improve the pharmacokinetics and bioavailability to the target site. However, there is an urgent need for translational studies to validate the drug delivery carriers for clinical administration in the pulmonary clinic.

Dua, K, Wadhwa, R, Singhvi, G, Rapalli, V, Shukla, SD, Shastri, MD, Gupta, G, Satija, S, Mehta, M, Khurana, N, Awasthi, R, Maurya, PK, Thangavelu, L, S, R, Tambuwala, MM, Collet, T, Hansbro, PM & Chellappan, DK 2019, 'The potential of siRNA based drug delivery in respiratory disorders: Recent advances and progress', Drug Development Research, vol. 80, no. 6, pp. 714-730.
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AbstractLung diseases are the leading cause of mortality worldwide. The currently available therapies are not sufficient, leading to the urgent need for new therapies with sustained anti‐inflammatory effects. Small/short or silencing interfering RNA (siRNA) has potential therapeutic implications through post‐transcriptional downregulation of the target gene expression. siRNA is essential in gene regulation, so is more favorable over other gene therapies due to its small size, high specificity, potency, and no or low immune response. In chronic respiratory diseases, local and targeted delivery of siRNA is achieved via inhalation. The effectual delivery can be attained by the generation of aerosols via inhalers and nebulizers, which overcomes anatomical barriers, alveolar macrophage clearance and mucociliary clearance. In this review, we discuss the different siRNA nanocarrier systems for chronic respiratory diseases, for safe and effective delivery. siRNA mediated pro‐inflammatory gene or miRNA targeting approach can be a useful approach in combating chronic respiratory inflammatory conditions and thus providing sustained drug delivery, reduced therapeutic dose, and improved patient compliance. This review will be of high relevance to the formulation, biological and translational scientists working in the area of respiratory diseases.

Duke, NC, Field, C, Mackenzie, JR, Meynecke, J-O & Wood, AL 2019, 'Rainfall and its possible hysteresis effect on the proportional cover of tropical tidal-wetland mangroves and saltmarsh–saltpans', Marine and Freshwater Research, vol. 70, no. 8, pp. 1047-1047.
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Mangrove–saltmarsh tidal wetlands are highly dynamic ecosystems, responding and adapting to climate and physical conditions at all spatial and temporal scales. Knowledge of the large-scale ecosystem processes involved and how they might be influenced by climate variables is highly relevant today. For tidal-wetland sites well within the latitudinal range of the mostly tropical mangrove communities, we confirm that average annual rainfall influences vegetative cover, as well as species composition and biomass of tidal wetlands. On the basis of 205 largely unmodified, tropical and subtropical estuaries of northern Australia, a sigmoidal relationship, with a centroid inflection point ~1368mm, was derived between rainfall and the relative amounts of high-biomass mangroves and low-biomass saltmarsh–saltpan vegetation. The presence and probability of observed combinations of these community types were quantified using the wetland cover index, which is the ratio of total mangrove area to that of mangroves plus intertidal saltmarsh and saltpans. Accordingly, periodic changes in rainfall trends are likely manifest as either encroachment or dieback of mangroves along the ecotones separating them from tidal saltmarsh–saltpans. Presented is a new conceptual framework and model that describes how such ecosystem-scale processes take place in tropical and subtropical tidal wetlands.

Duong, NMH, Glushkov, E, Chernev, A, Navikas, V, Comtet, J, Nguyen, MAP, Toth, M, Radenovic, A, Tran, TT & Aharonovich, I 2019, 'Facile Production of Hexagonal Boron Nitride Nanoparticles by Cryogenic Exfoliation', Nano Letters, vol. 19, no. 8, pp. 5417-5422.
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© 2019 American Chemical Society. Fluorescent nanoparticles with optically robust luminescence are imperative to applications in imaging and labeling. Here we demonstrate that hexagonal boron nitride (hBN) nanoparticles can be reliably produced using a scalable cryogenic exfoliation technique with sizes below 10 nm. The particles exhibit bright fluorescence generated by color centers that act as atomic-size quantum emitters. We analyze their optical properties, including emission wavelength, photon-statistics, and photodynamics, and show that they are suitable for far-field super-resolution fluorescence nanoscopy. Our results provide a foundation for exploration of hBN nanoparticles as candidates for bioimaging, labeling, as well as biomarkers that are suitable for quantum sensing.

Duong, NMH, Regan, B, Toth, M, Aharonovich, I & Dawes, J 2019, 'A Random Laser Based on Hybrid Fluorescent Dye and Diamond Nanoneedles', physica status solidi (RRL) – Rapid Research Letters, vol. 13, no. 2, pp. 1800513-1800513.
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Random lasers use radiative gain and multiple scatterers in disordered media to generate light amplification. In this study, a random laser based on diamond nanoneedles that act as scatterers in combination with fluorescent dye molecules that serve as a gain medium has been demonstrated. Random lasers realized using diamond possess high spectral radiance with angle‐free emission and thresholds of 0.16 mJ. The emission dependence on the pillar diameter and density is investigated, and optimum lasing conditions are measured for pillars with spacing and density of ≈336 ± 40 nm and ≈2.9 × 1010 cm−2. Our results expand the application space of diamond as a material platform for practical, compact photonic devices, and sensing applications.

Eapen, MS, Sharma, P, Gaikwad, AV, Lu, W, Myers, S, Hansbro, PM & Sohal, SS 2019, '<p>Epithelial–mesenchymal transition is driven by transcriptional and post transcriptional modulations in COPD: implications for disease progression and new therapeutics</p>', International Journal of Chronic Obstructive Pulmonary Disease, vol. Volume 14, pp. 1603-1610.
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© 2019 Eapen et al. COPD is a common and highly destructive disease with huge impacts on people and health services throughout the world. It is mainly caused by cigarette smoking though environmental pollution is also significant. There are no current treatments that affect the overall course of COPD; current drugs focus on symptomatic relief and to some extent reducing exacerbation rates. There is an urgent need for in-depth studies of the fundamental pathogenic mechanisms that underpin COPD. This is vital, given the fact that nearly 40%– 60% of the small airway and alveolar damage occurs in COPD well before the first measurable changes in lung function are detected. These individuals are also at a high risk of lung cancer. Current COPD research is mostly centered around late disease and/or innate immune activation within the airway lumen, but the actual damage to the airway wall has early onset. COPD is the end result of complex mechanisms, possibly triggered through initial epithelial activation. To change the disease trajectory, it is crucial to understand the mechanisms in the epithelium that are switched on early in smokers. One such mechanism we believe is the process of epithelial to mesenchymal transition. This article highlights the importance of this profound epithelial cell plasticity in COPD and also its regulation. We consider that understanding early changes in COPD will open new windows for therapy.

Eapen, MS, Sharma, P, Moodley, YP, Hansbro, PM & Sohal, SS 2019, 'Dysfunctional Immunity and Microbial Adhesion Molecules in Smoking-induced Pneumonia', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 2, pp. 250-251.
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Eapen, MS, Sharma, P, Thompson, IE, Lu, W, Myers, S, Hansbro, PM & Sohal, SS 2019, 'Heparin-binding epidermal growth factor (HB-EGF) drives EMT in patients with COPD: implications for disease pathogenesis and novel therapies', Laboratory Investigation, vol. 99, no. 2, pp. 150-157.
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© 2018, United States & Canadian Academy of Pathology. Chronic obstructive pulmonary disease (COPD) is a progressive and devastating chronic lung condition that has a significant global burden, both medically and financially. Currently there are no medications that can alter the course of disease. At best, the drugs in clinical practice provide symptomatic relief to suffering patients by alleviating acute exacerbations. Most of current clinical research activities are in late severe disease with lesser attention given to early disease manifestations. There is as yet, a lack of understanding of the underlying mechanisms of disease progression and the molecular switches that are involved in their manifestation. Small airway fibrosis and obliteration are known to cause fixed airflow obstruction in COPD, and the consequential damage to the lung has an early onset. So far, there is little evidence of the mechanisms that underlie this aspect of pathology. However, emerging research confirms that airway epithelial reprogramming or epithelial to mesenchymal transition (EMT) is a key mechanism that drives fibrotic remodelling changes in smokers and patients with COPD. A recent study by Lai et al. further highlights the importance of EMT in smoking-related COPD pathology. The authors identify HB-EGF, an EGFR ligand, as a key driver of EMT and a potential new therapeutic target for the amelioration of EMT and airway remodelling. There are also wider implications in lung cancer prophylaxis, which is another major comorbidity associated with COPD. We consider that improved molecular understanding of the intricate pathways associated with epithelial cell plasticity in smokers and patients with COPD will have major therapeutic implications.

Eggleton, BJ, Poulton, CG, Rakich, PT, Steel, MJ & Bahl, G 2019, 'Brillouin integrated photonics', Nature Photonics, vol. 13, no. 10, pp. 664-677.
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© 2019, Springer Nature Limited. A recent renaissance in Brillouin scattering research has been driven by the increasing maturity of photonic integration platforms and nanophotonics. The result is a new breed of chip-based devices that exploit acousto-optic interactions to create lasers, amplifiers, filters, delay lines and isolators. Here, we provide a detailed overview of Brillouin scattering in integrated waveguides and resonators, covering key concepts such as the stimulation of the Brillouin process, in which the optical field itself induces acoustic vibrations, the importance of acoustic confinement, methods for calculating and measuring Brillouin gain, and the diversity of materials platforms and geometries. Our Review emphasizes emerging applications in microwave photonics, signal processing and sensing, and concludes with a perspective for future directions.

Eijkelkamp, BA, Morey, JR, Neville, SL, Tan, A, Pederick, VG, Cole, N, Singh, PP, Ong, C-LY, Gonzalez de Vega, R, Clases, D, Cunningham, BA, Hughes, CE, Comerford, I, Brazel, EB, Whittall, JJ, Plumptre, CD, McColl, SR, Paton, JC, McEwan, AG, Doble, PA & McDevitt, CA 2019, 'Dietary zinc and the control of Streptococcus pneumoniae infection', PLOS Pathogens, vol. 15, no. 8, pp. e1007957-e1007957.
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© 2019 Eijkelkamp 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 zinc deficiency increases susceptibility to bacterial infection. Although zinc supplementation therapies can reduce the impact of disease, the molecular basis for protection remains unclear. Streptococcus pneumoniae is a major cause of bacterial pneumonia, which is prevalent in regions of zinc deficiency. We report that dietary zinc levels dictate the outcome of S. pneumoniae infection in a murine model. Dietary zinc restriction impacts murine tissue zinc levels with distribution post-infection altered, and S. pneumoniae virulence and infection enhanced. Although the activation and infiltration of murine phagocytic cells was not affected by zinc restriction, their efficacy of bacterial control was compromised. S. pneumoniae was shown to be highly sensitive to zinc intoxication, with this process impaired in zinc restricted mice and isolated phagocytic cells. Collectively, these data show how dietary zinc deficiency increases sensitivity to S. pneumoniae infection while revealing a role for zinc as a component of host antimicrobial defences.

Elbadawi, C, Fröch, JE, Aharonovich, I, Toth, M & Lobo, CJ 2019, 'One-Step Nanoscale Patterning of Silver Nanowire–Nitride Heterostructures Using Substrate-Assisted Chemical Etching', The Journal of Physical Chemistry C, vol. 123, no. 1, pp. 945-949.
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© 2018 American Chemical Society. Nanoscale etching and patterning of noble metals such as copper, silver, and gold are extremely difficult to achieve due to the low volatility of group 11 metal compounds. Here, we introduce a method of nanoscale chemical etching that involves reactions between H2O adsorbates and N radicals generated from electron-beam-induced etching (EBIE) of a hexagonal boron nitride or AlN substrate to achieve efficient and highly localized chemical etching of Ag nanowires and the underlying substrate. The volatilization of noble metal nanowires by radical species generated during EBIE of the underlying substrate represents a new class of EBIE reactions, which we term 'substrate-assisted chemical etching'.

Ende, JA, Ahmadzad, S, Christensen, JM, Oliver, B, Estephan, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'Isolated respiratory epithelials cell in suspension exhibiting ciliary activity', ASVIDE, vol. 6, pp. 62-62.
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Ende, JA, Ahmadzada, S, Christensen, JM, Oliver, B, Estepha, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'An ALI culture well with well-differentiated respiratory epithelium demonstrating coordinated ciliary activity and mucociliary clearance', ASVIDE, vol. 6, pp. 64-64.
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Ende, JA, Ahmadzada, S, Christensen, JM, Oliver, B, Estephan, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'An ALI culture well exhibiting well-differentiated respiratory epithelium with ciliary activity', ASVIDE, vol. 6, pp. 63-63.
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Ende, JA, Ahmadzada, S, Christensen, JM, Oliver, B, Estephan, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'Environmental responses of virally infected respiratory epithelial cells', Australian Journal of Otolaryngology, vol. 2, no. March, pp. 8-8.
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Background: Rhinovirus, airborne pollution, and allergens are thought to contribute to epithelial dysfunction in chronic airway disease. Objectives were to determine whether these factors act in synergism to induce inflammation and chronic airway disease. Methods: Respiratory mucosa from chronic rhinosinusitis with nasal polyps (CRSwNP) (n=7) or healthy (n=6) patients were cultured at air-liquid interface (ALI) (culture wells n=204). Cells were infected with rhinovirus, then exposed to combinations of vehicle, diesel particulate matter (DPM), and house dust mite (HDM). Ciliary beating frequency (CBF), interleukin (IL)-6 release, and cytotoxicity were assessed by Sisson-Ammons Video Analysis (SAVA) software, flow cytometry, and LDH assays. Results: Compared with healthy cultures, CRSwNP culture groups had lower baseline CBF. The CBF of virally infected ALI cultures was higher than healthy cultures. Challenges tended to impair CBF more in cells that were also virally infected. There was an elevation in IL-6 with viral infection. Challenge combinations did not cause a different IL-6 or CBF response within groups. Conclusions: An inherent mucosal dysfunction and environmental exposures can worsen sinus disease. Synergism in CBF impairment or IL-6 release was not seen.

Ernst, A, Fung, J, Singh, G & Zinder, Y 2019, 'Flexible flow shop with dedicated buffers', Discrete Applied Mathematics, vol. 261, pp. 148-163.
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© 2018 Elsevier B.V. A two-stage flexible flow shop is considered, where first- and second-stage machines form disjoint pairs, each with a buffer. The buffer capacity varies from pair to pair, and the buffer requirement varies from job to job. Each job is to be assigned to a pair of machines for processing and uses the required amount of buffer from the start till the end of its processing. Operations have equal duration. It is shown that, unless P=NP, no polynomial-time algorithm guarantees a makespan less than 4∕3 of the optimal. The paper presents two integer linear programs, compared by means of computational experiments. Both approaches utilise as a subroutine the developed polynomial-time algorithm for the case of equal buffers.

Espinoza-Vergara, G, Noorian, P, Silva-Valenzuela, CA, Raymond, BBA, Allen, C, Hoque, MM, Sun, S, Johnson, MS, Pernice, M, Kjelleberg, S, Djordjevic, SP, Labbate, M, Camilli, A & McDougald, D 2019, 'Vibrio cholerae residing in food vacuoles expelled by protozoa are more infectious in vivo', Nature Microbiology, vol. 4, no. 12, pp. 2466-2474.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Vibrio cholerae interacts with many organisms in the environment, including heterotrophic protists (protozoa). Several species of protozoa have been reported to release undigested bacteria in expelled food vacuoles (EFVs) when feeding on some pathogens. While the production of EFVs has been reported, their biological role as a vector for the transmission of pathogens remains unknown. Here we report that ciliated protozoa release EFVs containing V. cholerae. The EFVs are stable, the cells inside them are protected from multiple stresses, and large numbers of cells escape when incubated at 37 °C or in the presence of nutrients. We show that OmpU, a major outer membrane protein positively regulated by ToxR, has a role in the production of EFVs. Notably, cells released from EFVs have growth and colonization advantages over planktonic cells both in vitro and in vivo. Our results suggest that EFVs facilitate V. cholerae survival in the environment, enhancing their infectious potential and may contribute to the dissemination of epidemic V. cholerae strains. These results improve our understanding of the mechanisms of persistence and the modes of transmission of V. cholerae and may further apply to other opportunistic pathogens that have been shown to be released by protists in EFVs.

Eun-Sol Oh, J, Walsh, S & Zaslawski, C 2019, 'A snapshot of Chinese Medicine practice in Australia over a 10 year period (2006–2016): Moving towards integrative clinical care', Advances in Integrative Medicine, vol. 6, pp. S35-S35.
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Ewans, LJ, Colley, A, Gaston-Massuet, C, Gualtieri, A, Cowley, MJ, McCabe, MJ, Anand, D, Lachke, SA, Scietti, L, Forneris, F, Zhu, Y, Ying, K, Walsh, C, Kirk, EP, Miller, D, Giunta, C, Sillence, D, Dinger, M, Buckley, M & Roscioli, T 2019, 'Pathogenic variants in PLOD3 result in a Stickler syndrome-like connective tissue disorder with vascular complications', Journal of Medical Genetics, vol. 56, no. 9, pp. 629-638.
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BackgroundPathogenic PLOD3 variants cause a connective tissue disorder (CTD) that has been described rarely. We further characterise this CTD and propose a clinical diagnostic label to improve recognition and diagnosis of PLOD3-related disease.MethodsReported PLOD3 phenotypes were compared with known CTDs utilising data from three further individuals from a consanguineous family with a homozygous PLOD3 c.809C>T; p.(Pro270Leu) variant. PLOD3 mRNA expression in the developing embryo was analysed for tissue-specific localisation. Mouse microarray expression data were assessed for phylogenetic gene expression similarities across CTDs with overlapping clinical features.ResultsKey clinical features included ocular abnormalities with risk for retinal detachment, sensorineural hearing loss, reduced palmar creases, finger contractures, prominent knees, scoliosis, low bone mineral density, recognisable craniofacial dysmorphisms, developmental delay and risk for vascular dissection. Collated clinical features showed most overlap with Stickler syndrome with variable features of Ehlers-Danlos syndrome (EDS) and epidermolysis bullosa (EB). Human lysyl hydroxylase 3/PLOD3 expression was localised to the developing cochlea, eyes, skin, forelimbs, heart and cartilage, mirroring the clinical phenotype of this disorder.ConclusionThese data are consistent with pathogenic variants in PLOD3 resulting in a clinically distinct Stickler-like syndrome with vascular complications and variable features of EDS and EB. Early identification of PLOD3 variants would imp...

Facey, JA, Apte, SC & Mitrovic, SM 2019, 'A Review of the Effect of Trace Metals on Freshwater Cyanobacterial Growth and Toxin Production', Toxins, vol. 11, no. 11, pp. 643-643.
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Cyanobacterial blooms are becoming more common in freshwater systems, causing ecological degradation and human health risks through exposure to cyanotoxins. The role of phosphorus and nitrogen in cyanobacterial bloom formation is well documented and these are regularly the focus of management plans. There is also strong evidence that trace metals are required for a wide range of cellular processes, however their importance as a limiting factor of cyanobacterial growth in ecological systems is unclear. Furthermore, some studies have suggested a direct link between cyanotoxin production and some trace metals. This review synthesises current knowledge on the following: (1) the biochemical role of trace metals (particularly iron, cobalt, copper, manganese, molybdenum and zinc), (2) the growth limitation of cyanobacteria by trace metals, (3) the trace metal regulation of the phytoplankton community structure and (4) the role of trace metals in cyanotoxin production. Iron dominated the literature and regularly influenced bloom formation, with 15 of 18 studies indicating limitation or colimitation of cyanobacterial growth. A range of other trace metals were found to have a demonstrated capacity to limit cyanobacterial growth, and these metals require further study. The effect of trace metals on cyanotoxin production is equivocal and highly variable. Better understanding the role of trace metals in cyanobacterial growth and bloom formation is an essential component of freshwater management and a direction for future research.

Facey, JA, Steele, JR, Violi, JP, Mitrovic, SM & Cranfield, C 2019, 'An examination of microcystin-LR accumulation and toxicity using tethered bilayer lipid membranes (tBLMs)', Toxicon, vol. 158, pp. 51-56.
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Microcystin-LR (MC-LR) is a potent cyanobacterial toxin responsible for animal and human poisonings worldwide. MC-LR is found in organisms throughout the foodweb, however there is conjecture regarding whether it biomagnifies. Few studies have investigated how MC-LR interacts with lipid membranes, a determinant of biomagnification potential. We tested whether 1 μM MC-LR irreversibly associates with lipid bilayers or causes the creation of pore defects upon short and long-term exposure. Using tethered bilayer lipid membranes (tBLMs), we observed an increase in membrane conduction in tBLMs, representing an interaction of microcystin-LR with the lipid bilayer and a change in membrane packing properties. However, there were minimal changes in membrane capacitance upon short and long-term exposure, and MC-LR exhibited a rapid off-rate. Upon 24 h exposure to the toxin, no lipophilic multimeric complexes were detected capable of altering the toxin's off-rate. There was no evidence of the creation of new pores. This study demonstrates that MC-LR does not irreversibly imbed itself into lipids membranes after short or long-term exposure and suggests MC-LR does not biomagnify through the food web via lipid storage.

Faiz, A, Steiling, K, Roffel, MP, Postma, DS, Spira, A, Lenburg, ME, Borggrewe, M, Eijgenraam, TR, Jonker, MR, Koppelman, GH, Pouwels, SD, Liu, G, Alekseyev, YO, Lam, S, Hiemstra, PS, Sterk, PJ, Timens, W, Brandsma, C-A, Heijink, IH & van den Berge, M 2019, 'Effect of long-term corticosteroid treatment on microRNA and gene-expression profiles in COPD', European Respiratory Journal, vol. 53, no. 4, pp. 1801202-1801202.
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The aim was to investigate whether microRNA (miRNA) expression is modulated by inhaled corticosteroid (ICS) treatmentWe performed genome-wide miRNA analysis on bronchial biopsies of 69 moderate/severe chronic obstructive pulmonary disease (COPD) patients at baseline and after 6- and 30-month treatment with the ICS fluticasone propionate or placebo. The effect of ICS on miRNA expression was validated in differentiated primary bronchial epithelial cultures, and functional studies were conducted in BEAS-2B cells. MiRNAs affected by ICS and their predicted targets were compared to an independent miRNA dataset of bronchial brushings from COPD patients and healthy controls.Treatment with ICS for both 6 and 30 months significantly altered the expression of four miRNAs, including miR-320d, which was increased during ICS treatment compared with placebo. The ICS-induced increase of miR-320d was confirmed in primary airway epithelial cells. MiR-320d negatively correlated targets were enriched for pro-inflammatory genes and were increased in the bronchial brushes of patients with lower lung function in the independent dataset. Overexpression of miR-320d in BEAS-2B cells dampened cigarette smoke extract-induced pro-inflammatory activity via inhibition of nuclear factor-κB.Collectively, we identified miR-320d as a novel mediator of ICS, regulating the pro-inflammatory response of the airway epithelium.

Faiz, A, van den Berge, M, Vermeulen, CJ, ten Hacken, NHT, Guryev, V & Pouwels, SD 2019, 'AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers', Respiratory Research, vol. 20, no. 1.
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Cigarette smoking is one of the major risk factors for the development of chronic obstructive pulmonary disease (COPD). Evidence is accumulating that Receptor for Advanced Glycation-End products (RAGE)-signaling is a key pathway in the pathophysiology of COPD. To date, it is unknown how smoking affects RAGE expression. In the current study, we investigated the effect of smoking on AGER, the gene encoding RAGE, expression and on alternative splicing of AGER. To this end, we conducted RNA-Seq on bronchial biopsies for asymptomatic smokers (n = 36) and never smokers (n = 40). Total AGER gene expression was accessed using DESeq2, while alternative splicing was investigated by measuring the number of specific split reads spanning exon-exon junctions and the total split reads. One of the major isoforms of RAGE is endogenous soluble (es) RAGE, an anti-inflammatory decoy receptor, making up for approximately 10% of the total amount of soluble (s)RAGE. We found that smokers show decreased total gene expression of AGER in bronchial biopsies, while the relative abundance of the esRAGE isoform is increased. Furthermore, no difference in the serum levels of total sRAGE were observed between smokers and non-smokers. Our data indicates that smoking initiates a protective anti-inflammatory mechanism with decreased expression of the pro-inflammatory gene AGER and increased relative abundance of the anti-inflammatory isoform esRAGE.

Fan, X, McLaughlin, C, Robinson, C, Ravasini, J, Schelch, K, Johnson, T, Zandwijk, N, Reid, G & George, AM 2019, 'Zeolites ameliorate asbestos toxicity in a transgenic model of malignant mesothelioma', FASEB BioAdvances, vol. 1, no. 9, pp. 550-560.
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Fang, G, Lu, H, Law, A, Gallego-Ortega, D, Jin, D & Lin, G 2019, 'Gradient-sized control of tumor spheroids on a single chip', Lab on a Chip, vol. 19, no. 24, pp. 4093-4103.
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Gradient-sized spheroids can be simultaneously generated on a single chip using a liquid-dome method assisted by the surface tension. The facile method can be used for investigation of the size-dependent behaviors of spheroids in biomedical research.

Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Impacts of aluminum production: A cradle to gate investigation using life-cycle assessment', Science of The Total Environment, vol. 663, pp. 958-970.
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Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Life cycle analysis of copper-gold-lead-silver-zinc beneficiation process', Science of The Total Environment, vol. 659, pp. 41-52.
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Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Life cycle assessment of cobalt extraction process', Journal of Sustainable Mining, vol. 18, no. 3, pp. 150-161.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'A global life cycle assessment of manganese mining processes based on EcoInvent database', Science of The Total Environment, vol. 688, pp. 1102-1111.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'Impact analysis of gold silver refining processes through life-cycle assessment', Journal of Cleaner Production, vol. 228, pp. 867-881.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'Life-cycle assessment of solar integrated mining processes: A sustainable future', Journal of Cleaner Production, vol. 236, pp. 117610-117610.
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Farjana, SH, Huda, N, Parvez Mahmud, MA & Saidur, R 2019, 'A review on the impact of mining and mineral processing industries through life cycle assessment', Journal of Cleaner Production, vol. 231, pp. 1200-1217.
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Fergie, N, Todd, N, McClements, L, McAuley, D, O'Kane, C & Krasnodembskaya, A 2019, 'Hypercapnic acidosis induces mitochondrial dysfunction and impairs the ability of mesenchymal stem cells to promote distal lung epithelial repair', The FASEB Journal, vol. 33, no. 4, pp. 5585-5598.
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© The Author(s) Acute respiratory distress syndrome (ARDS) is a devastating disorder characterized by diffuse inflammation and edema formation. The main management strategy, low tidal volume ventilation, can be associated with the development of hypercapnic acidosis (HCA). Mesenchymal stem cells (MSCs) are a promising therapeutic candidate currently in early-phase clinical trials. The effects of HCA on the alveolar epithelium and capillary endothelium are not well established. The therapeutic efficacy of MSCs has never been reported in HCA. In the present study, we evaluated the effects of HCA on inflammatory response and reparative potential of the primary human small airway epithelial and lung microvasculature endothelial cells as well as on the capacity of bone marrow2derived MSCs to promote wound healing in vitro. We demonstrate that HCA attenuates the inflammatory response and reparative potential of primary human small airway epithelium and capillary endothelium and induces mitochondrial dysfunction. It was found that MSCs promote lung epithelial wound repair via the transfer of functional mitochondria; however, this proreparative effect of MSCs was lost in the setting of HCA. Therefore, HCA may adversely impact recovery from ARDS at the cellular level, whereas MSCs may not be therapeutically beneficial in patients with ARDS who develop HCA.

Ferreira, MA, Gamazon, ER, Al-Ejeh, F, Aittomäki, K, Andrulis, IL, Anton-Culver, H, Arason, A, Arndt, V, Aronson, KJ, Arun, BK, Asseryanis, E, Azzollini, J, Balmaña, J, Barnes, DR, Barrowdale, D, Beckmann, MW, Behrens, S, Benitez, J, Bermisheva, M, Białkowska, K, Blomqvist, C, Bogdanova, NV, Bojesen, SE, Bolla, MK, Borg, A, Brauch, H, Brenner, H, Broeks, A, Burwinkel, B, Caldés, T, Caligo, MA, Campa, D, Campbell, I, Canzian, F, Carter, J, Carter, BD, Castelao, JE, Chang-Claude, J, Chanock, SJ, Christiansen, H, Chung, WK, Claes, KBM, Clarke, CL, Adlard, J, Ahmed, M, Barwell, J, Brady, A, Brewer, C, Cook, J, Davidson, R, Donaldson, A, Eason, J, Eeles, R, Evans, DG, Gregory, H, Hanson, H, Henderson, A, Hodgson, S, Izatt, L, Kennedy, MJ, Lalloo, F, Miller, C, Morrison, PJ, Ong, K-R, Perkins, J, Porteous, ME, Rogers, MT, Side, LE, Snape, K, Walker, L, Harrington, PA, Arnold, N, Auber, B, Bogdanova-Markov, N, Borde, J, Caliebe, A, Ditsch, N, Dworniczak, B, Engert, S, Faust, U, Gehrig, A, Hahnen, E, Hauke, J, Hentschel, J, Herold, N, Honisch, E, Just, W, Kast, K, Larsen, M, Lemke, J, Nguyen, HP, Niederacher, D, Ott, C-E, Platzer, K, Pohl-Rescigno, E, Ramser, J, Rhiem, K, Steinemann, D, Sutter, C, Varon-Mateeva, R, Wang-Gohrke, S, Weber, BHF, Prieur, F, Pujol, P, Sagne, C, Sevenet, N, Sobol, H, Sokolowska, J, Stoppa-Lyonnet, D, Venat-Bouvet, L, Couch, FJ, Cox, A, Cross, SS, Czene, K, Daly, MB, de la Hoya, M, Dennis, J, Devilee, P, Diez, O, Dörk, T, Dunning, AM, Dwek, M, Eccles, DM, Ejlertsen, B, Ellberg, C, Engel, C, Eriksson, M, Fasching, PA, Fletcher, O, Flyger, H, Friedman, E, Frost, D, Gabrielson, M, Gago-Dominguez, M, Ganz, PA, Gapstur, SM, Garber, J, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Giles, GG, Glendon, G, Godwin, AK, Goldberg, MS, Goldgar, DE, González-Neira, A, Greene, MH, Gronwald, J, Guénel, P, Haiman, CA, Hall, P, Hamann, U, He, W, Heyworth, J, Hogervorst, FBL, Hollestelle, A, Hoover, RN, Hopper, JL, Hulick, PJ, Humphreys, K, Imyanitov, EN, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, SC, Marsh, D, Morey, A, Pathmanathan, N, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Heemskerk-Gerritsen, BAM, Rookus, MA, Seynaeve, CM, van der Baan, FH, van der Hout, AH, van der Kolk, LE, van der Luijt, RB, van Deurzen, CHM, van Doorn, HC, van Engelen, K, van Hest, L, van Os, TAM & et al. 2019, 'Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer', Nature Communications, vol. 10, no. 1, p. 1741.
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AbstractGenome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.

Figlioli, G, Bogliolo, M, Catucci, I, Caleca, L, Lasheras, SV, Pujol, R, Kiiski, JI, Muranen, TA, Barnes, DR, Dennis, J, Michailidou, K, Bolla, MK, Leslie, G, Aalfs, CM, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, CS, Marsh, D, Morey, A, Pathmanathan, N, Scott, R, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Zeps, N, Adank, MA, Adlard, J, Agata, S, Cadoo, K, Agnarsson, BA, Ahearn, T, Aittomäki, K, Ambrosone, CB, Andrews, L, Anton-Culver, H, Antonenkova, NN, Arndt, V, Arnold, N, Aronson, KJ, Arun, BK, Asseryanis, E, Auber, B, Auvinen, P, Azzollini, J, Balmaña, J, Barkardottir, RB, Barrowdale, D, Barwell, J, Beane Freeman, LE, Beauparlant, CJ, Beckmann, MW, Behrens, S, Benitez, J, Berger, R, Bermisheva, M, Blanco, AM, Blomqvist, C, Bogdanova, NV, Bojesen, A, Bojesen, SE, Bonanni, B, Borg, A, Brady, AF, Brauch, H, Brenner, H, Brüning, T, Burwinkel, B, Buys, SS, Caldés, T, Caliebe, A, Caligo, MA, Campa, D, Campbell, IG, Canzian, F, Castelao, JE, Chang-Claude, J, Chanock, SJ, Claes, KBM, Clarke, CL, Collavoli, A, Conner, TA, Cox, DG, Cybulski, C, Czene, K, Daly, MB, de la Hoya, M, Devilee, P, Diez, O, Ding, YC, Dite, GS, Ditsch, N, Domchek, SM, Dorfling, CM, dos-Santos-Silva, I, Durda, K, Dwek, M, Eccles, DM, Ekici, AB, Eliassen, AH, Ellberg, C, Eriksson, M, Evans, DG, Fasching, PA, Figueroa, J, Flyger, H, Foulkes, WD, Friebel, TM, Friedman, E, Gabrielson, M, Gaddam, P, Gago-Dominguez, M, Gao, C, Gapstur, SM, Garber, J, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Gayther, SA, Belotti, M, Bertrand, O, Birot, A-M, Buecher, B, Caputo, S, Dupré, A, Fourme, E, Gauthier-Villars, M, Golmard, L, Le Mentec, M, Moncoutier, V, de Pauw, A, Saule, C, Boutry-Kryza, N, Calender, A, Giraud, S, Léone, M, Bressac-de-Paillerets, B, Caron, O, Guillaud-Bataille, M, Bignon, Y-J, Uhrhammer, N, Bonadona, V, Lasset, C, Berthet, P, Castera, L, Vaur, D, Bourdon, V, Noguès, C, Noguchi, T, Popovici, C, Remenieras, A, Sobol, H, Coupier, I, Pujol, P, Adenis, C, Dumont, A, Révillion, F, Muller, D, Barouk-Simonet, E, Bonnet, F, Bubien, V, Longy, M, Sevenet, N, Gladieff, L, Guimbaud, R, Feillel, V, Toulas, C, Dreyfus, H, Leroux, CD, Peysselon, M, Rebischung, C, Legrand, C, Baurand, A, Bertolone, G, Coron, F, Faivre, L, Jacquot, C, Lizard, S, Kientz, C, Lebrun, M, Prieur, F, Fert-Ferrer, S, Mari, V, Vénat-Bouvet, L, Bézieau, S & et al. 2019, 'The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer', npj Breast Cancer, vol. 5, no. 1.
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AbstractBreast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM

Figueira, WF, Curley, B & Booth, DJ 2019, 'Can temperature-dependent predation rates regulate range expansion potential of tropical vagrant fishes?', Marine Biology, vol. 166, no. 6.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. The effect of temperature on predator–prey dynamics has the potential to be an important factor regulating ecological interactions and is becoming increasingly common due to climate-change-driven range shifts and species introductions. Here, we use mesocosm experiments to evaluate the thermal sensitivity of burst swimming (a proxy for prey escape ability) and mortality rates of cohorts of introduced tropical and resident temperate marine fishes in the presence of a local temperate predator. Increasing temperature (17–21–25 °C) resulted in a reduction in predation rates (by Hypoplectrodes maccullochi, family Serranidae) on the tropical prey species (Abudefduf vaigiensis, family Pomacentridae) which were more warm adapted, whereas predation rates on the temperate prey species (Atypichthys strigatus, family Kyphosidae) remained unchanged over the 17–21 °C range (25 °C not tested). These changes were linearly related to predator–prey burst swimming ratios, which decreased with increasing temperature for the tropical prey but remained largely unchanged for the temperate prey. By demonstrating the temperature sensitivity of predator–prey interactions, our work highlights the importance of linking physiology with ecology to understand the consequences of climate-driven range shifts and species introductions.

Filippini, G, Bugnot, AB, Johnston, EL, Ruszczyk, J, Potts, J, Scanes, P, Ferguson, A, Ostrowski, M, Varkey, D & Dafforn, KA 2019, 'Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)', Science of The Total Environment, vol. 693, pp. 133462-133462.
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© 2019 Elsevier B.V. Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur me...

Findlay, AD, Foot, JS, Buson, A, Deodhar, M, Jarnicki, AG, Hansbro, PM, Liu, G, Schilter, H, Turner, CI, Zhou, W & Jarolimek, W 2019, 'Identification and Optimization of Mechanism-Based Fluoroallylamine Inhibitors of Lysyl Oxidase-like 2/3', Journal of Medicinal Chemistry, vol. 62, no. 21, pp. 9874-9889.
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Copyright © 2019 American Chemical Society. Lysyl oxidase-like 2 (LOXL2) is a secreted enzyme that catalyzes the formation of cross-links in extracellular matrix proteins, namely, collagen and elastin, and is indicated in fibrotic diseases. Herein, we report the identification and subsequent optimization of a series of indole-based fluoroallylamine inhibitors of LOXL2. The result of this medicinal chemistry campaign is PXS-5120A (12k), a potent, irreversible inhibitor that is >300-fold selective for LOXL2 over LOX. PXS-5120A also shows potent inhibition of LOXL3, an emerging therapeutic target for lung fibrosis. Key to the development of this compound was the utilization of a compound oxidation assay. PXS-5120A was optimized to show negligible substrate activity in vitro for related amine oxidase family members, leading to metabolic stability. PXS-5120A, in a pro-drug form (PXS-5129A, 12o), displayed anti-fibrotic activity in models of liver and lung fibrosis, thus confirming LOXL2 as an important target in diseases where collagen cross-linking is implicated.

Fisher, A, Wangpraseurt, D, Larkum, AWD, Johnson, M, Kühl, M, Chen, M, Wong, HL & Burns, BP 2019, 'Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia', FEMS Microbiology Ecology, vol. 95, no. 1.
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© FEMS 2018. All rights reserved. Microbial mats and stromatolites are widespread in Hamelin Pool, Shark Bay, however the phototrophic capacity of these systems is unknown. This study has determined the optical properties and light-harvesting potential of these mats with light microsensors. These characteristics were linked via a combination of 16S rDNA sequencing, pigment analyses and hyperspectral imaging. Local scalar irradiance was elevated over the incident downwelling irradiance by 1.5-fold, suggesting light trapping and strong scattering by the mats. Visible light (400-700 nm) penetrated to a depth of 2 mm, whereas near-infrared light (700-800 nm) penetrated to at least 6 mm. Chlorophyll a and bacteriochlorophyll a (Bchl a) were found to be the dominant photosynthetic pigments present, with BChl a peaking at the subsurface (2-4 mm). Detailed 16S rDNA analyses revealed the presence of putative Chl f-containing Halomicronema sp. and photosynthetic members primarily decreased from the mat surface down to a depth of 6 mm. Data indicated high abundances of some pigments and phototrophic organisms in deeper layers of the mats (6-16 mm). It is proposed that the photosynthetic bacteria present in this system undergo unique adaptations to lower light conditions below the mat surface, and that phototrophic metabolisms are major contributors to ecosystem function.

Fleming, C, Gunawan, C, Golzan, M, Torpy, F, Irga, P & Mcgrath, K 2019, 'Investigating the effects of air pollutant nanoparticles on the onset or progression of Alzheimer's disease', IBRO Reports, vol. 6, pp. S329-S330.
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Fourment, M & Darling, AE 2019, 'Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics', PeerJ, vol. 7, no. 12, pp. e8272-e8272.
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Recent advances in statistical machine learning techniques have led to the creation of probabilistic programming frameworks. These frameworks enable probabilistic models to be rapidly prototyped and fit to data using scalable approximation methods such as variational inference. In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models. We show that many commonly used phylogenetic models including the general time reversible substitution model, rate heterogeneity among sites, and a range of coalescent models can be implemented using a probabilistic programming language. The posterior probability distributions obtained via the black box variational inference engine in Stan were compared to those obtained with reference implementations of Markov chain Monte Carlo (MCMC) for phylogenetic inference. We find that black box variational inference in Stan is less accurate than MCMC methods for phylogenetic models, but requires far less compute time. Finally, we evaluate a custom implementation of mean-field variational inference on the Jukes–Cantor substitution model and show that a specialized implementation of variational inference can be two orders of magnitude faster and more accurate than a general purpose probabilistic implementation.

Fritz, A, Hofmann, P, Majda, S, Dahms, E, Dröge, J, Fiedler, J, Lesker, TR, Belmann, P, DeMaere, MZ, Darling, AE, Sczyrba, A, Bremges, A & McHardy, AC 2019, 'CAMISIM: simulating metagenomes and microbial communities', Microbiome, vol. 7, no. 1.
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BACKGROUND:Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. RESULTS:We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. CONCLUSIONS:CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.

Fröch, JE, Hwang, Y, Kim, S, Aharonovich, I & Toth, M 2019, 'Photonic Nanostructures from Hexagonal Boron Nitride', Advanced Optical Materials, vol. 7, no. 4, pp. 1801344-1801344.
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AbstractGrowing interest in devices based on layered van der Waals (vdW) materials is motivating the development of new nanofabrication methods. Hexagonal boron nitride (hBN) is one of the most promising materials for studies of quantum photonics and phonon polaritonics. A promising nanofabrication process used to fabricate several hBN photonic devices using a hybrid reactive ion etching (RIE) and electron beam‐induced etching (EBIE) technique is reported in detail here. The shortcomings and benefits of RIE and EBIE are highlighted and the utility of the hybrid approach for the fabrication of suspended and supported device structures with nanoscale features and highly vertical sidewalls are demonstrated. Functionality of the fabricated devices is proven by measurements of high‐quality cavity optical modes (Q ≈ 1500). This nanofabrication approach constitutes an advance toward an integrated, monolithic quantum photonics platform based on hBN and other layered vdW materials.

Fröch, JE, Kim, S, Mendelson, N, Kianinia, M, Toth, M & Aharonovich, I 2019, 'Coupling hBN quantum emitters to 1D photonic crystal cavities', ACS nano, vol. 14, no. 6, pp. 7085-7091.
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Quantum photonics technologies require a scalable approach for integration ofnon-classical light sources with photonic resonators to achieve strong lightconfinement and enhancement of quantum light emission. Point defects fromhexagonal Boron Nitride (hBN) are amongst the front runners for single photonsources due to their ultra bright emission, however, coupling of hBN defects tophotonic crystal cavities has so far remained elusive. Here we demonstrateon-chip integration of hBN quantum emitters with photonic crystal cavities fromsilicon nitride (Si3N4) and achieve experimentally measured Q-factor of 3,300for hBN/Si3N4 hybrid cavities. We observed 9-fold photoluminescence enhancementof a hBN single photon emission at room temperature. Our work paves the waytowards hybrid integrated quantum photonics with hBN, and outlines an excellentpath for further development of cavity quantum electrodynamic experiments andon-chip integration of 2D materials.

Fronzi, M, Assadi, MHN & Hanaor, DAH 2019, 'Theoretical insights into the hydrophobicity of low index CeO2 surfaces', Applied Surface Science, vol. 478, pp. 68-74.
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© 2019 The hydrophobicity of CeO 2 surfaces is examined here. Since wettability measurements are extremely sensitive to experimental conditions, we propose a general approach to obtain contact angles between water and ceria surfaces of specified orientations based on density functional calculations. In particular, we analysed the low index surfaces of this oxide to establish their interactions with water. According to our calculations, the CeO 2 (111) surface was the most hydrophobic with a contact angle of Θ = 112.53° followed by (100) with Θ = 93.91°. The CeO 2 (110) surface was, on the other hand, mildly hydrophilic with Θ = 64.09°. By combining our calculations with an atomistic thermodynamic approach, we found that the O terminated (100) surface was unstable unless fully covered by molecularly adsorbed water. We also identified a strong attractive interaction between the hydrogen atoms in water molecules and surface oxygen, which gives rise to the hydrophilic behaviour of (110) surfaces. Interestingly, the adsorption of water molecules on the lower-energy (111) surface stabilises oxygen vacancies, which are expected to enhance the catalytic activity of this plane. The findings here shed light on the origin of the intrinsic wettability of rare earth oxides in general and CeO 2 surfaces in particular and also explain why CeO 2 (100) surface properties are so critically dependant on applied synthesis methods.

Fu, L, Chung, R & Shi, B 2019, 'Upconversion Nanoparticle-Based Strategy for Crossing the Blood-Brain Barrier to Treat the Central Nervous System Disease', pp. 263-282.
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Fu, S, Stove, C & Elliott, S 2019, 'Editorial: Advances in Analytical Methods for Drugs of Abuse Testing', Frontiers in Chemistry, vol. 7, pp. 589-589.
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Funari, R, Ripa, R, Söderström, B, Skoglund, U & Shen, AQ 2019, 'Detecting Gold Biomineralization by Delftia acidovorans Biofilms on a Quartz Crystal Microbalance', ACS Sensors, vol. 4, no. 11, pp. 3023-3033.
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© 2019 American Chemical Society. The extensive use of gold in sensing, diagnostics, and electronics has led to major concerns in solid waste management since gold and other heavy metals are nonbiodegradable and can easily accumulate in the environment. Moreover, gold ions are extremely reactive and potentially harmful for humans. Thus, there is an urgent need to develop reliable methodologies to detect and possibly neutralize ionic gold in aqueous solutions and industrial wastes. In this work, by using complementary measurement techniques such as quartz crystal microbalance (QCM), atomic force microscopy, crystal violet staining, and optical microscopy, we investigate a promising biologically induced gold biomineralization process accomplished by biofilms of bacterium Delftia acidovorans. When stressed by Au3+ ions, D. acidovorans is able to neutralize toxic soluble gold by excreting a nonribosomal peptide, which forms extracellular gold nanonuggets via complexation with metal ions. Specifically, QCM, a surface-sensitive transducer, is employed to quantify the production of these gold complexes directly on the D. acidovorans biofilm in real time. Detailed kinetics obtained by QCM captures the condition for maximized biomineralization yield and offers new insights underlying the biomineralization process. To the best of our knowledge, this is the first study providing an extensive characterization of the gold biomineralization process by a model bacterial biofilm. We also demonstrate QCM as a cheap, user-friendly sensing platform and alternative to standard analytical techniques for studies requiring high-resolution quantitative details, which offers promising opportunities in heavy-metal sensing, gold recovery, and industrial waste treatment.

Gan, W, Tserkezis, C, Cai, Q, Falin, A, Mateti, S, Nguyen, M, Aharonovich, I, Watanabe, K, Taniguchi, T, Huang, F, Song, L, Kong, L, Chen, Y & Li, LH 2019, 'Atomically Thin Boron Nitride as an Ideal Spacer for Metal-Enhanced Fluorescence', ACS Nano, vol. 13, no. 10, pp. 12184-12191.
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Metal-enhanced fluorescence (MEF) considerably enhances the luminescence for various applications, but its performance largely depends on the dielectric spacer between the fluorophore and plasmonic system. It is still challenging to produce a defect-free spacer having an optimized thickness with a sub-nanometer accuracy that enables reusability without affecting the enhancement. In this study, we demonstrate the use of atomically thin hexagonal boron nitride (BN) as an ideal MEF spacer owing to its multifold advantages over the traditional dielectric thin films. With rhodamine 6G as a representative fluorophore, it largely improves the enhancement factor (up to ∼95 ± 5), sensitivity (10-8 M), reproducibility, and reusability (∼90% of the plasmonic activity is retained after 30 cycles of heating at 350 °C in air) of MEF. This can be attributed to its two-dimensional structure, thickness control at the atomic level, defect-free quality, high affinities to aromatic fluorophores, good thermal stability, and excellent impermeability. The atomically thin BN spacers could increase the use of MEF in different fields and industries.

Ganesan, M, Trivedi, N, Gupta, V, Madhav, SV, Radhakrishna Reddy, C & Levine, IA 2019, 'Seaweed resources in India – current status of diversity and cultivation: prospects and challenges', Botanica Marina, vol. 62, no. 5, pp. 463-482.
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Abstract Seaweeds are an integral part of coastal ecosystems and offer invaluable ecosystem services supporting the life of many marine forms. The economic value of seaweeds significantly contributes to the sustainable development of rural coastal regions. Seaweeds are consumed as food in some Asian countries, but their utilization for production of phycocolloids is widespread across the globe, with an estimated value of more than one billion US$. In India, seaweeds have been utilized exclusively for the production of phycocolloids but recently they are used for the production of plant growth stimulants for agricultural applications. The domestic agar and alginate industry totally depends on the supplies from natural seaweed beds with some occasional imports. The recent success achieved in both upstream and downstream technologies in production and processing of seaweeds has boosted the prospects for commercialization of seaweed resources in the country. The present article briefly appraises the current status of Indian seaweed resources and their utilization, as well as developments in seaweed farming technologies, the status of seaweed industry and recent efforts to transform seaweed farming into a social enterprise. It also highlights the challenges encountered for mainstreaming these resources so as to evolve into a marine industry.

Gao, X, Feng, J, Su, D, Ma, Y, Wang, G, Ma, H & Zhang, J 2019, 'In-situ exfoliation of porous carbon nitride nanosheets for enhanced hydrogen evolution', Nano Energy, vol. 59, pp. 598-609.
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© 2019 Elsevier Ltd The development of water splitting technology is severely impeded by the limited strategies for preparing efficient photocatalyst with optimal structure. Herein, a facile structure and doping engineering strategy is proposed to obtain the atomic-thin mesoporous graphite carbon nitride (g-C 3 N 4 ) nanosheets with a large specific surface area of 212.5 m 2 g −1 , an ultra-large pore volume of 1.55 cm 3 g −1 , high C and O contents of ∼51.4 and 4.8% via an acid-assisted exfoliation route without any hard templates. The theoretical calculation reveals that the introduction of additional C/O atoms into g-C 3 N 4 matrix would boost the charge transfer rate and charge separation efficiency due to the enhanced electronic polarization effect (Bader Charge) and shortened bond lengths. Additionally, the electronic conductivity is demonstrated to be enhanced due to the formation of delocalized π-bonding both experimentally and theoretically. The synergic contribution of textural and electronic features renders an excellent photoelectrochemical (PEC) performance with 50–60 times larger photocurrent in comparison with the pristine g-C 3 N 4 and high hydrogen evolution rates of 830.1 and 115.5 μmol g −1 h −1 under the solar- and visible-light irradiation, respectively. This in-situ exfoliation approach demonstrates a facile yet efficient method to synthesize highly porous carbon nitride materials with optimal structure and composition for efficient water splitting.

Gao, X, Zhou, D, Chen, Y, Wu, W, Su, D, Li, B & Wang, G 2019, 'Strong charge polarization effect enabled by surface oxidized titanium nitride for lithium-sulfur batteries', Communications Chemistry, vol. 2, no. 1.
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AbstractThe commercialization of high-energy-density and low-cost lithium-sulfur batteries has been severely impeded by capacity fading and electrochemical polarization. Here we report a strategy to entrap polysulfides and boost the cathodic redox kinetics by embedding the surface oxidized quantum-dot-size TiN (TiN-O) within the highly ordered mesoporous carbon matrix. While the carbon scaffold offers sufficient electrical contact to the insulate sulfur, benefiting the full usage of sulfur and physical confinement of polysulfides. The surface oxygen renders TiN-O with a strong charge polarization effect for polysulfides via S-O-Ti bond as verified experimentally and theoretically. The suppressed shuttle effect and high lithium ion diffusion coefficient (7.9 × 10−8 cm2 s−1) lead to a high capacity of 1264 mA h g−1 at 0.2 C with a negligible capacity fading rate of 0.06% per cycle. Additionally, TiN-O based prototype soft-package cells also exhibit excellent cycling stability with flexibility, demonstrating their potential for practical applications.

Garcia, A, Lev, B, Hossain, KR, Gorman, A, Diaz, D, Pham, THN, Cornelius, F, Allen, TW & Clarke, RJ 2019, 'Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment', Journal of Biological Chemistry, vol. 294, no. 15, pp. 5956-5969.
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Cholesterol's effects on Na+,K+-ATPase reconstituted in phospholipid vesicles have been extensively studied. However, previous studies have reported both cholesterol-mediated stimulation and inhibition of Na+,K+-ATPase activity. Here, using partial reaction kinetics determined via stopped-flow experiments, we studied cholesterol's effect on Na+,K+-ATPase in a near-native environment in which purified membrane fragments were depleted of cholesterol with methyl-β-cyclodextrin (mβCD). The mβCD-treated Na+,K+-ATPase had significantly reduced overall activity and exhibited decreased observed rate constants for ATP phosphorylation (ENa3 + → E2P, i.e. phosphorylation by ATP and Na+ occlusion from the cytoplasm) and K+ deocclusion with subsequent intracellular Na+ binding (E2K2 + → E1Na3 +). However, cholesterol depletion did not affect the observed rate constant for K+ occlusion by phosphorylated Na+,K+-ATPase on the extracellular face and subsequent dephosphorylation (E2P → E2K2 +). Thus, partial reactions involving cation binding and release at the protein's intracellular side were most dependent on cholesterol. Fluorescence measurements with the probe eosin indicated that cholesterol depletion stabilizes the unphosphorylated E2 state relative to E1, and the cholesterol depletion-induced slowing of ATP phosphorylation kinetics was consistent with partial conversion of Na+,K+-ATPase into the E2 state, requiring a slow E2 → E1 transition before the phosphorylation. Molecular dynamics simulations of Na+,K+-ATPase in membranes with 40 mol % cholesterol revealed cholesterol interaction sites that differ markedly among protein conformations. They further indicated state-dependent effects on membrane shape, with the E2 state being likely disfavored in cholesterol-rich bilayers relative to the E1P state because of a greater hydrophobic mismatch. In summary, cholesterol extraction from membranes significantly decreases Na+,K+-ATPase steady-state activity.

Garcia, A, Zou, H, Hossain, KR, Xu, QH, Buda, A & Clarke, RJ 2019, 'Polar Interactions Play an Important Role in the Energetics of the Main Phase Transition of Phosphatidylcholine Membranes', ACS Omega, vol. 4, no. 1, pp. 518-527.
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© 2019 American Chemical Society. Conformational changes of membrane proteins are accompanied by deformation in the surrounding lipid bilayer. To gain insight into the energetics of membrane deformation, the phase behavior of dimyristoylphosphatidylcholine (DMPC) membranes in the presence of the dipole potential, d, modifiers was investigated by differential scanning calorimetry. 7-Ketocholesterol, which weakens d and reduces membrane-perpendicular dipole-dipole repulsion, causes a discrete second peak on the high-temperature side of the main transition, whereas 6-ketocholestanol, which strengthens d and increases membrane-perpendicular dipole-dipole repulsion, merely produces a shoulder. Measurements on pure DMPC vesicles showed that the observed temperature profile could not be explained by a single endothermic process, that is, breaking of van der Waals forces between hydrocarbon chains alone. Removal of NaCl from the buffer caused an increase in the main transition temperature and the appearance of an obvious shoulder, implicating polar interactions. Consideration of the phosphatidylcholine (PC) head group dipole moment indicates direct interactions between PC dipoles that are unlikely to account for the additional process. It seems more likely that the breaking of an in-plane hydrogen-bonded network consisting of hydrating water dipoles together with zwitterionic lipid head groups is responsible. The evidence presented supports the idea that the breaking of van der Waals forces between lipid tails required for the main phase transition of PC membranes is coupled to partial breaking of a hydrogen-bonded network at the membrane surface.

Gardner, SG, Camp, EF, Smith, DJ, Kahlke, T, Osman, EO, Gendron, G, Hume, BCC, Pogoreutz, C, Voolstra, CR & Suggett, DJ 2019, 'Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave', Ecology and Evolution, vol. 9, no. 3, pp. 938-956.
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AbstractRepeat marine heat wave‐induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral‐associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad‐scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2‐sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host‐specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching‐resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome commun...

Gassner, A-L, Manganelli, M, Werner, D, Rhumorbarbe, D, Maitre, M, Beavis, A, Roux, CP & Weyermann, C 2019, 'Secondary transfer of organic gunshot residues: Empirical data to assist the evaluation of three scenarios', Science & Justice, vol. 59, no. 1, pp. 58-66.
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© 2018 The Chartered Society of Forensic Sciences The present study aimed at providing data to assess the secondary transfer of organic gunshot residues (OGSR). Three scenarios were evaluated in controlled conditions, namely displacing a firearm from point A to point B, a simple handshake and an arrest involving handcuffing on the ground. Specimens were collected from the firearm, the hands of the shooter and the non-shooter undergoing the secondary transfer in order to compare the amounts detected. Secondary transfer was observed for the three scenarios, but to a different extent. It was found that displacing a firearm resulted in secondary transfer in <50% of the experiments. The firearm also had an influence, as contrary to the pistol, no secondary OGSR were detected using the revolver. Shaking the hand of the shooter also transferred OGSR to the non-shooter's hand. In that case, the amount of OGSR was generally higher on the shooter than on the non-shooter. Finally, the largest secondary transfer was observed after the arrest with handcuffing with positive results in all cases using the pistol. In that scenario, the amounts on the shooter and the non-shooter were in the same range. This study highlights that the secondary transfer must be taken into account in the interpretation of OGSR. Indeed, an individual's hands might be contaminated by handling a firearm or having physical contact with a shooter.

Gaw, S, Harford, A, Pettigrove, V, Sevicke‐Jones, G, Manning, T, Ataria, J, Cresswell, T, Dafforn, KA, Leusch, FDL, Moggridge, B, Cameron, M, Chapman, J, Coates, G, Colville, A, Death, C, Hageman, K, Hassell, K, Hoak, M, Gadd, J, Jolley, DF, Karami, A, Kotzakoulakis, K, Lim, R, McRae, N, Metzeling, L, Mooney, T, Myers, J, Pearson, A, Saaristo, M, Sharley, D, Stuthe, J, Sutherland, O, Thomas, O, Tremblay, L, Wood, W, Boxall, ABA, Rudd, MA & Brooks, BW 2019, 'Towards Sustainable Environmental Quality: Priority Research Questions for the Australasian Region of Oceania', Integrated Environmental Assessment and Management, vol. 15, no. 6, pp. 917-935.
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ABSTRACTEnvironmental challenges persist across the world, including the Australasian region of Oceania, where biodiversity hotspots and unique ecosystems such as the Great Barrier Reef are common. These systems are routinely affected by multiple stressors from anthropogenic activities, and increasingly influenced by global megatrends (e.g., the food–energy–water nexus, demographic transitions to cities) and climate change. Here we report priority research questions from the Global Horizon Scanning Project, which aimed to identify, prioritize, and advance environmental quality research needs from an Australasian perspective, within a global context. We employed a transparent and inclusive process of soliciting key questions from Australasian members of the Society of Environmental Toxicology and Chemistry. Following submission of 78 questions, 20 priority research questions were identified during an expert workshop in Nelson, New Zealand. These research questions covered a range of issues of global relevance, including research needed to more closely integrate ecotoxicology and ecology for the protection of ecosystems, increase flexibility for prioritizing chemical substances currently in commerce, understand the impacts of complex mixtures and multiple stressors, and define environmental quality and ecosystem integrity of temporary waters. Some questions have specific relevance to Australasia, particularly the uncertainties associated with using toxicity data from exotic species to protect unique indigenous species. Several related priority questions deal with the theme of how widely international ecotoxicological data and databases can be applied to regional ecosystems. Other timely questions, which focus on improving predictive chemistry and toxicology tools and techniques, will be important to answer several of the priority questions identified here. Another important question raised was how to protect local cultural...

Gemikonakli, G, Keay, KA, Kendig, MD, Kang, JWM, Corbit, LH & Mor, D 2019, 'Altered monoamine levels in the dorsal striatum of the rat are associated with alterations in behavioural selection and motivation following peripheral nerve injury and acute stress', European Journal of Neuroscience, vol. 50, no. 5, pp. 2786-2800.
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AbstractChronic neuropathic pain and psychological stress interact to compromise goal‐directed control over behaviour following mild psychological stress. The dorsomedial (DMS) and dorsolateral (DLS) striatum in the rat are crucial for the expression of goal‐directed and habitual behaviours, respectively. This study investigated whether changes in monoamine levels in the DMS and DLS following nerve injury and psychological stress reflect these behavioural differences. Neuropathic pain was induced by a chronic constriction injury (CCI) of the sciatic nerve in Sprague–Dawley rats. Acute stress was induced using a 15‐min restraint. Behavioural flexibility was assessed using the outcome devaluation paradigm. Noradrenaline, serotonin, dopamine and associated metabolites were measured bilaterally from the DLS and DMS. In uninjured rats, restraint increased dopaminergic markers in the left and serotonergic markers in the right of both the DMS and DLS, indicating a possible left hemisphere‐mediated dominance. CCI led to a slightly different lateralised effect, with a larger effect in the DMS than in the DLS. Individual differences in behavioural flexibility following Translational Neurodegeneration, vol. 8, no. 1, p. 30.
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Abstract Background A great body of evidence suggests that there are retinal functional and structural changes that occur in Alzheimer’s disease (AD). However, whether such changes are primary or secondary remains to be elucidated. We studied a range of retinal functional and structural parameters in association with AD- specific pathophysiological markers in the double transgenic APP/PS1 and control mice across age. Methods Electroretinogram (ERG) and optical coherence tomography (OCT) was performed in APP/PS1 and wild type (WT) control mice every 3 months from 3 to 12 months of age. For functional assessment, the a- and b-wave of the ERG, amplitude of oscillatory potentials (OP) and the positive scotopic threshold response (pSTR) were quantified at each time point. For structural assessment, the inner and outer retinal thickness was segmented and measured from OCT scans. Episodic memory was evaluated at 6, 9 and 12 months of age using the novel object recognition test. Amyloid beta (Aβ) distribution in the hippocampus and the retina were visualised at 3, 6 and 12 months of age. Inter- and intra- group analysis was performed to study rate of change for each parameter between the two groups. Results Inter-group analysis revealed a significant difference in b-wave and OPs of APP/PS1 compared to WT controls starting from 3 months (p < 0.001). There was also a significant difference in the amplitude of pSTR between the two groups starting from 6 months (p < 0.001). Furthermore, a significant difference in the inner retinal thickness, betwe...

Gerace, D, Martiniello-Wilks, R, Habib, R & Simpson, AM 2019, 'Luciferase-based reporting of suicide gene activity in murine mesenchymal stem cells', PLOS ONE, vol. 14, no. 7, pp. e0220013-e0220013.
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© 2019 Gerace 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. Due to their ease of isolation, gene modification and tumor-homing properties, mesenchymal stem cells (MSCs) are an attractive cellular vehicle for the delivery of toxic suicide genes to a variety of cancers in pre-clinical models. In addition, the incorporation of suicide genes in stem cell-derived cell replacement therapies improves their safety profile by permitting graft destruction in the event of unexpected tumorigeneses or unwanted differentiation. Due to the functional requirement of ATP for the Firefly luciferase gene Luc2 to produce light, luciferase-based reporting of cytotoxicity can be engineered into potential cell therapies. Consequently, we nucleofected mammalian expression plasmids containing both the Luc2 and the yeast fusion cytosine deaminase uracil phosphoribosyltransferase (CDUPRT) genes for expression in murine MSCs to assess luciferase as a reporter of suicide gene cytotoxicity, and MSC as vehicles of suicide gene therapy. In vitro bioluminescence imaging (BLI) showed that following the addition of the non-toxic prodrug fluorocytosine (5-FC), CDUPRT-expressing MSCs displayed enhanced cytotoxicity in comparison to Luc2 reporter MSC controls. This study demonstrates the utility of luciferase as a reporter of CDUPRT-mediated cytotoxicity in murine MSC using BLI.

Gerace, D, Martiniello-Wilks, R, Habib, R, Ren, B, Nassif, NT, O’Brien, BA & Simpson, AM 2019, 'Ex Vivo Expansion of Murine MSC Impairs Transcription Factor-Induced Differentiation into Pancreatic β-Cells', Stem Cells International, vol. 2019, pp. 1-15.
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Combinatorial gene and cell therapy as a means of generating surrogate β-cells has been investigated for the treatment of type 1 diabetes (T1D) for a number of years with varying success. One of the limitations of current cell therapies for T1D is the inability to generate sufficient quantities of functional transplantable insulin-producing cells. Due to their impressive immunomodulatory properties, in addition to their ease of expansion and genetic modification ex vivo, mesenchymal stem cells (MSCs) are an attractive alternative source of adult stem cells for regenerative medicine. To overcome the aforementioned limitation of current therapies, we assessed the utility of ex vivo expanded bone marrow-derived murine MSCs for their persistence in immune-competent and immune-deficient animal models and their ability to differentiate into surrogate β-cells. CD45-/Ly6+ murine MSCs were isolated from the bone marrow of nonobese diabetic (NOD) mice and nucleofected to express the bioluminescent protein, Firefly luciferase (Luc2). The persistence of a subcutaneous (s.c.) transplant of Luc2-expressing MSCs was assessed in immune-competent (NOD) (n=4) and immune-deficient (NOD/Scid) (n=4) animal models of diabetes. Luc2-expressing MSCs persisted for 2 and 12 weeks, respectively, in NOD and NOD/Scid mice. Ex vivo expanded MSCs were transduced with the HMD lentiviral vector (MOI = 10) to express furin-...

Gharib, DH, Lock, P, Moulton, SE, Malherbe, F & Langford, SJ 2019, 'Molecular Design of Core Substituted Naphthalene Diimides for the Exfoliation of Graphite to Graphene in Chloroform', ChemNanoMat, vol. 5, no. 10, pp. 1303-1310.
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AbstractA significant challenge of liquid phase exfoliation (LPE) of graphite to yield graphene resides in the fact that most conventional solvents used are high boiling points and thus extremely difficult to eliminate, especially during processing of graphene into composites or films. Here, we advance the ability to produce high yield graphene in a low boiling point organic solvent, chloroform, using core‐substituted naphthalene diimides (cNDIs). Through the use of cNDIs it is possible to obtain high graphene concentrations of up to 0.13 mg/mL in chloroform. This yield represents a 69% improvement from graphene yields previously obtained in chloroform using unsubstituted NDIs. Characterisation of the products by UV‐Vis, X‐ray diffraction (XRD), Transmission electron microscopy (TEM), Raman spectroscopy and X‐ray photoelectron spectroscopy (XPS) support the use of cNDIs as an appropriate exfoliating agent in chloroform.

Ghazilou, A, Shokri, MR & Gladstone, W 2019, 'Comparison of baited remote underwater video (BRUV) and underwater visual census (UVC) for assessment of reef fish in a marginal reef in the Northern Persian gulf', Iranian Journal of Ichthyology, vol. 6, no. 3, pp. 197-207.
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Underwater Visual Census (UVC) and Baited Remote Underwater Video (BRUV) are broadly used methods to study fish assemblages in marine and estuarine environments. This study compared the results of BRUV and UVC methods for assessing seasonal trends in coral reef fish assemblages in a marginal reef in the northern Persian Gulf. In doing so, seasonal surveys of coral reef fishes were done using BRUV and UVC methods. Comparison of assemblage metrics driven from each method indicated that both methods may reveal similar patterns of seasonal changes in fish and trophic group assemblages while there may be between-method differences in species richness, total abundance, and trophic group abundances. The observed differences may be related to the longer sampling times of BRUV.

Giannopoulos, S, Samardzic, K, Raymond, BBA, Djordjevic, SP & Rodgers, KJ 2019, 'L-DOPA causes mitochondrial dysfunction in vitro: A novel mechanism of L-DOPA toxicity uncovered', The International Journal of Biochemistry & Cell Biology, vol. 117, pp. 105624-105624.
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In Parkinson's disease (PD), as in many other neurodegenerative disorders, mitochondrial dysfunction, protein misfolding, and proteotoxic stress underly the disease process. For decades, the primary symptomatic treatment for PD has been the dopamine precursor L-DOPA (Levodopa). L-DOPA however can initiate protein misfolding through its ability to mimic the protein amino acid L-tyrosine, resulting in random errors in aminoacylation and L-DOPA becoming mistakenly inserted into the polypeptide chain of proteins in place of L-tyrosine. In the present study we examined the impact that the generation of DOPA-containing proteins had on human neuroblastoma cell (SH-SY5Y) function in vitro. We showed that even in the presence of antioxidants there was a significant accumulation of cytosolic ubiquitin in DOPA-treated cells, an upregulation in the endosomal-lysosomal degradation system, deleterious changes to mitochondrial morphology and a marked decline in mitochondrial function.The effects of L-DOPA on mitochondrial function were not observed with D-DOPA, the stereoisomer of L-DOPA that cannot be inserted into proteins so did not result from oxidative stress. We could fully protect against these effects by co-treatment with L-tyrosine, supporting the view that misincorporation of L-DOPA into proteins contributed to these cytotoxic effects, leading us to suggest that co-treatment with L-tyrosine could be beneficial therapeutically.

Gibb, BC & Gale, PA 2019, '2019 Sessler Early Career Researcher Prize', Supramolecular Chemistry, vol. 31, no. 9, pp. 607-607.
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Gill, AJ, Lim, G, Cheung, VKY, Andrici, J, Perry-Keene, JL, Paik, J, Sioson, L, Clarkson, A, Sheen, A, Luxford, C, Elston, MS, Meyer-Rochow, GY, Nano, MT, Kruijff, S, Engelsman, AF, Sywak, M, Sidhu, SB, Delbridge, LW, Robinson, BG, Marsh, DJ, Toon, CW, Chou, A & Clifton-Bligh, RJ 2019, 'Parafibromin-deficient (HPT-JT Type, CDC73 Mutated) Parathyroid Tumors Demonstrate Distinctive Morphologic Features', American Journal of Surgical Pathology, vol. 43, no. 1, pp. 35-46.
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The gene CDC73 (previously known as HRPT2) encodes the protein parafibromin. Biallelic mutation of CDC73 is strongly associated with malignancy in parathyroid tumors. Heterozygous germline mutations cause hyperparathyroidism jaw tumor syndrome,which is associated with a high life-time risk of parathyroid carcinoma. Therefore loss of parafibromin expression by immunohistochemistry may triage genetic testing for hyperparathyroidism jaw tumor syndrome and be associated with malignant behavior in atypical parathyroid tumors. We share our experience that parafibromin-negative parathyroid tumors show distinctive morphology. We searched our institutional database for parathyroid tumors demonstrating complete loss of nuclear expression of parafibromin with internal positive controls. Forty-three parafibromin-negative tumors from 40 (5.1%) of 789 patients undergoing immunohistochemistry were identified. Thirty-three (77%) were external consultation cases; the estimated incidence in unselected tumors was 0.19%. Sixteen (37.2%) fulfilled World Health Organization 2017 criteria for parathyroid carcinoma and 63% had serum calcium greater than 3mmol/L. One of 27 (3.7%) noninvasive but parafibromin-negative tumors subsequently metastasized. Parafibromin-negative patients were younger (mean, 36 vs. 63 y; P<0.001) and had larger tumors (mean, 3.04 vs. 0.62 g; P<0.001). Not all patients had full testing, but 26 patients had pathogenic CDC73 mutation/deletions confirmed in tumor (n=23) and/or germline (n=16). Parafibromin-negative tumors demonstrated distinctive morphology including extensive sheet-like rather than acinar growth, eosinophilic cytoplasm, nuclear enlargement with distinctive coarse chromatin, perinuclear cyt...

Gissibl, A, Care, A, Sun, A, Hobba, G, Nevalainen, H & Sunna, A 2019, 'Development of screening strategies for the identification of paramylon-degrading enzymes', Journal of Industrial Microbiology and Biotechnology, vol. 46, no. 6, pp. 769-781.
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Abstract Enzymatic degradation of the β-1,3-glucan paramylon could enable the production of bioactive compounds for healthcare and renewable substrates for biofuels. However, few enzymes have been found to degrade paramylon efficiently and their enzymatic mechanisms remain poorly understood. Thus, the aim of this work was to find paramylon-degrading enzymes and ways to facilitate their identification. Towards this end, a Euglena gracilis-derived cDNA expression library was generated and introduced into Escherichia coli. A flow cytometry-based screening assay was developed to identify E. gracilis enzymes that could hydrolyse the fluorogenic substrate fluorescein di-β-d-glucopyranoside in combination with time-saving auto-induction medium. In parallel, four amino acid sequences of potential E. gracilis β-1,3-glucanases were identified from proteomic data. The open reading frame encoding one of these candidate sequences (light_m.20624) was heterologously expressed in E. coli. Finally, a Congo Red dye plate assay was developed for the screening of enzyme preparations potentially able to degrade paramylon. This assay was validated with enzymes assumed to have paramylon-degrading activity and then used to identify four commercial preparations with previously unknown paramylon degradation ability.

Gissibl, A, Sun, A, Care, A, Nevalainen, H & Sunna, A 2019, 'Bioproducts From Euglena gracilis: Synthesis and Applications', Frontiers in Bioengineering and Biotechnology, vol. 7, no. MAY, p. 108.
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In recent years, the versatile phototrophic protist Euglena gracilis has emerged as an interesting candidate for application-driven research and commercialisation, as it is an excellent source of dietary protein, pro(vitamins), lipids, and the β-1,3-glucan paramylon only found in euglenoids. From these, paramylon is already marketed as an immunostimulatory agent in nutraceuticals. Bioproducts from E. gracilis can be produced under various cultivation conditions discussed in this review, and their yields are relatively high when compared with those achieved in microalgal systems. Future challenges include achieving the economy of large-scale cultivation. Recent insights into the complex metabolism of E. gracilis have highlighted unique metabolic pathways, which could provide new leads for product enhancement by genetic modification of the organism. Also, development of molecular tools for strain improvement are emerging rapidly, making E. gracilis a noteworthy challenger for microalgae such as Chlorella spp. and their products currently on the market.

Gleason, FH, Larkum, AWD, Raven, JA, Manohar, CS & Lilje, O 2019, 'Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments', Fungal Ecology, vol. 39, pp. 380-387.
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© 2018 Rhodopsin transmembrane proton pumps (fuelled by visible light which is absorbed by retinal (carotenoid) chromophores) exist in all three domains of living species and in all groups of true fungi studied. Light driven proton and sodium pumps are likely to be essential for some marine fungi, especially hypersaline tolerant and endolithic species. Rhodopsin macromolecular machines, using visible light, drive metabolic reactions in addition to those provided by aerobic respiration, providing extra energy needed for the maintenance and growth of fungi, especially in euphotic environments where oxygen concentration is limited. In addition, dissimilatory nitrate and metal oxide reduction can provide sources of energy for fungi in the absence of oxygen, for example, in fungal species growing in marine sediments. Finally, the oxidation of elemental sulphur, iron and manganese can be a source of energy. Some fungi are, therefore, lithotrophs and photoheterotrophs. The ecological implications of these latter processes are discussed.

GOH, CJ, PARK, D, LEE, JS, DAVEY, PA, PERNICE, M, RALPH, PJ & HAHN, Y 2019, 'Zostera virus T – a novel virus of the genus Tepovirus identified in the eelgrass, Zostera muelleri', Acta virologica, vol. 63, no. 04, pp. 366-372.
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Analysis of a transcriptome dataset obtained from tissue samples of the eelgrass Zostera muelleri, an aquatic flowering plant species of the family Zosteraceae, yielded three genome sequence contigs of a novel RNA virus. Sequence comparison and phylogenetic analysis revealed that the novel RNA virus, named Zostera virus T (ZoVT), belongs to the genus Tepovirus of the family Betaflexiviridae. The three genome contigs of ZoVT showed 88.2‒97.2% nucleotide sequence identity to each other, indicating that they descended from a common ancestor. The ZoVT genome contains three open reading frames (ORFs): ORF1 encodes a 1816 amino acid (aa) replicase (REP) with RNA-dependent RNA polymerase (RdRp) activity; ORF2, a 398 aa movement protein (MP); and ORF3, a 240 aa coat protein (CP). The phylogenetic analysis using REP sequences of ZoVT and other Betaflexiviridae viruses showed that Prunus virus T is the closest known virus to ZoVT, whereas potato virus T, the type species of the genus Tepovirus, is the second closest virus. Genome sequences of ZoVT, which is the third tepovirus species identified to date, may be useful for investigating the evolution and molecular biology of tepoviruses. Keywords: Zostera virus T; Tepovirus; Betaflexiviridae; eelgrass; Zostera muelleri.

González de Vega, R, Clases, D, Fernández-Sánchez, ML, Eiró, N, González, LO, Vizoso, FJ, Doble, PA & Sanz-Medel, A 2019, 'MMP-11 as a biomarker for metastatic breast cancer by immunohistochemical-assisted imaging mass spectrometry', Analytical and Bioanalytical Chemistry, vol. 411, no. 3, pp. 639-646.
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© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. MMP-11 is a member of the matrix metalloproteinase family (MMPs) which are overexpressed in cancer cells, stromal cells and the adjacent microenvironment. The MMP protein family encompasses zinc-dependent endopeptidases that degrade the extracellular matrix (ECM), facilitating the breakdown of the basal membrane and matrix connective tissues. This function is believed to be important in cancer development and metastasis. This paper investigated a gold nanoparticle-based immunohistochemical assay to visualise the distribution of MMP-11 in human breast cancer tissues from eight patients with and without metastases by employing laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The expression of MMP-11 was increased and more heterogeneous in metastatic specimens compared to non-metastatic tumour samples. These findings demonstrate that imaging breast tumours by LA-ICP-MS may be a useful tool to aid the prognosis and treatment of breast cancer. As an example, samples of two patients are presented who were diagnosed with matching characteristics and grades of breast cancer. Although both patients had a similar prognosis and treatment, only one developed metastases.

Gonzalez-Bayon, R, Shen, Y, Groszmann, M, Zhu, A, Wang, A, Allu, AD, Dennis, ES, Peacock, WJ & Greaves, IK 2019, 'Senescence and Defense Pathways Contribute to Heterosis', Plant Physiology, vol. 180, no. 1, pp. 240-252.
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Abstract Hybrids are used extensively in agriculture due to their superior performance in seed yield and plant growth, yet the molecular mechanisms underpinning hybrid performance are not well understood. Recent evidence has suggested that a decrease in basal defense response gene expression regulated by reduced levels of salicylic acid (SA) may be important for vigor in certain hybrid combinations. Decreasing levels of SA in the Arabidopsis (Arabidopsis thaliana) accession C24 through the introduction of the SA catabolic enzyme salicylate1 hydroxylase (NahG) increases plant size, phenocopying the large-sized C24/Landsberg erecta (Ler) F1 hybrids. C24♀ × Ler♂ F1 hybrids and C24 NahG lines shared differentially expressed genes and pathways associated with plant defense and leaf senescence including decreased expression of SA biosynthetic genes and SA response genes. The expression of TL1 BINDING TRANSCRIPTION FACTOR1, a key regulator in resource allocation between growth and defense, was decreased in both the F1 hybrid and the C24 NahG lines, which may promote growth. Both C24 NahG lines and the F1 hybrids showed decreased expression of the key senescence-associated transcription factors WRKY53, NAC-CONTAINING PROTEIN29, and ORESARA1 with a delayed onset of senescence compared to C24 plants. The delay in senescence resulted in an extension of the photosynthetic period in the leaves of F1 hybrids compared to the parental lines, potentially allowing each leaf to contribute more resources toward growth.

Gottscholl, A, Kianinia, M, Soltamov, V, Bradac, C, Kasper, C, Krambrock, K, Sperlich, A, Toth, M, Aharonovich, I & Dyakonov, V 2019, 'Room Temperature Initialisation and Readout of Intrinsic Spin Defects in a Van der Waals Crystal', Nature Materials (2020), vol. 19, no. 5, pp. 540-545.
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Optically addressable spins in widebandgap semiconductors have become one ofthe most prominent platforms for exploring fundamental quantum phenomena. Whileseveral candidates in 3D crystals including diamond and silicon carbide havebeen extensively studied, the identification of spindependent processes inatomically thin 2D materials has remained elusive. Although opticallyaccessible spin states in hBN are theoretically predicted, they have not yetbeen observed experimentally. Here, employing rigorous electron paramagneticresonance techniques and photoluminescence spectroscopy, we identifyfluorescence lines in hexagonal boron nitride associated with a particulardefect, the negatively charged boron vacancy and determine the parameters ofits spin Hamiltonian. We show that the defect has a triplet ground state with azero field splitting of 3.5 GHz and establish that the centre exhibitsoptically detected magnetic resonance at room temperature. We also demonstratethe spin polarization of this centre under optical pumping, which leads tooptically induced population inversion of the spin ground state a prerequisitefor coherent spin manipulation schemes. Our results constitute a leap forwardin establishing two dimensional hBN as a prime platform for scalable quantumtechnologies, with extended potential for spin based quantum information andsensing applications, as our ODMR studies on hBN NV diamonds hybrid structuresshow.

Gough, R, Ellis, J & Stark, D 2019, 'Comparison and Recommendations for Use of Dientamoeba fragilis Real-Time PCR Assays', Journal of Clinical Microbiology, vol. 57, no. 5.
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Dientamoeba fragilis is a gastrointestinal trichomonad parasite whose pathogenicity is yet to be determined. The difficulty involved in microscopically diagnosing D. fragilis in feces led to the development of real-time PCR methodologies for the detection of D. fragilis in stool samples.

Gow, I, Millar, D, Ellis, J, Melki, J & Stark, D 2019, 'Semi-Quantitative, Duplexed qPCR Assay for the Detection of Leishmania spp. Using Bisulphite Conversion Technology', Tropical Medicine and Infectious Disease, vol. 4, no. 4, pp. 135-135.
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Leishmaniasis is caused by the flagellated protozoan Leishmania, and is a neglected tropical disease (NTD), as defined by the World Health Organisation (WHO). Bisulphite conversion technology converts all genomic material to a simplified form during the lysis step of the nucleic acid extraction process, and increases the efficiency of multiplex quantitative polymerase chain reaction (qPCR) reactions. Through utilization of qPCR real-time probes, in conjunction with bisulphite conversion, a new duplex assay targeting the 18S rDNA gene region was designed to detect all Leishmania species. The assay was validated against previously extracted DNA, from seven quantitated DNA and cell standards for pan-Leishmania analytical sensitivity data, and 67 cutaneous clinical samples for cutaneous clinical sensitivity data. Specificity was evaluated by testing 76 negative clinical samples and 43 bacterial, viral, protozoan and fungal species. The assay was also trialed in a side-by-side experiment against a conventional PCR (cPCR), based on the Internal transcribed spacer region 1 (ITS1 region). Ninety-seven percent of specimens from patients that previously tested positive for Leishmania were positive for Leishmania spp. with the bisulphite conversion assay, and a limit of detection (LOD) of 10 copies per PCR was achieved, while the LOD of the ITS1 methodology was 10 cells/1000 genomic copies per PCR. This method of rapid, accurate and simple detection of Leishmania can lead to improved diagnosis, treatment and public health outcomes.

Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunensse, T, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 815-830.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. High-latitude coral communities are distinct from their tropical counterparts, and how they respond to recent heat wave events that have decimated tropical reefs remains unknown. In Australia, the 2016 El Niño resulted in the largest global mass coral bleaching event to date, reaching as far south as Sydney Harbour (~ 34°S). Coral bleaching was observed for the first time (affecting ca., 60% of all corals) as sea surface temperatures in Sydney Harbour remained > 2 °C above the long-term mean summer maxima, enabling us to examine whether high-latitude corals bleached in a manner described for tropical corals. Responses of the geographically cosmopolitan Plesiastrea versipora and southerly restricted Coscinaraea mcneilli were contrasted across two harbour sites, both in situ and among samples-maintained ex situ in aquaria continually supplied with Sydney Harbour seawater. While both coral taxa hosted the same species of microalgal endosymbiont (Breviolum spp; formerly clade B), only P. versipora bleached both in situ and ex situ via pronounced losses of endosymbiont cells. Both species displayed very different metabolic responses (growth, photosynthesis, respiration and calcification) and bleaching susceptibilities under elevated temperatures. Bacterial microbiome profiling, however, revealed a convergence of bacterial community composition across coral species throughout the bleaching. Corals species found in temperate regions, including the generalist P. versipora, will therefore likely be highly susceptible to future change as heat waves grow in frequency and severity unless their thermal thresholds increase. Our observations provide further evidence that high-latitude systems are susceptible to community reorganisation under climate change.

Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunesse, TC, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Correction to: Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 877-877.
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Gramaglia, I, Velez, J, Chang, Y-S, Caparros-Wanderley, W, Combes, V, Grau, G, Stins, MF & van der Heyde, HC 2019, 'Citrulline protects mice from experimental cerebral malaria by ameliorating hypoargininemia, urea cycle changes and vascular leak', PLOS ONE, vol. 14, no. 3, pp. e0213428-e0213428.
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© 2019 Gramaglia 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. Clinical and model studies indicate that low nitric oxide (NO) bioavailability due in part to profound hypoargininemia contributes to cerebral malaria (CM) pathogenesis. Protection against CM pathogenesis may be achieved by altering the diet before infection with Plasmodium falcIParum infection (nutraceutical) or by administering adjunctive therapy that decreases CM mortality (adjunctive therapy). This hypothesis was tested by administering citrulline or arginine in experimental CM (eCM). We report that citrulline injected as prophylaxis immediately post infection (PI) protected virtually all mice by ameliorating (i) hypoargininemia, (ii) urea cycle impairment, and (iii) disruption of blood brain barrier. Citrulline prophylaxis inhibited plasma arginase activity. Parasitemia was similar in citrulline- And vehicle control-groups, indicating that protection from pathogenesis was not due to decreased parasitemia. Both citrulline and arginine administered from day 1 PI in the drinking water significantly protected mice from eCM. These observations collectively indicate that increasing dietary citrulline or arginine decreases eCM mortality. Citrulline injected IP on day 4 PI with quinine-injected IP on day 6 PI partially protected mice from eCM; citrulline plus scavenging of superoxide with pegylated superoxide dismutase and pegylated catalase protected all recIPients from eCM. These findings indicate that ameliorating hypoargininemia with citrulline plus superoxide scavenging decreases eCM mortality.

Gray, CM, Carroll, RJ, Lentjes, MAH & Keogh, RH 2019, 'Correcting for measurement error in fractional polynomial models using Bayesian modelling and regression calibration, with an application to alcohol and mortality', Biometrical Journal, vol. 61, no. 3, pp. 558-573.
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AbstractExposure measurement error can result in a biased estimate of the association between an exposure and outcome. When the exposure–outcome relationship is linear on the appropriate scale (e.g. linear, logistic) and the measurement error is classical, that is the result of random noise, the result is attenuation of the effect. When the relationship is non‐linear, measurement error distorts the true shape of the association. Regression calibration is a commonly used method for correcting for measurement error, in which each individual's unknown true exposure in the outcome regression model is replaced by its expectation conditional on the error‐prone measure and any fully measured covariates. Regression calibration is simple to execute when the exposure is untransformed in the linear predictor of the outcome regression model, but less straightforward when non‐linear transformations of the exposure are used. We describe a method for applying regression calibration in models in which a non‐linear association is modelled by transforming the exposure using a fractional polynomial model. It is shown that taking a Bayesian estimation approach is advantageous. By use of Markov chain Monte Carlo algorithms, one can sample from the distribution of the true exposure for each individual. Transformations of the sampled values can then be performed directly and used to find the expectation of the transformed exposure required for regression calibration. A simulation study shows that the proposed approach performs well. We apply the method to investigate the relationship between usual alcohol intake and subsequent all‐cause mortality using an error model that adjusts for the episodic nature of alcohol consumption.

Gray, R, Jones, HA, Hitchcock, JN, Hardwick, L, Pepper, D, Lugg, A, Seymour, JR & Mitrovic, SM 2019, 'Mitigation of cold‐water thermal pollution downstream of a large dam with the use of a novel thermal curtain', River Research and Applications, vol. 35, no. 7, pp. 855-866.
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AbstractHypolimnial releases from dams during periods of thermal stratification modify the downstream riverine thermal regime by decreasing water temperature and reducing natural diel thermal variability. This cold‐water thermal pollution in rivers can persist for hundreds of kilometres downstream of dams and impact important ecological processes such as fish spawning. To mitigate this problem, a first‐of‐its‐kind thermal curtain was fitted to the large bottom release Burrendong Dam on the Macquarie River, Australia. The thermal curtain acts by directing warmer, near‐surface epilimnial water to the low‐level hypolimnial offtake. This study aimed to test the efficacy of the thermal curtain by measuring temperatures before and after the curtains installation, quantifying the magnitude and extent of cold‐water thermal pollution along the Macquarie River downstream of Burrendong Dam. Epilimnial releases with use of the curtain increased diel temperature ranges and the mean monthly water temperature below the dam. Epilimnial releases with use of the curtain increased diel temperature ranges from 0.9°C to 2.5°C and reduced the difference between the mean monthly water temperature of an upstream control and a downstream site by up to 3.5°C. A comparison of the monthly temperature means along the river, indicated that thermal recovery, whereby temperatures returned to within the natural range of upstream temperatures occurred 45 km downstream of the dam during summer when the thermal curtain was deployed, compared with approximately 200 km prior to deployment of the curtain. Our study suggests that the use of thermal curtains can reduce cold‐water thermal pollution and improve ecological outcomes for river ecosystems downstream of dams.

Green, TJ, Siboni, N, King, WL, Labbate, M, Seymour, JR & Raftos, D 2019, 'Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event', Microbial Ecology, vol. 77, no. 3, pp. 736-747.
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.

Gu, Y, Guo, Z, Yuan, W, Kong, M, Liu, Y, Liu, Y, Gao, Y, Feng, W, Wang, F, Zhou, J, Jin, D & Li, F 2019, 'High-sensitivity imaging of time-domain near-infrared light transducer', Nature Photonics, vol. 13, no. 8, pp. 525-531.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. The optically transparent biological window in the near-infrared (NIR) spectral range allows deep-tissue excitation and the detection of fluorescence signals1,2. Spectrum-domain discrimination of NIR contrast agents via an upconversion or downshifting scheme requires sufficient (anti-) Stokes shift to separate excitation and fluorescence emission. Here, we report a time-domain (τ) scheme in which about 5,000 ytterbium signal transducers are condensed within an optically inert and biocompatible CaF2 shell (2.3 nm), which forms a 14.5 nm τ-dot. Because of the long-lived and spectrally narrowly defined excited state of pure ytterbium ions, the NIR τ-dot can convert the NIR pulsed excitation into long-decaying luminescence with an efficiency approaching 100%. Within a safe injection dosage of 13 μg g−1, an excitation power density of 1.1 mW cm−2 was sufficient to image organs with a signal-to-noise ratio of >9. The high brightness of τ-dots further allows long-term in vivo passive targeting and dynamic tracking in a tumour-bearing mouse model.

Gu, Y, Guo, Z, Yuan, W, Kong, M, Liu, Y, Liu, Y, Gao, Y, Feng, W, Wang, F, Zhou, J, Jin, D & Li, F 2019, 'Publisher Correction: High-sensitivity imaging of time-domain near-infrared light transducer', Nature Photonics, vol. 13, no. 8, pp. 580-580.
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Gulzar, A, Xu, J, Wang, C, He, F, Yang, D, Gai, S, Yang, P, Lin, J, Jin, D & Xing, B 2019, 'Tumour microenvironment responsive nanoconstructs for cancer theranostic', Nano Today, vol. 26, pp. 16-56.
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© 2019 Elsevier Ltd The tumour mass is made up of not only of a heterogeneous population of cancer cells nonetheless also a mixture of resident as well as the infiltrating host cells, secreted factors besides extracellular matrix proteins, together recognized as the tumour microenvironment (TME). Tumour development is overwhelmingly affected through the dealings of cancer cells with their environment which eventually conclude whether the primary tumour is eliminated, metastasizes or creates dormant micro metastases. The TME may perhaps shape therapeutic responses as well as resistance. Some inimitable features of TME, for example vascular abnormalities, hypoxia, acidic pH and glutathione (GSH) are comparative to normal tissue. Several types of cells, together with tumour cells, macrophages, immune and fibroblast cells are nourished by flawed blood vessels in the solid tumour. To dispense anticancer agents to tumour sites nanovehicles can be competent carts. For augmented therapeutic efficacy, TME is the key for designing of nanoparticles (NPs). In this review, we will discuss the TME and summarize the current advancement in several nano-formulations for cancer therapy, with an extraordinary stress on TME-responsive ones. Scheme 1 highlights several TME modulation tactics with positive cancer therapeutic competence. The design of nanoconstructs and future challenges, consideration and opportunities are also discussed in detail. We have confidence in that these modulation approaches of TME tender a reliable opportunity for the practical translation of nanoparticle formulas into clinic.

Gunawan, C, Lord, MS, Lovell, E, Wong, RJ, Jung, MS, Oscar, D, Mann, R & Amal, R 2019, 'Oxygen-Vacancy Engineering of Cerium-Oxide Nanoparticles for Antioxidant Activity', ACS Omega, vol. 4, no. 5, pp. 9473-9479.
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© 2019 American Chemical Society. To address an important challenge in the engineering of antioxidant nanoparticles, the present work devised a surface-to-bulk migration of oxygen vacancies in the oxygen radical-scavenging cerium-oxide nanoparticles. The study highlights the significance of surface oxygen vacancies in the intended cellular internalization and, subsequently, the radical scavenging activity of the nanoparticles inside the cells. The findings advise future development of therapeutic antioxidant nanomaterials to also include engineering of the particles for enhanced surface defects not only for the accessibility of their oxygen vacancies but also, equally important, rendering them bioavailable for cellular uptake.

Guo, J, Huo, J, Liu, Y, Wu, W, Wang, Y, Wu, M, Liu, H & Wang, G 2019, 'Nitrogen‐Doped Porous Carbon Supported Nonprecious Metal Single‐Atom Electrocatalysts: from Synthesis to Application', Small Methods, vol. 3, no. 9, pp. 1900159-1900159.
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AbstractNonprecious metal single‐atom materials have attracted extensive attention in the field of electrocatalysis due to their low cost, high reactivity, high selectivity, and high atomic utilization. However, the high surface energy of a single atom causes agglomeration during preparation and catalytic measurement, resulting in damage to the catalytic sites. The strong interaction between substrate and monoatoms is the key factor to prevent the aggregation of individual metal atoms, and the geometry and electronic structure of the catalysts can be adjusted to optimize the catalytic activity. Due to the hierarchically pores, high specific surface area, and defect effect, nitrogen‐doped porous carbon (NPC) has been widely studied as an ideal nonprecious metal single‐atom support, which synergistically enhance the electrocatalytic performance toward oxygen reduction reaction, oxygen evolution reaction, hydrogen evolution reaction, carbon dioxide reduction reaction, and nitrogen reduction reaction with non‐noble metal single atoms. This review summarizes the controllable synthesis, characterization, theoretical calculation, and application of M (M = Co, Fe, Ni, Cu, Zn, Mo, etc.) single atoms on nitrogen‐doped porous carbon. Finally, the future development and challenges of nitrogen‐doped porous carbon supported nonprecious metal single‐atom electrocatalysts for practical commercialization are concluded.

Guo, X, Zhang, J, Zhao, Y, Sun, B, Liu, H & Wang, G 2019, 'Ultrathin Porous NiCo₂O₄ Nanosheets for Lithium–Oxygen Batteries: An Excellent Performance Deriving from an Enhanced Solution Mechanism', ACS Applied Energy Materials, vol. 2, no. 6, pp. 4215-4223.
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© Copyright 2019 American Chemical Society. Lithium-oxygen batteries are of interest for long-range electric vehicles owing to their high theoretical energy density. However, the poor cycling performance and low round-trip efficiency deriving from the sluggish oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) kinetics severely impede their practical application. Ingenious design of cathode catalysts is imperative to overcome these challenges. Here, we report ultrathin porous NiCo2O4 nanosheets with abundant oxygen vaccines as an efficient cathode catalyst toward both OER and ORR for Li-O2 batteries. From combined theoretical calculation with experimental results, a unique enhanced solution mechanism is proposed in the ether-based electrolyte system. Benefiting from the porous 2D architecture of the cathode and the hierarchical toroidal products, the Li-O2 batteries using NiCo2O4 cathodes deliver a high discharge capacity of 16 400 mAh g-1 at 200 mA g-1 and an excellent cycling performance up to 150 cycles with a restricted capacity of 1000 mAh g-1.

Gupta, A, Martinez-Lopez, C, Curran, JM & Almirall, JR 2019, 'Multi-element comparisons of tapes evidence using dimensionality reduction for calculating likelihood ratios', Forensic Science International, vol. 301, pp. 426-434.
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Computing the likelihood ratio (LR), as a measure of weight of evidence, has traditionally been difficult for multi-element evidence. A solution based on multivariate random effects models has been adopted by the forensic community but suffers from instability and has a tendency toward extreme values. This problem is magnified by increasing the number of variables. In this study, we consider reducing the dimensionality of the problem using principal component analysis (PCA) and a post-hoc calibration step suggested by van Es et al. [1] and evaluate the performance of this method using multi-element data collected from electrical tapes with up to 18 elements measured. A set of 90 tapes known to originate from different sources were analyzed by LA-ICP-MS. We used additive log-ratio transformation with respect to the signal of 208Pb to transform the 18-dimensional data. This transformation altered the scale of the signals and more importantly, the transformed signals exhibited characteristics similar to a normal distribution. We used scores of the first five principal components (PCs) as input to the LR formula given by Aitken and Lucy [2] where we assumed multivariate normal between-sources distribution (LR MVN) to compare the tapes. We observed that the calculated LRs were extremely positive and negative and did not conform with the definition of well-calibrated LRs. Thus, we used the post-hoc calibration method given by van Es et al. [1] to calibrate the likelihood ratios. The calibrated LRs were obtained within an appropriate range. Five scenarios, each related to the number of principal components used to compare the samples formed part of this study. The first scenario made the comparisons using only the first PC, the second scenario used the first two PCs together and so on. The last scenario, LR5, used 5 PCs for the comparisons. Comparing the results of these 5 scenarios provided an understanding around sensitivity of the method based on the percen...

Gupta, V, Kumar, R, Kumar, R, Mahajan, R, Mehta, M, Satija, S, Vyas, M, Khurana, N & Sharma, N 2019, 'Pharmacological actions of sinomenium acutum : A brief review', Plant Archives, vol. 19, pp. 1732-1736.
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Sinomenine is an alkaloid, found in the roots of the Sinomenium acutum, which is a popular Chinese medicinal plant. It contains alkaloids, sterols, and phospholipids. Sinomenine have a great therapeutic benefit in rheumatic disease due to its analgesic, anti-arrhythmic and anti-inflammatory property. It is a morphinan derivative which is related to opioids such as levorphenol. It is reported to have activity against oligomeric Aβ protein, that support its neuroprotective potential, specifically to hippocampal cells. It also possesses anti-inflammatory effect against various neurological disorders. The current review mainly focuses on the action of sinomenine on immune system, cardiovascular system, and nervous system.

Gutiérrez Moreno, JJ, Fronzi, M, Lovera, P, O’Riordan, A, Ford, MJ, Li, W & Nolan, M 2019, 'Structure, stability and water adsorption on ultra-thin TiO₂ supported on TiN', Physical Chemistry Chemical Physics, vol. 21, no. 45, pp. 25344-25361.
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Water adsorbs dissociatively on O-defective ultra-thin TiO_1.75 supported on TiN. The Ti³⁺ states reduce the energy gap compared to TiO₂.

Hajduk, IV, Mann, R, Rodrigues, CDA & Harry, EJ 2019, 'The ParB homologs, Spo0J and Noc, together prevent premature midcell Z ring assembly when the early stages of replication are blocked in Bacillus subtilis', Molecular Microbiology, vol. 112, no. 3, pp. 766-784.
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SummaryPrecise cell division in coordination with DNA replication and segregation is of utmost importance for all organisms. The earliest stage of cell division is the assembly of a division protein FtsZ into a ring, known as the Z ring, at midcell. What still eludes us, however, is how bacteria precisely position the Z ring at midcell. Work in B. subtilis over the last two decades has identified a link between the early stages of DNA replication and cell division. A recent model proposed that the progression of the early stages of DNA replication leads to an increased ability for the Z ring to form at midcell. This model arose through studies examining Z ring position in mutants blocked at different steps of the early stages of DNA replication. Here, we show that this model is unlikely to be correct and the mutants previously studied generate nucleoids with different capacity for blocking midcell Z ring assembly. Importantly, our data suggest that two proteins of the widespread ParB family, Noc and Spo0J are required to prevent Z ring assembly over the bacterial nucleoid and help fine tune the assembly of the Z ring at midcell during the cell cycle.

Hamidian, M & Nigro, SJ 2019, 'Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii', Microbial Genomics, vol. 5, no. 10.
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Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of high levels of resistance to many antibiotics, particularly those considered to be last-resort antibiotics, such as carbapenems. Although alterations in the efflux pump and outer membrane proteins can cause carbapenem resistance, the main mechanism is the acquisition of carbapenem-hydrolyzing oxacillinase-encoding genes. Of these, oxa23 is by far the most widespread in most countries, while oxa24 and oxa58 appear to be dominant in specific regions. Historically, much of the global spread of carbapenem resistance has been due to the dissemination of two major clones, known as global clones 1 and 2, although new lineages are now common in some parts of the world. The analysis of all publicly available genome sequences performed here indicates that ST2, ST1, ST79 and ST25 account for over 71 % of all genomes sequenced to date, with ST2 by far the most dominant type and oxa23 the most widespread carbapenem resistance determinant globally, regardless of clonal type. Whilst this highlights the global spread of ST1 and ST2, and the dominance of oxa23 in both clones, it could also be a result of preferential selection of carbapenem-resistant strains, which mainly belong to the two major clones. Furthermore, ~70 % of the sequenced strains have been isolated from five countries, namely the USA, PR China, Australia, Thailand and Pakistan, with only a limited number from other coun...

Hamidian, M, Hawkey, J, Wick, R, Holt, KE & Hall, RM 2019, 'Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1', Microbial Genomics, vol. 5, no. 1.
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© 2019 The Authors. Resistance to carbapenem and aminoglycoside antibiotics is a critical problem in Acinetobacter baumannii, particularly when genes conferring resistance are acquired by multiply or extensively resistant members of successful globally distributed clonal complexes, such as global clone 1 (GC1). Here, we investigate the evolution of an expanding clade of lineage 1 of the GC1 complex via repeated acquisition of carbapenem-and aminoglycoside-resistance genes. Lineage 1 arose in the late 1970s and the Tn6168/OCL3 clade arose in the late 1990s from an ancestor that had already acquired resistance to third-generation cephalosporins and fluoroquinolones. Between 2000 and 2002, two distinct subclades have emerged, and they are distinguishable via the presence of an integrated phage genome in subclade 1 and AbaR4 (carrying the oxa23 carbapenem-resistance gene in Tn2006) at a specific chromosomal location in subclade 2. Part or all of the original resistance gene cluster in the chromosomally located AbaR3 has been lost from some isolates, but plasmids carrying alternate resistance genes have been gained. In one group in subclade 2, the chromosomally located AbGRI3, carrying the armA aminoglycoside-resistance gene, has been acquired from a GC2 isolate and incorporated via homologous recombination. ISAba1 entered the common ancestor of this clade as part of the cephalosporin-resistance transposon Tn6168 and has dispersed differently in each subclade. Members of subclade 1 share an ISAba1 in one specific position in the chromosome and in subclade 2 two different ISAba1 locations are shared. Further shared ISAba1 locations distinguish further divisions, potentially providing simple markers for epidemiological studies.

Hamidian, M, Wick, RR, Hartstein, RM, Judd, LM, Holt, KE & Hall, RM 2019, 'Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2', Microbial Genomics, vol. 5, no. 10.
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The Acinetobacter baumannii global clone 1 isolate AB307-0294, recovered in the USA in 1994, and the global clone 2 (GC2) isolate ACICU, isolated in 2005 in Italy, were among the first A. baumannii isolates to be completely sequenced. AB307-0294 is susceptible to most antibiotics and has been used in many genetic studies, and ACICU belongs to a rare GC2 lineage. The complete genome sequences, originally determined using 454 pyrosequencing technology, which is known to generate sequencing errors, were re-determined using Illumina MiSeq and MinION (Oxford Nanopore Technologies) technologies and a hybrid assembly generated using Unicycler. Comparison of the resulting new high-quality genomes to the earlier 454-sequenced versions identified a large number of nucleotide differences affecting protein coding sequence (CDS) features, and allowed the sequences of the long and highly repetitive bap and blp1 genes to be properly resolved for the first time in ACICU. Comparisons of the annotations of the original and revised genomes revealed a large number of differences in the protein CDS features, underlining the impact of sequence errors on protein sequence predictions and core gene determination. On average, 400 predicted CDSs were longer ...

Hamidian, M, Wick, RR, Judd, LM, Holt, KE & Hall, RM 2019, 'Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece', Microbiology Resource Announcements, vol. 8, no. 41.
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Acinetobacter baumannii isolate A388, recovered in Greece in 2002, represents a distinct antibiotic-resistant lineage of global clone 1 (GC1) producing the OXA-58 carbapenemase. We present the complete 4.332-Mbp genome sequence (chromosome plus 1 plasmid), generated by combining long (MinION) and short (Illumina HiSeq) read sequencing data.

Han, N, Wei, Q, Tian, H, Zhang, S, Zhu, Z, Liu, J & Liu, S 2019, 'Highly Stable Dual‐Phase Membrane Based on Ce_0.9Gd_0.1O_2–δ—La₂NiO_4+δ for Oxygen Permeation under Pure CO₂ Atmosphere', Energy Technology, vol. 7, no. 5, pp. 1800701-1800701.
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Dense oxygen ion–conducting ceramic membranes with CO2 resistance can promote many advanced applications such as membrane reactors for green chemical synthesis and oxy‐fuel combustion for clean energy delivery. The state‐of‐the‐art perovskite oxide membranes are characterized by their high O2 flux but low stability in a CO2‐containing atmosphere. To solve this problem, dual‐phase membranes have captured the imagination of researchers. Herein, a novel dual‐phase hollow fiber membrane with a composition of 40 wt% Ce0.9Gd0.1O2–δ (GDC)–60 wt% La2NiO4+δ (LNO) is developed via a combined phase inversion sintering process. During the high temperature treatment, La‐doping behavior is observed with La leaching out from the LNO phase and diffusing into the GDC phase. This dual phase membrane displays the O2 flux of 1.47 at 950 °C, which is reduced by 10% to 1.31 mL min−1 cm−2 when the sweep gas is switched from helium to pure CO2. Such minor O2 flux reduction is due to the strong CO2 adsorption on membrane surface occupying the O2 vacancies without permanent membrane damage, which is fully eliminated by an inert gas purge. Such a robust dual‐phase membrane exhibits the potential to overcome the low stability problem under the CO2‐containing atmosphere.

Han, R, Khan, MH, Angeloski, A, Casillas, G, Yoon, CW, Sun, X & Huang, Z 2019, 'Hexagonal Boron Nitride Nanosheets Grown via Chemical Vapor Deposition for Silver Protection', ACS Applied Nano Materials, vol. 2, no. 5, pp. 2830-2835.
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© 2019 American Chemical Society. In this study, hexagonal boron nitride nanosheets (h-BNNS) have been grown on polycrystalline silver substrates via chemical vapor deposition (CVD) using ammonia borane as a precursor. The h-BNNS are of few-atomic-layer thickness and form continuous coverage over the whole Ag substrate. The atomically thin coating poses negligible interference to the reflectivity in the UV-visible range. The nanosheet coating also proves very effective in protecting Ag foil chemically. In contrast to bare Ag foil, the coated foil displayed only minor decolorization under high concentration of H2S. The study indicates that h-BNNS can be a promising protective coating for Ag based items such as jewelry or mirrors used in astronomical telescopes.

Hardy, S, Mabotuwana, NS, Murtha, LA, Coulter, B, Bezenilla, SS, Al-Omary, MS, Senanayake, T, Loering, S, Rech, CLS, Starkey, M, Lee, RJ, Rainer, P, Hansbro, PM & Boyle, AJ 2019, 'P6296The role of extracellular matrix protein 1 (ECM1) - a novel link between inflammation and cardiac fibrosis', European Heart Journal, vol. 40, no. Supplement_1.
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Abstract Introduction Cardiac fibrosis is a severe consequence of cardiovascular disease and aging, in which we currently have no effective treatments. The mechanisms underpinning the development of cardiac fibrosis remains poorly understood. Our preliminary data suggested extracellular matrix protein 1 (ECM1) is involved in cardiac fibrosis. We therefore aimed to investigate the role of ECM1 in several fibrotic cardiac diseases. Methods Young and ageing (3m/18m) male C57BL/6 mice, and primary mouse cardiac fibroblast (cFB) cultures, commercial human cardiac fibroblasts (Hu-cFB), human coronary artery endothelial cell (HCAEC)/smooth muscle cell (HCASMC), and human cardiac myocyte (HCM) cell lines were used. Young mice were subject to myocardial infarction (MI, 3-day/28-day, n=6/6), or pressure overload (TAC, 3-day/13-week, n=4/4). Left ventricle (LV) was collected at all time-points, and at 18m (ageing; n=3). Spleen and bone marrow was extracted from young control mice. Hu-cFB cells were treated with recombinant ECM1 (20ng/ml) for either 10, 30 or 50 min, or 48h. Immunoblotting was conducted on all samples, qPCR on LV tissue only, density gradient centrifugation and multicolour flow cytometry coupled with fluorescent ECM1 mRNA in-situ hybridisation (FISH-Flow) on bone marrow cells. Results ECM1 expression was upregulated in ageing LV (mRNA 2.2±0.1-fold, p=0.0002; protein 2.0-fold, p=0.0006), day-3 post-MI (mRNA, 4.9±2.0-fold, p=0.004; protein, 3.0-fold, p=0.004), a trend of ECM1 upregulation was observed at day-28 post-MI (mRNA, 13.2±12.0-fold, p=0.003; protein, 1.8-fold, p=0.2)...

Hardy, S, Mabotuwana, NS, Murtha, LA, Coulter, B, Bezenilla, SS, Al-Omary, MS, Senanayake, T, Loering, S, Rech, CLS, Starkey, M, Lee, RJ, Rainer, P, Hansbro, PM & Boyle, AJ 2019, 'The role of extracellular matrix protein 1 (ECM1) - a novel link between inflammation and cardiac fibrosis', EUROPEAN HEART JOURNAL, vol. 40, pp. 3900-3900.

Hardy, SA, Mabotuwana, NS, Murtha, LA, Coulter, B, Sanchez-Bezanilla, S, Al-Omary, MS, Senanayake, T, Loering, S, Starkey, M, Lee, RJ, Rainer, PP, Hansbro, PM & Boyle, AJ 2019, 'Novel role of extracellular matrix protein 1 (ECM1) in cardiac aging and myocardial infarction', PLOS ONE, vol. 14, no. 2, pp. e0212230-e0212230.
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© 2019 Hardy 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. Introduction The prevalence of heart failure increases in the aging population and following myocardial infarction (MI), yet the extracellular matrix (ECM) remodeling underpinning the development of aging- and MI-associated cardiac fibrosis remains poorly understood. A link between inflammation and fibrosis in the heart has long been appreciated, but has mechanistically remained undefined. We investigated the expression of a novel protein, extracellular matrix protein 1 (ECM1) in the aging and infarcted heart. Methods Young adult (3-month old) and aging (18-month old) C57BL/6 mice were assessed. Young mice were subjected to left anterior descending artery-ligation to induce MI, or transverse aortic constriction (TAC) surgery to induce pressure-overload cardiomyopathy. Left ventricle (LV) tissue was collected early and late post-MI/TAC. Bone marrow cells (BMCs) were isolated from young healthy mice, and subject to flow cytometry. Human cardiac fibroblast (CFb), myocyte, and coronary artery endothelial & smooth muscle cell lines were cultured; human CFbs were treated with recombinant ECM1. Primary mouse CFbs were cultured and treated with recombinant angiotensin-II or TGF-β1. Immunoblotting, qPCR and mRNA fluorescent in-situ hybridization (mRNA-FISH) were conducted on LV tissue and cells. Results ECM1 expression was upregulated in the aging LV, and in the infarct zone of the LV early post-MI. No significant differences in ECM1 expression were found late post-MI or at any time-point post-TAC. ECM1 was not expressed in any resident cardiac cells, but ECM1 was highly expressed in BMCs, with high ECM1 expression in granulocytes. Flow cytometry of bone marrow revealed ECM1 expression in large granular leucocy...

Hare, DJ, Braat, S, Cardoso, BR, Morgan, C, Szymlek-Gay, EA & Biggs, B-A 2019, 'Health outcomes of iron supplementation and/or food fortification in iron-replete children aged 4–24 months: protocol for a systematic review and meta-analysis', Systematic Reviews, vol. 8, no. 1.
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Abstract Background Direct supplementation or food fortification with iron are two public health initiatives intended to reduce the prevalence of iron deficiency (ID) and iron deficiency anaemia (IDA) in 4–24-month-old infants. In most high-income countries where IDA prevalence is < 15%, the recommended daily intake levels of iron from supplements and/or consumption of fortified food products are at odds with World Health Organisation (WHO) guidelines that recommend shorter-term (3 months/year) supplementation only in populations with IDA prevalence > 40%. Emerging concerns about delayed neurological effects of early-life iron overexposure have raised questions as to whether recommended guidelines in high-income countries are unnecessarily excessive. This systematic review will gather evidence from supplementation/fortification trials, comparing health outcomes in studies where iron-replete children did or did not receive additional dietary iron; and determine if replete children at study outset were not receiving additional iron show changes in haematological indices of ID/IDA over the trial duration. Methods We will perform a systematic review of the literature, including all studies of iron supplementation and/or fortification, including study arms with confirmed iron-replete infants at the commencement of the trial. This includes both dietary iron intervention or placebo/average dietary intakes. One reviewer will conduct searches in electronic databases of published and ongoing trials (Medline, Web of Science, Scopus, CENTRAL, EBSCO [e.g. CINAHL Complete, Food Science and Technology Abstracts], Embase, ClinicalTrials.gov, ClinicalTrialsRegister.eu and who.it/trialsearch), digital theses and dissertations (Wo...

Harrison, JA, Kelso, C, Padula, MP, Nicholson, GM & Beck, JL 2019, 'Structural characterization of protein toxins from Australian snake venoms using native mass spectrometry', Toxicon, vol. 158, pp. S43-S43.
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Harvey, KL, Jarocki, VM, Charles, IG & Djordjevic, SP 2019, 'The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis', Frontiers in Microbiology, vol. 10, no. OCT, p. 2351.
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© 2019 Harvey, Jarocki, Charles and Djordjevic. Elongation factor thermal unstable Tu (EF-Tu) is a G protein that catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome inside living cells. Structural and biochemical studies have described the complex interactions needed to effect canonical function. However, EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein. Here we explore the diverse moonlighting functions relating to pathogenesis of EF-Tu in bacteria and examine putative SLiMs on surface-exposed regions of the molecule.

Häußler, S, Benedikter, J, Bray, K, Regan, B, Dietrich, A, Twamley, J, Aharonovich, I, Hunger, D & Kubanek, A 2019, 'Diamond photonics platform based on silicon vacancy centers in a single-crystal diamond membrane and a fiber cavity', Physical Review B, vol. 99, no. 16.
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© 2019 American Physical Society. We realize a potential platform for an efficient spin-photon interface, namely negatively-charged silicon-vacancy centers in a diamond membrane coupled to the mode of a fully-tunable, fiber-based, optical resonator. We demonstrate that introducing the thin (∼200nm), single crystal diamond membrane into the mode of the resonator does not change the cavity properties, which is one of the crucial points for an efficient spin-photon interface. In particular, we observe constantly high Finesse values of up to 3000 and a linear dispersion in the presence of the membrane. We observe cavity-coupled fluorescence from an ensemble of SiV- centers with an enhancement factor of ∼1.9. Furthermore from our investigations we extract the ensemble absorption and extrapolate an absorption cross section of (2.9±2)×10-12cm2 for a single SiV- center, much higher than previously reported.

Hayman, TJ, Hsu, AC, Kolesnik, TB, Dagley, LF, Willemsen, J, Tate, MD, Baker, PJ, Kershaw, NJ, Kedzierski, L, Webb, AI, Wark, PA, Kedzierska, K, Masters, SL, Belz, GT, Binder, M, Hansbro, PM, Nicola, NA & Nicholson, SE 2019, 'RIPLET, and not TRIM25, is required for endogenous RIG‐I‐dependent antiviral responses', Immunology & Cell Biology, vol. 97, no. 9, pp. 840-852.
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AbstractThe innate immune system is our first line of defense against viral pathogens. Host cell pattern recognition receptors sense viral components and initiate immune signaling cascades that result in the production of an array of cytokines to combat infection. Retinoic acid–inducible gene‐I (RIG‐I) is a pattern recognition receptor that recognizes viral RNA and, when activated, results in the production of type I and III interferons (IFNs) and the upregulation of IFN‐stimulated genes. Ubiquitination of RIG‐I by the E3 ligases tripartite motif‐containing 25 (TRIM25) and Riplet is thought to be requisite for RIG‐I activation; however, recent studies have questioned the relative importance of these two enzymes for RIG‐I signaling. In this study, we show that deletion of Trim25 does not affect the IFN response to either influenza A virus (IAV), influenza B virus, Sendai virus or several RIG‐I agonists. This is in contrast to deletion of either Rig‐i or Riplet, which completely abrogated RIG‐I‐dependent IFN responses. This was consistent in both mouse and human cell lines, as well as in normal human bronchial cells. With most of the current TRIM25 literature based on exogenous expression, these findings provide critical evidence that Riplet, and not TRIM25, is required endogenously for the ubiquitination of RIG‐I. Despite this, loss of TRIM25 results in greater susceptibility to IAV infection in vivo, suggesting that it may have an alternative role in host antiviral defense. This study refines our understanding of RIG‐I signaling in viral infections and will inform future studies in the field.

Hayward, RJ, Marsh, JW, Humphrys, MS, Huston, WM & Myers, GSA 2019, 'Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution', Frontiers in Cellular and Infection Microbiology, vol. 9.
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Chlamydia are Gram-negative obligate intracellular bacterial pathogens responsible for a variety of disease in humans and animals worldwide. Chlamydia trachomatis causes trachoma in disadvantaged populations, and is the most common bacterial sexually transmitted infection in humans, causing reproductive tract disease. Antibiotic therapy successfully treats diagnosed chlamydial infections, however asymptomatic infections are common. High-throughput transcriptomic approaches have explored chlamydial gene expression and infected host cell gene expression. However, these were performed on large cell populations, averaging gene expression profiles across all cells sampled and potentially obscuring biologically relevant subsets of cells. We generated a pilot dataset, applying single cell RNA-Seq (scRNA-Seq) to C. trachomatis infected and mock-infected epithelial cells to assess the utility, pitfalls and challenges of single cell approaches applied to chlamydial biology, and to potentially identify early host cell biomarkers of chlamydial infection. Two hundred sixty-four time-matched C. trachomatis-infected and mock-infected HEp-2 cells were collected and subjected to scRNA-Seq. After quality control, 200 cells were retained for analysis. Two distinct clusters distinguished 3-h cells from 6- and 12-h. Pseudotime analysis identified a possible infection-specific cellular trajectory for Chlamydia-infected cells, while differential expression analyses found temporal expression of metallothioneins and genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis and cellular stress. We find that changes to the host cell transcriptome at early times of C. trachomatis infection are readily discernible by scRNA-Seq, supporting the utility of single cell approaches to identify host cell biomarkers of chlamydial infection, and to further deconvolute the complex host response to infection.

He, P, Smith, A, Gelissen, IC & Ammit, AJ 2019, 'The effect of statins and the synthetic LXR agonist T0901317 on expression of ABCA1 transporter protein in human lung epithelial cell lines in vitro', Pharmacological Reports, vol. 71, no. 6, pp. 1219-1226.
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BACKGROUND: The pathogenesis of chronic obstructive pulmonary disease (COPD) is associated with dyslipidemia, an established co-morbidity. Statins treat hypercholesterolemia, but more recently have been trailed in the setting of COPD for their potential anti-inflammatory benefits. The outcomes of prospective trials however have been inconsistent. Thus, we hypothesize that the variation in results may have been due to statin-induced downregulation of ATP-binding cassette transporter A1 (ABCA1), thereby reducing cholesterol export. This study aims to elucidate whether statin treatment in a cellular model of COPD leads to a decrease in ABCA1 protein expression. METHODS: To mimic the inflammatory environment of COPD, two commonly used lung epithelial cell lines (BEAS-2B and A549) were treated with tumor necrosis factor (TNF), and co-treated with cholesterol/25-hydroxycholesterol (25-OH) to mimic dyslipidemia. ABCA1 protein was detected by Western Blotting. RESULTS: We unexpectedly showed that statins did not affect ABCA1 expression. However, the LXR agonist T0901317 significantly increased ABCA1 expression in both cell lines, while TNF, cholesterol or 25-OH induced ABCA1 protein upregulation in BEAS-2B cells, indicating cell line differences in response. There was also evidence of synergistic impacts of combined treatments on ABCA1 upregulation in BEAS-2B cells. CONCLUSION: Statins did not have an impact on ABCA1 expression in lung epithelial cell lines, disproving our original hypothesis. However, we showed for the first time, the effect of the inflammatory cytokine TNF, cholesterol/25-OH, statins and the LXR agonist T0901317 on expression of ABCA1 transporter protein in human lung epithelial cell lines in vitro. We hope that these in vitro studies may prove beneficial for addressing dyslipidemia in COPD in the future.

Hewson, I, Sullivan, B, Jackson, EW, Xu, Q, Long, H, Lin, C, Quijano Cardé, EM, Seymour, J, Siboni, N, Jones, MRL & Sewell, MA 2019, 'Perspective: Something Old, Something New? Review of Wasting and Other Mortality in Asteroidea (Echinodermata)', Frontiers in Marine Science, vol. 6.
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Hing, ML, Klanten, OS, Wong, MYL & Dowton, M 2019, 'Drivers of sociality in Gobiodon fishes: An assessment of phylogeny, ecology and life-history', Molecular Phylogenetics and Evolution, vol. 137, pp. 263-273.
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What drives the evolution of sociality in animals? Many robust studies in terrestrial organisms have pointed toward various kinship-based, ecological and life-history traits or phylogenetic constraint which have played a role in the evolution of sociality. These traits are not mutually exclusive and the exact combination of traits is likely taxon-specific. Phylogenetic comparative analyses have been instrumental in identifying social lineages and comparing various traits with non-social lineages to give broad evolutionary perspectives on the development of sociality. Few studies have attempted this approach in marine vertebrate systems. Social marine fishes are particularly interesting because many have a pelagic larval phase and non-conventional life-history strategies (e.g. bi-directional sex-change) not often observed in terrestrial animals. Such strategies provide novel insights into terrestrially-derived theories of social evolution. Here, we assess the strength of the phylogenetic signal of sociality in the Gobiodon genus with Pagel's lambda and Blomberg's K parameters. We found some evidence of a phylogenetic signal of sociality, but factors other than phylogenetic constraint also have a strong influence on the extant social state of each species. We then use phylogenetic generalized least squares analyses to examine several ecological and life-history traits that may have influenced the evolution of sociality in the genus. We found an interaction of habitat size and fish length was the strongest predictor of sociality. Sociality in larger species was more dependent on coral size than in smaller species, but smaller species were more social overall, regardless of coral size. Finally, we comment on findings regarding the validity of the species G. spilophthalmus which arose during the course of our research. These findings in a group of marine fishes add a unique perspective on the evolution of sociality to the excellent terrestrial work conducted in this f...

Hinko-Najera, N, Najera Umaña, JC, Smith, MG, Löw, M, Griebel, A & Bennett, LT 2019, 'Relationships of intra-annual stem growth with climate indicate distinct growth niches for two co-occurring temperate eucalypts', Science of The Total Environment, vol. 690, pp. 991-1004.
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Forests are an important global carbon sink but their responses to climate change are uncertain. Tree stems, as the predominant carbon pool, represent net productivity in temperate eucalypt forests but the drivers of growth in these evergreen forests remain poorly understood partly because the dominant tree species lack distinct growth rings. Disentangling eucalypt species' growth responses to climate from other factors, such as competition and disturbances like fire, remains challenging due to a lack of long-term growth data. We measured monthly stem-diameter changes (as basal area increment, BAI) of two co-occurring dominant eucalypts from different sub-genera (Eucalyptus obliqua and E. rubida) over nearly four years. Our study included seven sites in a natural temperate forest of south-eastern Australia, and we used linear mixed-effects models to examine the relative importance to monthly BAI of species, monthly climate variables (temperature and rainfall), inter-tree competition, and recent fire history (long-unburnt, prescribed fire, wildfire). Monthly BAI peaked in spring and autumn and was significantly different between species during spring and summer. BAI variation was most clearly associated with temperature, increasing in hyperbolic response curves up to maximum mean temperatures of ~ 15-17 °C and thereafter decreasing. Temperature optima for maximum monthly BAI were 1 to 2 °C warmer for E. rubida than E. obliqua. While less important than temperature, rainfall, particularly autumn rainfall, also helped explain patterns in monthly BAI, with inter-tree competition and recent fire history of comparatively minor importance. Our study provides the first comprehensive field-based evidence of different growth niches for eucalypts from different subgenera in natural temperate mixed forests. It highlights the importance of intra-annual climate to understanding productivity variation in temperate evergreen forests and provides insights into the mechanisms unde...

Hitchcock, JN & Mitrovic, SM 2019, 'Microplastic pollution in estuaries across a gradient of human impact', Environmental Pollution, vol. 247, pp. 457-466.
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Microplastic (MP) pollution is an emerging issue in aquatic sciences. Little comparative information currently exists about the problem in coastal systems exposed to different levels of human impact. Here we report a year-long study on the abundance of MP in the water column of three estuaries on the east-coast of Australia. The estuaries are subject to different scales of human impact; the Clyde estuary has little human modification, the Bega estuary has a small township and single wastewater treatment works discharging to its waters, and the Hunter estuary which has multiple townships, multiple wastewater treatment plants, and heavy industry. MP abundance followed an expected pattern with the lowest abundance in the low-impact Clyde estuary (98 part. m3), moderate levels of MP in the moderately impacted Bega estuary (246 part. m3), and high MP abundance in the highly impacted Hunter estuary (1032 part. m3). The majority of particles were <200 μm and fragment-like rather than fiber-like. MP abundance was positively related to maximum antecedent rainfall in the Bega estuary, however there are no clear environmental factors that could explain MP variation in the other systems. MP were generally higher in summer and following freshwater inflow events. On the Hunter estuary MP abundance was at times as high as zooplankton abundance, and within the range of numbers reported in other highly impacted systems globally. The results confirm that higher levels of human impact lead to greater plastic pollution and highlight the need to examine aquatic ecosystems under a range of conditions in order to adequately characterize the extent of MP pollution in rivers and coastal systems.

Hogan, AL, Don, EK, Rayner, SL, Lee, A, Laird, AS, Watchon, M, Winnick, C, Tarr, IS, Morsch, M, Fifita, JA, Gwee, SSL, Formella, I, Hortle, E, Yuan, KC, Molloy, MP, Williams, KL, Nicholson, GA, Chung, RS, Blair, IP & Cole, NJ 2019, 'Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype', Human Molecular Genetics, vol. 28, no. 4, pp. 698-698.
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Holt, KE, Kenyon, JJ, Hamidian, M, Schultz, MB, Pickard, DJ, Dougan, G & Hall, RM 2019, 'Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1', Microbial Genomics, vol. 5, no. 7.
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Hoppenrath, M, Kretzschmar, AL, Kaufmann, MJ & Murray, SA 2019, 'Morphological and molecular phylogenetic identification and record verification of Gambierdiscus excentricus (Dinophyceae) from Madeira Island (NE Atlantic Ocean)', Marine Biodiversity Records, vol. 12, no. 1.
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Hoppstädter, J & Ammit, AJ 2019, 'Role of Dual-Specificity Phosphatase 1 in Glucocorticoid-Driven Anti-inflammatory Responses', Frontiers in Immunology, vol. 10, no. JUN, p. 1446.
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Copyright © 2019 Hoppstädter and Ammit. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Glucocorticoids (GCs) potently inhibit pro-inflammatory responses and are widely used for the treatment of inflammatory diseases, such as allergies, autoimmune disorders, and asthma. Dual-specificity phosphatase 1 (DUSP1), also known as mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1), exerts its effects by dephosphorylation of MAPKs, i.e., extracellular-signal-regulated kinase (ERK), p38, and c-Jun N-terminal kinase (JNK). Endogenous DUSP1 expression is tightly regulated at multiple levels, involving both transcriptional and post-transcriptional mechanisms. DUSP1 has emerged as a central mediator in the resolution of inflammation, and upregulation of DUSP1 by GCs has been suggested to be a key mechanism of GC actions. In this review, we discuss the impact of DUSP1 on the efficacy of GC-mediated suppression of inflammation and address the underlying mechanisms.

Hortle, E, Johnson, KE, Johansen, MD, Nguyen, T, Shavit, JA, Britton, WJ, Tobin, DM & Oehlers, SH 2019, 'Thrombocyte Inhibition Restores Protective Immunity to Mycobacterial Infection in Zebrafish', The Journal of Infectious Diseases, vol. 220, no. 3, pp. 524-534.
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Abstract Background Infection-induced thrombocytosis is a clinically important complication of tuberculosis infection. Recent studies have highlighted the utility of aspirin as a host-directed therapy modulating the inflammatory response to infection but have not investigated the possibility that the effect of aspirin is related to an antiplatelet mode of action. Methods In this study, we utilize the zebrafish-Mycobacterium marinum model to show mycobacteria drive host hemostasis through the formation of granulomas. Treatment of infected zebrafish with aspirin markedly reduced mycobacterial burden. This effect is reproduced by treatment with platelet-specific glycoprotein IIb/IIIa inhibitors demonstrating a detrimental role for infection-induced thrombocyte activation. Results We find that the reduction in mycobacterial burden is dependent on macrophages and granuloma formation, providing the first in vivo experimental evidence that infection-induced platelet activation compromises protective host immunity to mycobacterial infection. Conclusions Our study illuminates platelet activation as an efficacious target of aspirin, a widely available and affordable host-directed therapy candidate for tuberculosis.

Hortle, E, Starrs, L, Brown, FC, Jane, SM, Curtis, DJ, McMorran, BJ, Foote, SJ & Burgio, G 2019, 'KCC1 Activation protects Mice from the Development of Experimental Cerebral Malaria', Scientific Reports, vol. 9, no. 1.
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AbstractPlasmodium falciparummalaria causes half a million deaths per year, with up to 9% of this mortality caused by cerebral malaria (CM). One of the major processes contributing to the development of CM is an excess of host inflammatory cytokines. Recently K+ signaling has emerged as an important mediator of the inflammatory response to infection; we therefore investigated whether mice carrying an ENU induced activation of the electroneutral K+ channel KCC1 had an altered response toPlasmodium berghei. Here we show that Kcc1M935K/M935Kmice are protected from the development of experimental cerebral malaria, and that this protection is associated with an increased CD4+ and TNFa response. This is the first description of a K+ channel affecting the development of experimental cerebral malaria.

Hossain, KR & Clarke, RJ 2019, 'General and specific interactions of the phospholipid bilayer with P-type ATPases', Biophysical Reviews, vol. 11, no. 3, pp. 353-364.
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© 2019, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature. Protein structure and function are modulated via interactions with their environment, representing both the surrounding aqueous media and lipid membranes that have an active role in shaping the structural topology of membrane proteins. Compared to a decade ago, there is now an abundance of crystal structural data on membrane proteins, which together with their functional studies have enhanced our understanding of the salient features of lipid-protein interactions. It is now important to recognize that membrane proteins are regulated by both (1) general lipid-protein interactions, where the general physicochemical properties of the lipid environment affect the conformational flexibility of a membrane protein, and (2) by specific lipid-protein interactions, where lipid molecules directly interact via chemical interactions with specific lipid-binding sites located on the protein. However, due to local differences in membrane composition, thickness, and lipid packing, local membrane physical properties and hence the associated lipid-protein interactions also differ due to membrane location, even for the same protein. Such a phenomenon has been shown to be true for one family of integral membrane ion pumps, the P2-type adenosine triphosphatases (ATPases). Despite being highly homologous, individual members of this family have distinct structural and functional activity and are an excellent candidate to highlight how the local membrane physical properties and specific lipid-protein interactions play a vital role in facilitating the structural rearrangements of these proteins necessary for their activity. Hence in this review, we focus on both the general and specific lipid-protein interactions and will mostly discuss the structure-function relationships of the following P2-type ATPases, Na+,K+-ATPase (NKA), gastric H+,K+-ATPase (HKA),...

Hossain, KR, Turkewitz, DR, Holt, SA, Herson, L, Brown, LJ, Cornell, BA, Curmi, PMG & Valenzuela, SM 2019, 'A conserved GXXXG motif in the transmembrane domain of CLIC proteins is essential for their cholesterol-dependant membrane interaction', Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1863, no. 8, pp. 1243-1253.
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© 2019 Elsevier B.V. Background: Sterols have been reported to modulate conformation and hence the function of several membrane proteins. One such group is the Chloride Intracellular Ion Channel (CLIC)family of proteins. The CLIC protein family consists of six evolutionarily conserved protein members in vertebrates. These proteins exist as both monomeric soluble proteins and as membrane bound proteins. To date, the structure of their membrane-bound form remains unknown. In addition to several studies indicating cellular redox environment and pH as facilitators of CLIC1 insertion into membranes, we have also demonstrated that the spontaneous membrane insertion of CLIC1 is regulated by membrane cholesterol. Method: We have performed Langmuir-film, Impedance Spectroscopy and Molecular Docking Simulations to study the role of this GXXXG motif in CLIC1 interaction with cholesterol. Results: Unlike CLIC1-wild-type protein, the G18A and G22A mutants, that form part of the GXXXG motif, showed much slower initial kinetics and lower ion channel activity compared to the native protein. This difference can be attributed to the significantly reduced membrane interaction and insertion rate of the mutant proteins and/or slower formation of the final membrane configuration of the mutant proteins once in the membrane. Conclusion: In this study, our findings uncover the identification of a GXXXG motif in CLIC1, which likely serves as the cholesterol-binding domain, that facilitates the protein's membrane interaction and insertion. Furthermore, we were able to postulate a model by which CLIC1 can autonomously insert into membranes to form functional ion channels. General significance: Members of the CLIC family of proteins demonstrate unusual structural and dual functional properties – as ion channels and enzymes. Elucidating how the CLIC proteins' interact with membranes, thus allowing them to switch between their soluble and membrane form, will provide key information a...

Howe, ENW & Gale, PA 2019, 'Fatty Acid Fueled Transmembrane Chloride Transport', Journal of the American Chemical Society, vol. 141, no. 27, pp. 10654-10660.
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Hu, M, Schulze, KE, Ghildyal, R, Henstridge, DC, Kolanowski, JL, New, EJ, Hong, Y, Hsu, AC, Hansbro, PM, Wark, PAB, Bogoyevitch, MA & Jans, DA 2019, 'Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production', eLife, vol. 8.
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Although respiratory syncytial virus (RSV) is responsible for more human deaths each year than influenza, its pathogenic mechanisms are poorly understood. Here high-resolution quantitative imaging, bioenergetics measurements and mitochondrial membrane potential- and redox-sensitive dyes are used to define RSV’s impact on host mitochondria for the first time, delineating RSV-induced microtubule/dynein-dependent mitochondrial perinuclear clustering, and translocation towards the microtubule-organizing centre. These changes are concomitant with impaired mitochondrial respiration, loss of mitochondrial membrane potential and increased production of mitochondrial reactive oxygen species (ROS). Strikingly, agents that target microtubule integrity the dynein motor protein, or inhibit mitochondrial ROS production strongly suppresses RSV virus production, including in a mouse model with concomitantly reduced virus-induced lung inflammation. The results establish RSV’s unique ability to co-opt host cell mitochondria to facilitate viral infection, revealing the RSV-mitochondrial interface for the first time as a viable target for therapeutic intervention.

Hu, P, Hu, S, Huang, Y, Reimers, JR, Rappe, AM, Li, Y, Stroppa, A & Ren, W 2019, 'Bioferroelectric Properties of Glycine Crystals', The Journal of Physical Chemistry Letters, vol. 10, no. 6, pp. 1319-1324.
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© 2019 American Chemical Society. Biological ferroelectric materials have great potential in biosensing and disease diagnosis and treatment. Glycine crystals form the simplest bioferroelectric materials, and here we investigate the polarizations of its β- and γ-phases. Using density functional theory, we predict that glycine crystals can develop polarizations even larger than those of conventional inorganic ferroelectrics. Further, using systematic molecular dynamics simulations utilizing polarized crystal charges, we predict the Curie temperature of γ-glycine to be 630 K, with a required coercive field to switch its polarization states of 1 V·nm -1 , consistent with experimental evidence. This work sheds light on the microscopic mechanism of electric dipole ordering in biomaterials, helping in the material design of novel bioferroelectrics.

Hundal, AK, Agarwal, A, Jameel, M, Chen, J-Y, Li, J-L, Jones, L, Kaur, N, Langford, S & Gupta, A 2019, 'Improvement of the optoelectronic and photovoltaic properties of a cyanopyrid-2,6-dione-based donor via molecular engineering', Dyes and Pigments, vol. 170, pp. 107661-107661.
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Huo, J, Chen, Y, Liu, Y, Guo, J, Lu, L, Li, W, Wang, Y & Liu, H 2019, 'Bifunctional iron nickel phosphide nanocatalysts supported on porous carbon for highly efficient overall water splitting', Sustainable Materials and Technologies, vol. 22, pp. e00117-e00117.
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© 2019 The development of low-cost and earth-abundant materials for efficient oxygen and hydrogen evolution is critical for water splitting as a feasible energy conversion system. Metallic phosphides as promising bifunctional catalysts for water splitting tend to aggregate during the preparation and application. Thus, constructing metal phosphide-based composites with well-exposed active sites and stable structure is essential. Here, bi-metallic iron nickel phosphide nanoparticles (NPs) loaded on three-dimensional (3D) porous carbon (denoted as FexNi2-xP (0 < x < 2)) is synthesized through a facile co-deposition method followed by in situ phosphidation. The interconnected porous carbon with large specific area, abundant microporous and oxygen-containing functional groups contribute to the generation of ultra-small Fe–Ni–P NPs by confining growth of Fe–Ni layered double hydroxide (Fe–Ni–LDH) precursor. The ultra-small FexNi2-xP NPs loaded on 3D interconnected porous carbon with large active surface area and high conductivity can offer abundant catalytic active sites, facilitate mass transport and optimize electronic configuration, thereby promoting the reaction kinetics and accelerating catalytic performance. By tailoring the Ni/Fe ratios, the optimal bimetallic phosphide exhibits a small overpotential of 210 mV at current density of 10 mA cm−2 for oxygen evolution reaction. When applying for water splitting as cathode and anode materials in an alkaline electrolyzer, the potential of 1.63 V is required to reach 10 mA cm−2. The catalyst obtained from this strategy is a promising bi-functional catalyst for water splitting.

Hurtado Silva, M, Berry, I, Strange, N, Djordjevic, S & Padula, M 2019, 'Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets', Proteomes, vol. 7, no. 2, pp. 11-11.
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Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.

Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2019, 'Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome', Frontiers in Microbiology, vol. 10, no. MAY.
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Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify “core microbiome” members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with “core” taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenviron...

Huston, W 2019, 'Spotlight on…Wilhelmina M. Huston', FEMS Microbiology Letters, vol. 366, no. 20.
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Huston, WM, Coers, J & Garzino-Demo, A 2019, 'Fresh faces and new approaches at Pathogens and Disease', Pathogens and Disease, vol. 77, no. 1.
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Huston, WM, Cranfield, CG, Forbes, SL & Leigh, A 2019, 'A sponsorship action plan for increasing diversity in STEMM', Ecology and Evolution, vol. 9, no. 5, pp. 2340-2345.
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AbstractThere are numerous structural and cultural barriers to the progression of women and marginalized groups to leadership in academia, especially in Science, Technology, Engineering, Mathematics and Medicine (STEMM). A range of interventions have been described to address this inequity, with varying success. Here, we suggest that sponsorship could be one effective intervention and propose an institutional action plan to implement a sponsorship program in academia. We outline why sponsorship could be an effective strategy, especially if implemented through a deliberate program by an institution. We then detail the three components of an action plan to be considered in implementation: the elements of the program, the activities that sponsorship in academia likely encompasses, and the selection of sponsors and protégés. The plan could also be enacted by academic leadership in the absence of an institutional program and could serve as a guide to individuals in academia aspiring to address diversity and inclusion in STEMM.

Idowu, O, Semple, KT, Ramadass, K, O'Connor, W, Hansbro, P & Thavamani, P 2019, 'Beyond the obvious: Environmental health implications of polar polycyclic aromatic hydrocarbons', Environment International, vol. 123, pp. 543-557.
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© 2018 The genotoxic, mutagenic and carcinogenic effects of polar polycyclic aromatic hydrocarbons (polar PAHs) are believed to surpass those of their parent PAHs; however, their environmental and human health implications have been largely unexplored. Oxygenated PAHs (oxy-PAHs) is a critical class of polar PAHs associated with carcinogenic effects without enzymatic activation. They also cause an upsurge in reactive oxygen species (ROS) in living cells. This results in oxidative stress and other consequences, such as abnormal gene expressions, altered protein activities, mutagenesis, and carcinogenesis. Similarly, some nitrated PAHs (N-PAHs) are probable human carcinogens as classified by the International Agency for Research on Cancer (IARC). Heterocyclic PAHs (polar PAHs containing nitrogen, sulphur and oxygen atoms within the aromatic rings) have been shown to be potent endocrine disruptors, primarily through their estrogenic activities. Despite the high toxicity and enhanced environmental mobility of many polar PAHs, they have attracted only a little attention in risk assessment of contaminated sites. This may lead to underestimation of potential risks, and remediation end points. In this review, the toxicity of polar PAHs and their associated mechanisms of action, including their role in mutagenic, carcinogenic, developmental and teratogenic effects are critically discussed. This review suggests that polar PAHs could have serious toxicological effects on human health and should be considered during risk assessment of PAH-contaminated sites. The implications of not doing so were argued and critical knowledge gaps and future research requirements discussed.

Imkamp, K, Bernal, V, Grzegorzcyk, M, Horvatovich, P, Vermeulen, CJ, Heijink, IH, Guryev, V, Kerstjens, HAM, van den Berge, M & Faiz, A 2019, 'Gene network approach reveals co-expression patterns in nasal and bronchial epithelium', Scientific Reports, vol. 9, no. 1.
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AbstractNasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate <0.05, |Fold-change|>2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking.

Indigo, N, Smith, J, Webb, JK & Phillips, BL 2019, 'Bangers and cash: Baiting efficiency in a heterogeneous population', Wildlife Society Bulletin, vol. 43, no. 4, pp. 669-677.
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ABSTRACTUptake of baits is a key variable in management actions aimed at the vaccination, training, or control of many vertebrate species. Increasingly, however, it is apparent that individuals of the target species vary in their likelihood of taking baits. To optimize a baiting program, knowledge on the rate of bait uptake, how this rate changes with bait availability, and the proportion of the target population that will take a bait is required. The invasive cane toad (Rhinella marina) in Australia is a major threat to northern quolls (Dasyurus hallucatus), which are poisoned when they attack this novel toxic prey item. Conditioned‐taste‐aversion baits (cane toad sausages) can be delivered in the field to train northern quolls to avoid toads. We conducted a large‐scale field trial among 11 sites across one large property in Western Australia from 19–26 July 2017. We used camera traps and statistical modelling to estimate the proportion of baitable animals in the population, their encounter rate with baits, and survival rate of baits in the environment. Population estimates varied at each site from 2.5 to 16.8 quolls per site, resulting in a range among sites of 0.7–4.6 baits available/individual. Approximately 64% of individual quolls were bait‐susceptible. Both encounter rate and bait survival were low, resulting in our baiting regime treating <30% of the bait‐susceptible population. Using our model parameters, we estimate that we would need to increase our bait density 6‐fold to treat all bait‐susceptible individuals in the population. Without accounting for heterogeneity in bait‐susceptibility, our model would suggest we would need a 10‐fold increase in bait density. Thus, accounting for heterogeneity provides a more efficient baiting design. Data and models such as ours provide wildlife managers with information critical to informed decision‐making and are fu...

Insuasty, A, Carrara, S, Tang, L, Forsyth, C, Hogan, CF, McNeill, CR & Langford, SJ 2019, 'A Family of Heterocyclic Naphthalene Diimide (NDI) Analogues: Comparing Parent Isoquinoline Diimides and Phthalazine Diimides with NDI', ChemPlusChem, vol. 84, no. 10, pp. 1638-1642.
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AbstractParent isoquinoline diimide (IQDI) and phthalazine diimide (PTDI), as two new heterocyclic analogues of naphthalene diimides (NDIs), have been synthesized through an oxidative strategy in 35–79 % yield. X‐ray crystallography has been used to support the formation of IQDI, which also show fluorescence quantum yields of 3.5 %. The electrochemical and electrical properties of these molecules have been studied. The electrochemical results show an interesting trend in first reduction potential PTDI<IQDI<NDI and 0.1 eV changes in the optical band gap (Eg) leading to the trend IQDI<NDI<PTDI, as supported by DFT calculations. While initial top gate OFET devices yield charge mobilities less than NDIs, the basis of this study intimates that IQDIs and PTDIs hold promise for applications commensurate with NDIs.

Insuasty, A, Maniam, S & Langford, SJ 2019, 'Frontispiece: Recent Advances in the Core‐Annulation of Naphthalene Diimides', Chemistry – A European Journal, vol. 25, no. 29.
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Insuasty, A, Maniam, S & Langford, SJ 2019, 'Recent Advances in the Core‐Annulation of Naphthalene Diimides', Chemistry – A European Journal, vol. 25, no. 29, pp. 7058-7073.
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AbstractThis review focuses on describing all known synthetic strategies leading to core‐annulation of naphthalene diimides (NDIs). Strategies presented involve the formation of four‐, five‐ and six‐membered ring annulations bearing different heteroatomic and carbocyclic derivatives, including annulenes. The core‐annulation method opens the possibility for obtaining designer molecules with tuneable electronic characteristics such as a reduced energy band gap, and enhanced intermolecular overlap of π‐systems that improve electronic coupling between molecules—which is highly desirable for charge transport properties summarised in the final pages for applications in electronic devices such as organic field‐effect transistors (OFETs) and organic photovoltaic (OPV) cells. Molecular recognition in pH and fluoride sensing, or as a DNA probe, are some of additional applications of core‐annulated NDIs presented here. Additionally, recent advances in core modification of NDIs are presented, opening an entire new chemical avenue to be explored. Finally, the outlook on the future prospect of annulated NDIs in various applications is summarised.

Irga, PJ, Pettit, T, Irga, RF, Paull, NJ, Douglas, ANJ & Torpy, FR 2019, 'Does plant species selection in functional active green walls influence VOC phytoremediation efficiency?', Environmental Science and Pollution Research, vol. 26, no. 13, pp. 12851-12858.
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© Springer-Verlag GmbH Germany, part of Springer Nature 2019. Volatile organic compounds (VOCs) are of public concern due to their adverse health effects. Botanical air filtration is a promising technology for reducing indoor air contaminants, but the underlying mechanisms are not fully understood. This study assessed active botanical biofilters for their single-pass removal efficiency (SPRE) for benzene, ethyl acetate and ambient total volatile organic compounds (TVOCs), at concentrations of in situ relevance. Biofilters containing four plant species (Chlorophytum orchidastrum, Nematanthus glabra, Nephrolepis cordifolia ‘duffii’ and Schefflera arboricola) werecompared to discern whether plant selection influenced VOC SPRE. Amongst all tested plant species, benzene SPREs were between 45.54 and 59.50%, with N. glabra the most efficient. The botanical biofilters removed 32.36–91.19% of ethyl acetate, with C. orchidastrum and S. arboricola recording significantly higher ethyl acetate SPREs than N. glabra and N. cordifolia. These findings thus indicate that plant type influences botanical biofilter VOC removal. It is proposed that ethyl acetate SPREs were dependent on hydrophilic adsorbent sites, with increasing root surface area, root diameter and root mass all associated with increasing ethyl acetate SPRE. The high benzene SPRE of N. glabra is likely due to the high wax content in its leaf cuticles. The SPREs for the relatively low levels of ambient TVOCs were consistent amongst plant species, providing no evidence to suggest that in situ TVOC removal is influenced by plant choice. Nonetheless, as inter-species differences do exist for some VOCs, botanical biofilters using a mixture of plants is proposed.

Jain, D, Ghonse, SS, Trivedi, T, Fernandes, GL, Menezes, LD, Damare, SR, Mamatha, SS, Kumar, S & Gupta, V 2019, 'CO2 fixation and production of biodiesel by Chlorella vulgaris NIOCCV under mixotrophic cultivation', Bioresource Technology, vol. 273, pp. 672-676.
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Jarocki, V 2019, 'Mycoplasma hyopneumoniae' proteases: Investigating their role in pathogenesis and chronic infection', Journal and Proceedings of the Royal Society of New South Wales, vol. 152, no. 471/472, pp. 145-146.

Jarocki, VM, Raymond, BBA, Tacchi, JL, Padula, MP & Djordjevic, SP 2019, 'Mycoplasma hyopneumoniae surface-associated proteases cleave bradykinin, substance P, neurokinin A and neuropeptide Y', Scientific Reports, vol. 9, no. 1, p. 14585.
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AbstractMycoplasma hyopneumoniae is an economically-devastating and geographically-widespread pathogen that colonises ciliated epithelium, and destroys mucociliary function. M. hyopneumoniae devotes ~5% of its reduced genome to encode members of the P97 and P102 adhesin families that are critical for colonising epithelial cilia, but mechanisms to impair mucociliary clearance and manipulate host immune response to induce a chronic infectious state have remained elusive. Here we identified two surface exposed M. hyopneumoniae proteases, a putative Xaa-Pro aminopeptidase (MHJ_0659; PepP) and a putative oligoendopeptidase F (MHJ_0522; PepF), using immunofluorescence microscopy and two orthogonal proteomic methodologies. MHJ_0659 and MHJ_0522 were purified as polyhistidine fusion proteins and shown, using a novel MALDI-TOF MS assay, to degrade four pro-inflammatory peptides that regulate lung homeostasis; bradykinin (BK), substance P (SP), neurokinin A (NKA) and neuropeptide Y (NPY). These findings provide insight into the mechanisms used by M. hyopneumoniae to influence ciliary beat frequency, impair mucociliary clearance, and initiate a chronic infectious disease state in swine, features that are a hallmark of disease caused by this pathogen.

Jarocki, VM, Reid, CJ, Chapman, TA & Djordjevic, SP 2019, 'Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements', Frontiers in Microbiology, vol. 10, p. 3098.
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aEPEC are associated with persistent diarrhea, and diarrheal outbreaks in both humans and animals worldwide. They are differentiated from typical EPEC by the lack of bundle-forming pili, and from EHEC by the lack of phage-mediated stx toxins. However, phylogenetic analyses often associate aEPEC with EHEC, promoting the hypothesis that aEPEC are the progenitors of EHEC, which is supported by aEPEC conversion to EHEC by stx-carrying phages. While aEPEC can cause disease outright, the potential to acquire stx, one of the most potent bacterial toxins known, merits close monitoring. Escherichia coli ST302 (O108:H9, O182:H9, O45:H9) are aEPEC that have been isolated from diarrheic human, pig and rabbit hosts, as well as in healthy pigs, however, no study to date has focused on E. coli ST302 strains. Through WGS and hybrid assembly we present the first closed chromosome, and two circularized plasmids of an ST302 strain - F2_18C, isolated from a healthy pig in Australia. A phylogenetic analysis placed E. coli ST302 strains in proximity to EHEC ST32 (O145:H28) strains. Public databases were interrogated for WGSs of E. coli ST302 strains and short-read gene screens were used to compare their virulence-associated gene (VAG) and antimicrobial resistance gene (ARG) cargo. E. coli ST302 strains carry diverse VAGs, including those that typically associated with extraintestinal pathogenic E. coli (ExPEC). Plasmid comparisons showed that pF2_18C_FIB shared homology with EHEC virulence plasmids such as pO103 while pF2_18C_HI2 is a large multidrug resistance IncHI2:ST3 plasmid. A comparison of 33 HI2:ST3 plasmids demonstrated that those of Australian origin have not acquired resistances to extended-spectrum beta-lactams, colistin, fosfomycin or rifampicin, unlike those originating from Asia. F2_18C was shown to carry two additional pathogenicity islands - ETT2, and the STEC-associated PAI CL 3, plasmid-associated heavy metal resistance genes, as well as several unoccupied...

Jarocki, VM, Steele, JR, Widjaja, M, Tacchi, JL, Padula, MP & Djordjevic, SP 2019, 'Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation', International Journal of Medical Microbiology, vol. 309, no. 5, pp. 288-298.
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© 2019 Elsevier GmbH N-terminal methionine excision (NME) is a proteolytic pathway that cleaves the N-termini of proteins, a process that influences where proteins localise in the cell and their turnover rates. In bacteria, protein biosynthesis is initiated by formylated methionine start tRNA (fMet-tRNAfMet). The formyl group is attached by formyltransferase (FMT) and is subsequently removed by peptide deformylase (PDF) in most but not all proteins. Methionine aminopeptidase then cleaves deformylated methionine to complete the process. Components of NME, particularly PDF, are promising therapeutic targets for bacterial pathogens. In Mycoplasma hyopneumoniae, a genome-reduced, major respiratory pathogen of swine, pdf and fmt are absent from its genome. Our bioinformatic analysis uncovered additional enzymes involved in formylated N-terminal methionine (fnMet) processing missing in fourteen mycoplasma species, including M. hyopneumoniae but not in Mycoplasma pneumoniae, a major respiratory pathogen of humans. Consistent with our bioinformatic studies, an analysis of in-house tryptic peptide libraries confirmed the absence of fnMet in M. hyopneumoniae proteins but, as expected fnMet peptides were detected in the proteome of M. pneumoniae. Additionally, computational molecular modelling of M. hyopneumoniae translation initiation factors reveal structural and sequence differences in areas known to interact with fMet-tRNAfMet. Our data suggests that some mycoplasmas have evolved a translation process that does not require fnMet.

Jaspers, C, Fraune, S, Arnold, AE, Miller, DJ, Bosch, TCG & Voolstra, CR 2019, 'Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches', Zoology, vol. 133, pp. 81-87.
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Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of th...

Jean-Richard-dit-Bressel, P, Ma, C, Bradfield, LA, Killcross, S & McNally, GP 2019, 'Punishment insensitivity emerges from impaired contingency detection, not aversion insensitivity or reward dominance', eLife, vol. 8.
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Our behaviour is shaped by its consequences – we seek rewards and avoid harm. It has been reported that individuals vary markedly in their avoidance of detrimental consequences, that is in their sensitivity to punishment. The underpinnings of this variability are poorly understood; they may be driven by differences in aversion sensitivity, motivation for reward, and/or instrumental control. We examined these hypotheses by applying several analysis strategies to the behaviour of rats (n = 48; 18 female) trained in a conditioned punishment task that permitted concurrent assessment of punishment, reward-seeking, and Pavlovian fear. We show that punishment insensitivity is a unique phenotype, unrelated to differences in reward-seeking and Pavlovian fear, and due to a failure of instrumental control. Subjects insensitive to punishment are afraid of aversive events, they are simply unable to change their behaviour to avoid them.

Jerotic, D, Matic, M, Suvakov, S, Vucicevic, K, Damjanovic, T, Savic-Radojevic, A, Pljesa-Ercegovac, M, Coric, V, Stefanovic, A, Ivanisevic, J, Jelic-Ivanovic, Z, McClements, L, Dimkovic, N & Simic, T 2019, 'Association of Nrf2, SOD2 and GPX1 Polymorphisms with Biomarkers of Oxidative Distress and Survival in End-Stage Renal Disease Patients', Toxins, vol. 11, no. 7, pp. 431-431.
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The oxidative stress response via Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) interlinks inflammation- and metabolism-related pathways in chronic kidney disease. We assessed the association between polymorphisms in Nrf2, superoxide dismutase (SOD2), glutathione peroxidase (GPX1), and the risk of end-stage renal disease (ESRD). The modifying effect of these polymorphisms on both oxidative phenotype and ESRD prognosis, both independently and/or in combination with the glutathione S-transferase M1 (GSTM1) deletion polymorphism, was further analyzed. Polymorphisms in Nrf2 (rs6721961), SOD2 (rs4880), GPX1 (rs1050450), and GSTM1 were determined by PCR in 256 ESRD patients undergoing hemodialysis and 374 controls. Byproducts of oxidative stress were analyzed spectrophotometically or by ELISA. Time-to-event modeling was performed to evaluate overall survival and cardiovascular survival. The SOD2 Val/Val genotype increased ESRD risk (OR = 2.01, p = 0.002), which was even higher in combination with the GPX1 Leu/Leu genotype (OR = 3.27, p = 0.019). Polymorphism in SOD2 also showed an effect on oxidative phenotypes. Overall survival in ESRD patients was dependent on a combination of the Nrf2 (C/C) and GPX1 (Leu/Leu) genotypes in addition to a patients’ age and GSTM1 polymorphism. Similarly, the GPX1 (Leu/Leu) genotype contributed to longer cardiovascular survival. Conclusions: Our results show that SOD2, GPX1, and Nrf2 polymorphisms are associated with ESRD development and can predict survival.

Ji, D, Wen, Q, Cao, L, Kang, Q, Lin, S, Zhang, X, Jiang, L & Guo, W 2019, 'Electrokinetically Controlled Asymmetric Ion Transport through 1D/2D Nanofluidic Heterojunctions', Advanced Materials Technologies, vol. 4, no. 7.
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AbstractSupported 2D layered materials are widely used in gas separation, water treatment, energy conversion, etc. In conventional viewpoint, the atop 2D membrane functions as an active layer for mass or charge separation in vapor or liquid phase, while the substrate membrane, containing aligned or tortuous 1D micro or nanoscaled fluidic channels, functions as a mechanical support. However, asymmetric transport property induced by the mixed‐dimensional composite structure is an equally very important, yet long‐overlooked element that endows new features to the membrane‐scale nanofluidic systems and contributes to the promotion of overall performance. Here, reported are asymmetric ion transport properties through 1D/2D nanofluidic heterojunction membrane (NFHM) under three different types of electrokinetic driving force. The 1D/2D NFHM comprises of self‐assembled graphene oxide multi‐layers (2DM, negatively charged) supported on a polydopamine‐coated 1D nanopore array (1DM, ampholytic). Intriguingly, it is found that the preferential direction for electric‐field‐driven ionic transport is from the 2DM to the 1DM, while under the concentration difference or the hydraulic flow, the preferred direction for diffusion or streaming ionic current goes in the reversed direction, from the 1DM to the 2DM. A theoretical model based on coupled Poisson–Nernst–Planck and Navier–Stokes equations is employed to explain the asymmetric ion transport phenomena.

Jia, P, Wen, Q, Liu, D, Zhou, M, Jin, X, Ding, L, Dong, H, Lu, D, Jiang, L & Guo, W 2019, 'Highly Efficient Ionic Photocurrent Generation through WS₂‐Based 2D Nanofluidic Channels', Small, vol. 15, no. 50, p. e1905355.
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AbstractThe unique feature of nacre‐like 2D layered materials provides a facile, yet highly efficient way to modulate the transmembrane ion transport from two orthogonal transport directions, either vertical or horizontal. Recently, light‐driven active transport of ionic species in synthetic nanofluidic systems attracts broad research interest. Herein, taking advantage of the photoelectric semiconducting properties of 2D transition metal dichalcogenides, the generation of a directional and greatly enhanced cationic flow through WS2‐based 2D nanofluidic membranes upon asymmetric visible light illumination is reported. Compared with graphene‐based materials, the magnitude of the ionic photocurrent can be enhanced by tens of times, and its photo‐responsiveness can be 2–3.5 times faster. This enhancement is explained by the coexistence of semiconducting and metallic WS2 nanosheets in the hybrid membrane that facilitates the asymmetric diffusion of photoexcited charge carriers on the channel wall, and the high ionic conductance due to the neat membrane structure. To further demonstrate its application, photonic ion switches, photonic ion diodes, and photonic ion transistors as the fundamental elements for light‐controlled nanofluidic circuits are further developed. Exploring new possibilities in the family of liquid processable colloidal 2D materials provides a way toward high‐performance light‐harvesting nanofluidic systems for artificial photosynthesis and sunlight‐driven desalination.

Jian, X, Wang, H, Rao, G, Jiang, L, Wang, H, Subramaniyam, CM, Mahmood, A, Zhang, W, Xiang, Y, Dou, SX, Zhou, Z, Hui, D, Kalantar-Zadeh, K & Mahmood, N 2019, 'Self-tunable ultrathin carbon nanocups as the electrode material of sodium-ion batteries with unprecedented capacity and stability', Chemical Engineering Journal, vol. 364, pp. 578-588.
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Jo, Y, Johir, MAH, Cho, Y, Naidu, G, Rice, SA, McDougald, D, Kandasamy, J, Vigneswaran, S & Sun, S 2019, 'A comparative study on nitric oxide and hypochlorite as a membrane cleaning agent to minimise biofilm growth in a membrane bioreactor (MBR) process', Biochemical Engineering Journal, vol. 148, pp. 9-15.
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© 2019 Elsevier B.V. Reverse osmosis concentrates (ROC) produced from water reclamation plants can threaten the environment if it is not appropriately treated before discharge. A membrane bioreactor (MBR) process to treat ROC was used in this project. In an MBR, fouling is an essential and inevitable phenomenon which leads to higher operational and capital costs. A comparative study on chemical cleaning, such as sodium hypochlorite (NaOCl) and nitric oxide (NO), was experimentally evaluated together with the influence of filtration flux. Exposure to a low concentration of NO reduced biofilms in an MBR system. NO treatment delayed the formation of new biofilm biomass on the membrane. NO also showed good performance in reducing membrane fouling and had no adverse effect on activated sludge and the environment. In MBR, the bacterial community was dominated by Proteobacteria (61%), with Alpha and Beta-proteobacteria representing approximately 54% of the community. After NO treatment, the relative abundance of the Proteobacteria decreased to 44%, and this was also reflected in a reduction in Alpha and Beta-proteobacteria, to 30% and 5% respectively. Thus, NO treatment resulted in the decrease of the relative biofilms associated with reduced MBR performance.

Johansen, MD, de Silva, K, Plain, KM, Whittington, RJ & Purdie, AC 2019, 'Mycobacterium avium subspecies paratuberculosis is able to manipulate host lipid metabolism and accumulate cholesterol within macrophages', Microbial Pathogenesis, vol. 130, pp. 44-53.
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Johne's disease is a chronic wasting disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Closely related pathogenic mycobacteria such as M. tuberculosis are capable of altering host lipid metabolism, highlighting the need to explore the role of lipid metabolism contributing to intracellular survival. This study aimed to identify whether MAP is able to manipulate host lipid metabolic pathways and accumulate host cholesterol during early infection. Macrophages were exposed to four different MAP strains and non-pathogenic M. phlei for up to 72 h, with changes to lipid metabolism examined using fluorescent microscopy and gene expression. MAP-infected macrophages displayed strain-dependent differences to intracellular cholesterol levels during early infection, however showed similarly increased intracellular cholesterol at later timepoints. Gene expression revealed that MAP strains similarly activate the host immune response in a conserved manner compared to M. phlei. MAP significantly upregulated host genes associated with lipid efflux and endocytosis. Moreover, lipid biosynthesis genes were differentially regulated in a strain-dependent manner following MAP infection. Collectively, these results demonstrate that MAP manipulates host lipid metabolism during early infection, however the extent of these modulations are strain-dependent. These findings reflect a conserved pathway contributing to intracellular MAP survival.

Johnson, L, Cameron, M, Waters, L, Padula, MP & Marks, DC 2019, 'The impact of refrigerated storage of UVC pathogen inactivated platelet concentrates on in vitro platelet quality parameters', Vox Sanguinis, vol. 114, no. 1, pp. 47-56.
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Background and ObjectivesRefrigeration (cold‐storage) of pathogen inactivated (PI) platelet components may increase the shelf‐life and safety profile of platelet components, compared to conventional room‐temperature (RT) storage. Whilst there is substantial knowledge regarding the impact of these individual treatments on platelets, the combined effect has not been assessed.Materials and methodsUsing a pool‐and‐split study design, paired buffy‐coat derived platelets in 70% platelet additive solution (SSP+; MacoPharma) were left untreated or PI‐treated using the THERAFLEX UV‐Platelets System (UVC; MacoPharma). Units from each pair were split and stored at room temperature (20–24°C) or cold‐stored (2–6°C) to yield RT, cold, RT‐UVC and cold‐UVC study groups (n = 8 in each group). In vitro quality and function was tested over 9 days.ResultsCold‐storage of UVC‐treated platelets reduced glycolytic metabolism (glucose consumption and lactate production) compared to RT‐

JOHNSTON, NP, WALLMAN, JF & PAPE, T 2019, 'First record of Miltogramminae from New Caledonia: a new species of Protomiltogramma (Diptera: Sarcophagidae)', Zootaxa, vol. 4612, no. 4, pp. zootaxa.4612.4.12-595.
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New Caledonia is described as one of Earth’s key biodiversity hotspots, with high species endemism, particularly for plants and vertebrate animals (Myers et al. 2000; Kier et al. 2009). The distinct biodiversity of this country has been attributed to the Gondwanan origins of the New Caledonian archipelago, its relative isolation from neighbouring countries (such as Australia) and the stability of its climate. These factors are suggested to have led to the accumulation of many Gondwanan species, with few instances of extinction, which has allowed for marked species diversification (Espeland & Murienne 2011). 

Jolly, CJ, Lee, Q, Padula, MP, Pinello, N, Williams, SH, O’Rourke, MB, Fumagalli, MJ, Orkin, JD, Shaban, B, Brenner, O, Weninger, W, de Souza, WM, Melin, AD, Wong, JJ-L, Crim, MJ, Monette, S & Roediger, B 2019, 'MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2'.
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AbstractMouse kidney parvovirus (MKPV) is a member of the provisionalChapparvovirusgenus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four MKPV transcripts, created by alternative splicing, to a common transcription initiation region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and a splicing-dependent putative accessory protein NS2 are conserved in all near-complete tetrapod chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbedNephroparvovirus, which is consistent with nomenclature for the genusErythroparvovirus.

Jolly, CJ, Webb, JK, Gillespie, GR, Hughes, NK & Phillips, BL 2019, 'Bias averted: personality may not influence trappability', Behavioral Ecology and Sociobiology, vol. 73, no. 9.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Abstract: If bold animals are more likely to be trapped than shy animals, we take a biased sample of personalities—a problem for behavioural research. Such a bias is problematic, also, for population estimation using mark-recapture models that assume homogeneity in detection probabilities. In this study, we investigated whether differences in boldness result in differences in detection probability in a native Australian rodent, the grassland melomys (Melomys burtoni). During a mark-recapture study of this species, we used modified open field tests to assess the boldness (via emergence, and interaction with a novel object) of melomys trapped on the last night of four trapping nights in each of two trapping sessions. Despite melomys showing repeatable variation in these behavioural traits, neither boldness nor emergence latency had an effect on detection probability, and we found no evidence that detection probability varied between individuals. This result suggests that any neophobia is experienced and resolved in individuals of this species on a scale of minutes, rather than the hours across which traps are made available each night. Our work demonstrates that personality-caused sampling bias may not be inevitable, even in situations where animals are required to respond to novelty to be detected, such as in baited traps. Heterogeneity in personality does not inevitably lead to heterogeneity in detection probability. Significance statement: Historically, passive traps were assumed a non-biased means of sampling animal populations. Increasingly behavioural ecologists suggest that personality traits, particularly individual boldness, may influence behaviour and, as a consequence, could result in sampling bias. Here, we present a comprehensive example of when animal personality has no effect on detection probability. Despite having distinct personalities, detection probabilities of a native Aus...

Jones, MWM, Phillips, NW, Abbey, B, Hare, DJ, van Riessen, GA, Vine, DJ, de Jonge, MD & McColl, G 2019, 'Simultaneous nanostructure and chemical imaging of intact whole nematodes', Chemical Communications, vol. 55, no. 8, pp. 1052-1055.
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Accurately locating biologically relevant elements at high resolution: simultaneous ptychography and fluorescence imaging of large specimens comes of age.

Jones, PM, Mazzio, E, Soliman, K & George, AM 2019, 'In Silico Investigation of the Binding of MCoTI-II Plant Defense Knottin to the γ-NGF Serine Protease of the 7S Nerve Growth Factor Complex and Biological Activity of Its NGF Mimetic Properties', The Journal of Physical Chemistry B, vol. 123, no. 43, pp. 9104-9110.
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Jowett, LA & Gale, PA 2019, 'Supramolecular methods: the chloride/nitrate transmembrane exchange assay', Supramolecular Chemistry, vol. 31, no. 5, pp. 297-312.
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Jung, JY, Kang, P-W, Kim, E, Chacon, D, Beck, D & McNevin, D 2019, 'Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations', International Journal of Legal Medicine, vol. 133, no. 6, pp. 1711-1719.
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Inference of ancestry from biological evidence can provide investigative information, especially for unknown DNA donors. Although tools for predicting ancestry have been developing, ancestry research focusing on populations relevant for South Korea is not common and markers are seldom chosen specifically to differentiate Koreans from other East Asian and South East Asian populations. Here, we report ancestry informative markers (AIMs) for distinguishing six East/South East Asian regional populations: China, Japan, Indonesia, Philippines, South Korea and Thailand. Individual genotypes from these six populations were available in PanSNPdb: The HUGO Pan-Asian SNP Database. To select AIMs, we calculated four population divergence metrics for each SNP: Nei's FST, Rosenberg's Informativeness (In), the average absolute allele frequency difference between populations (δFmean) and the maximum allele frequency difference between populations (δFmax). Based on these values, we selected 100 single nucleotide polymorphisms (SNPs) for distinguishing the six populations, 13 of which exhibited large allele frequency differences between Koreans and non-Koreans. To assess the performance of the AIMs, we performed principal coordinates analysis (PCoA) on the individuals from all six populations and inferred ancestral population clusters using the STRUCTURE program. In conclusion, we found that the selected AIMs can be applied to distinguish the six East/South East Asian groups and we suggest the markers in this study will be helpful to establish ancestry panels for Korea and neighbouring populations.

Kamachi, K, Otsuka, N, Fumimoto, R, Ozawa, K, Yao, S-M, Chiang, C-S, Luu, LDW, Lan, R, Shibayama, K & Watanabe, M 2019, 'A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis', Journal of Medical Microbiology, vol. 68, no. 11, pp. 1671-1676.
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Purpose. Human-adapted Bordetella parapertussis is one of the causative agents of whooping cough; however, there are currently no genotyping systems with high discriminatory power for this bacterial pathogen. We therefore aimed to develop a multilocus variable-number tandem repeat analysis (MLVA) for human-adapted B. parapertussis.Methodology. Four highly polymorphic variable number tandem repeat (VNTR) loci in the B. parapertussis genome were selected and amplified by multiplex PCR. MLVA was performed based on the number of tandem repeats at VNTR loci. The discriminatory power of MLVA was evaluated with three laboratory reference strains and 50 human isolates of B. parapertussis.Results. Multiplex PCR-based MLVA characterized 53 B. parapertussis reference strains and isolates into 25 MLVA types and the Simpson diversity index was 0.91 (95 % confidence interval, 0.86-0.97). The three reference strains exhibited different MLVA types. Thirty-one Japanese isolates, ten French isolates and three Taiwanese isolates belonged to fourteen, nine and three MLVA types, respectively. In contrast, all five Australian isolates belonged to the same type. Two Japanese isolates collected from patients with known epidemiological links had the same type.Conclusion. Our novel MLVA method has high discriminatory power for genotyping human B. parapertussis. Regarding this organism, this genotyping system is a promising tool for epidemiological surveillance and investigating outbreaks.

Kanodarwala, FK, Moret, S, Spindler, X, Lennard, C & Roux, C 2019, 'Nanoparticles used for fingermark detection—A comprehensive review', WIREs Forensic Science, vol. 1, no. 5.
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AbstractNanoparticles (NPs) have been used in numerous fields such as medicine, imaging, and electronics to cite just a few. In forensic science, NPs have been researched specifically for the detection of fingermarks. Their small size, surface functionalization ability, and luminescence properties can potentially lead to better resolution, increased sensitivity, and selectivity. This paper offers an extensive review of the various NP types investigated over the past three decades. NPs are sorted into seven categories, namely metal, metal oxide, quantum dots (QDs), carbon dots (C‐dots), silica (SiO2), and upconverters NPs (UCNPs) as well as a miscellaneous section. Each type is discussed in details from a critical viewpoint. The most promising NP types are also identified.This article is categorized under:Forensic Chemistry and Trace Evidence > Fingermarks and Other Marks

Karacan, I, Ben-Nissan, B, Wang, HA, Juritza, A, Swain, MV, Müller, WH, Chou, J, Stamboulis, A, Macha, IJ & Taraschi, V 2019, 'Mechanical testing of antimicrobial biocomposite coating on metallic medical implants as drug delivery system', Materials Science and Engineering: C, vol. 104, no. 109757, pp. 109757-109757.
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Kaufer, A, Barratt, J, Stark, D & Ellis, J 2019, 'The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae', Infection, Genetics and Evolution, vol. 70, pp. 90-100.
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© 2019 Elsevier B.V. The mitochondrial DNA (mtDNA) is a potentially valuable phylogenetic marker given its presence across all eukaryotic taxa and its relative conservation in structure and sequence. In trypanosomatids, a homologue of the mtDNA referred to as the maxicircle DNA, is located within a specialised structure in the single mitochondrion of the trypanosomatids called the kinetoplast; a high molecular weight network of DNA composed of thousands of catenated minicircles and a smaller number of larger maxicircles. Unique to the kinetoplastid protists, the maxicircle component of this complex network could represent a desirable target for taxonomic inquiry that may also facilitate exploration of the evolutionary history of this important group of parasites. The aim of this study was to investigate the phylogenetic value of the trypanosomatid maxicircle for these applications. Maxicircle sequences were obtained either by assembling raw sequence data publicly accessible in online databases (i.e., NCBI), or by amplification of novel maxicircle sequences from trypanosomatid DNA using long-range (LR) PCR with subsequent Illumina sequencing. This procedure facilitated the generation of nearly complete maxicircle sequences (i.e., excluding the divergent region) for numerous dixenous and monoxenous trypanosomatid species. Annotation of each maxicircle sequence confirmed that their structure was conserved across all taxa examined. Phylogenetic analyses confirmed that Z. australiensis showed a greater genetic relatedness with the dixenous trypanosomatids of the genera Leishmania and Endotrypanum, as opposed to members of the monoxenous genera Crithidia and Leptomonas. Additionally, molecular clock analysis supported that the dixenous Leishmaniinae appeared approximately 75 million years ago during the breakup of Gondwana. In line with previous studies, our results support the Supercontinents hypothesis regarding the origin of dixenous Leishmaniinae. Ultimat...

Kaufer, A, Ellis, J & Stark, D 2019, 'Identification of Clinical Infections of Leishmania Imported into Australia: Revising Speciation with Polymerase Chain Reaction-RFLP of the Kinetoplast Maxicircle', The American Journal of Tropical Medicine and Hygiene, vol. 101, no. 3, pp. 590-601.
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Kaufer, Stark & Ellis 2019, 'Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast', Pathogens, vol. 8, no. 3, pp. 157-157.
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Advancements in next-generation sequencing techniques have led to a substantial increase in the genomic information available for analyses in evolutionary biology. As such, this data requires the exponential growth in bioinformatic methods and expertise required to understand such vast quantities of genomic data. Alignment-free phylogenomics offer an alternative approach for large-scale analyses that may have the potential to address these challenges. The evolutionary relationships between various species within the trypanosomatid family, specifically members belonging to the genera Leishmania and Trypanosoma have been extensively studies over the last 30 years. However, there is a need for a more exhaustive analysis of the Trypanosomatidae, summarising the evolutionary patterns amongst the entire family of these important protists. The mitochondrial DNA of the trypanosomatids, better known as the kinetoplast, represents a valuable taxonomic marker given its unique presence across all kinetoplastid protozoans. The aim of this study was to validate the reliability and robustness of alignment-free approaches for phylogenomic analyses and its applicability to reconstruct the evolutionary relationships between the trypanosomatid family. In the present study, alignment-free analyses demonstrated the strength of these methods, particularly when dealing with large datasets compared to the traditional phylogenetic approaches. We present a maxicircle genome phylogeny of 46 species spanning the trypanosomatid family, demonstrating the superiority of the maxicircle for the analysis and taxonomic resolution of the Trypanosomatidae.

Kaur, S, Sharma, N, Vyas, M, Mahajan, R, Satija, S, Mehta, M & Khurana, N 2019, 'A review on pharmacological activities of betaine', Plant Archives, vol. 19, pp. 1021-1034.
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Betaine is an important phytoconstituent found in plant Beta vulgaris. It is found abundantly in various common foods like beets, spinach and cereals, whereas wheat is its major source in human diet. Chemically, betaine is termed as trimethylglycine. It plays an important physiological role in the body. It has found to be a an organis osmolyte and it participates in methionine-homocysteine cycle as a methyl group donor due to which it possesses many physiological activities. It has widely been studied for its promising antioxidant properties, neuroprotective effects, anti-Inflammatory effects, inhibition of NF-κB signaling pathway, inhibition of NLRP3 inflammasome activation, regulating energy metabolism to relieve chronic inflammation, mitigation of endoplasmic reticulum stress and apoptosis, canonical and noncanonical inflammasome-mediated processing of IL-1β, against neurodegenerative diseases, anticonvulsant effects, reducing the total homocysteine content in brain and its role in performance and action. The present article firstly aims to review the pharmacological effects including neuroprotective effects, physiological effects of betaine including effects on performance and human body composition, secondly to study the safety concerns of betaine and its future prospects.

Keadle, S, Kravitz, E, Matthews, CE, Tseng, M & Carroll, RJ 2019, 'Development And Testing Of An Integrated Score For Physical Behaviors', Medicine & Science in Sports & Exercise, vol. 51, no. 6S, pp. 164-164.
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KEADLE, SK, KRAVITZ, ES, MATTHEWS, CE, TSENG, M & CARROLL, RJ 2019, 'Development and Testing of an Integrated Score for Physical Behaviors', Medicine & Science in Sports & Exercise, vol. 51, no. 8, pp. 1759-1766.
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ABSTRACT Purpose Interest in a variety of physical behaviors (e.g., exercise, sitting time, sleep) in relation to health outcomes creates a need for new statistical approaches to analyze the joint effects of these distinct but inter-related physical behaviors. We developed and tested an integrated physical behavior score (PBS). Methods National Institutes of Health-American Association of Retired Persons Diet and Health Study participants (N = 163,016) completed a questionnaire (2004–2006) asking about time spent in five exercise and nonexercise physical activities, two sedentary behaviors (television and nontelevision), and sleep. In half of the sample, we used shape-constrained additive regression to model the relationship between each behavior and survival. Maximum logit scores from each of the eight behavior-survival functions were summed to produce a PBS that was proportionally rescaled to range from 0 to 100. We examined predictive validity of the PBS in the other half-sample using Cox Proportional Hazards models after adjustment for covariates for all-cause and cause-specific mortality. Results In the testing sample, over an average of 6.6 yr of follow-up, 8732 deaths occurred. We found a strong graded decline in risk of all-cause mortality across quintiles of PBS (Q5 vs Q1 hazard ratio [95% CI] = 0.53 [0.49, 0.57]). Risk estimates for the PBS were higher than any of the components in isolation. Results were similar but stronger for cardiovascular disease (Q5 vs Q1 = 0.42 [0.39, 0.48]) and other mortality (Q5 vs Q1 = 0.42 [0.36, 0.48]). The relationship between PBS and mortality was observed ...

Keenan, CR, Iannarella, N, Garnham, AL, Brown, AC, Kim, RY, Horvat, JC, Hansbro, PM, Nutt, SL & Allan, RS 2019, 'Polycomb repressive complex 2 is a critical mediator of allergic inflammation', JCI Insight, vol. 4, no. 10.
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© 2019 American Society for Clinical Investigation. Strategies that intervene with the development of immune-mediated diseases are urgently needed, as current treatments mostly focus on alleviating symptoms rather than reversing the disease. Targeting enzymes involved in epigenetic modifcations to chromatin represents an alternative strategy that has the potential to perturb the function of the lymphocytes that drive the immune response. Here, we report that 2 major epigenetic silencing pathways are increased after T cell activation. By specifc inactivation of these molecules in the T cell compartment in vivo, we demonstrate that the polycomb repressive complex 2 (PRC2) is essential for the generation of allergic responses. Furthermore, we show that small-molecule inhibition of the PRC2 methyltransferase, enhancer of zeste homolog 2 (Ezh2), reduces allergic inflammation in mice. Therefore, by systematically surveying the pathways involved in epigenetic gene silencing we have identifed Ezh2 as a target for the suppression of allergic disease.

Kendig, MD & Morris, MJ 2019, 'Fizzing out: No effect of acute carbohydrate consumption on mood', Neuroscience & Biobehavioral Reviews, vol. 104, pp. 56-57.
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Kendig, MD & Morris, MJ 2019, 'Reviewing the effects of dietary salt on cognition: mechanisms and future directions.', Asia Pac J Clin Nutr, vol. 28, no. 1, pp. 6-14.
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BACKGROUND AND OBJECTIVES: Consumption of salt exceeds dietary guidelines for many countries around the world, despite efforts to increase awareness of the potential cardiovascular health risks. Emerging evidence, primarily from rodent models, indicates that high salt intake may also impair aspects of cognitive function. To our knowledge, here we provide the first review of the effects of salt on cognition. To review literature on the effects of high-salt diets on cognitive measures across human and non-human animal research to generate targeted questions for future studies. METHODS AND STUDY DESIGN: Non-systematic literature review of studies manipulating (in rodents) or measuring (in humans) salt intake and assessing performance on cognitive measures. RESULTS: Studies in humans have focused on older populations and show mixed associations between salt intake and cognitive performance. By contrast, most rodent studies have found impairments in cognition following chronic consumption of high-salt (typically 7-8%) diets. Most report impairments in tasks assessing spatial memory with corresponding increases in hippocampal oxidative stress and inflammatory responses originating in the gut. Notably, several rodent studies reported that high-salt diets impaired cognitive function in the absence of blood pressure changes. CONCLUSIONS: Contrasting results from human and animal studies emphasise the need for further studies to clarify whether salt intake affects cognition. Testing cognition in high-salt diet models that induce hypertension will increase the translatability of future studies in rodents. A challenge for research in humans is isolating the effects of salt from those of fat and sugar that tend to co-occur in 'western' diets.

Kendig, MD, Westbrook, RF & Morris, MJ 2019, 'Pattern of access to cafeteria-style diet determines fat mass and degree of spatial memory impairments in rats', Scientific Reports, vol. 9, no. 1, p. 13516.
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AbstractRepeated ‘cycling’ between healthy and unhealthy eating is increasingly common but the effects of such cycling on cognitive function are unknown. Here we tested the effects of cycling between chow and a cafeteria diet (CAF) rich in saturated fat and refined carbohydrates on fat mass and place recognition memory in rats. Rats fed the chow diet (control group) were compared with groups fed CAF for either: 3 consecutive days per week followed by 4 days of chow, (3CAF:4CHOW group); 5 consecutive days per week followed by 2 days of chow (5CAF:2CHOW group); or 7 days per week (7CAF group). Total days of exposure to CAF were matched between the latter groups by staggering the introduction of CAF diet. After 16–18 days of CAF, spatial recognition memory was significantly worse in the 7CAF group relative to controls. After 23–25 days of CAF, both the 7CAF and 5CAF:2CHOW groups, but not the 3CAF:4CHOW group, were impaired relative to controls, mirroring changes in fat mass measured by EchoMRI. CAF feeding did not affect object recognition memory or total exploration time. These results indicate that even when matching total exposure, the pattern of access to unhealthy diets impairs spatial memory in a graded fashion.

Keshvardoust, P, Huron, VAA, Clemson, M, Constancias, F, Barraud, N & Rice, SA 2019, 'Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria', npj Biofilms and Microbiomes, vol. 5, no. 1, p. 22.
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AbstractDespite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.

Kim, JH, Kim, H, Kang, D, Lim, YK, Ajani, P, Jung, SW & Baek, SH 2019, 'Field application and validity of a red-tide acoustic sensing system (RASS) for monitoring and alerting of harmful algal blooms (HABs) in Korean coastal waters', Journal of Applied Phycology, vol. 31, no. 6, pp. 3737-3748.
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Kim, M, Pernice, M, Watson-Lazowski, A, Guagliardo, P, Kilburn, MR, Larkum, AWD, Raven, JA & Ralph, PJ 2019, 'Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri', Marine Environmental Research, vol. 149, pp. 80-89.
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Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.

Kim, S, Duong, NMH, Nguyen, M, Lu, T-J, Kianinia, M, Mendelson, N, Solntsev, A, Bradac, C, Englund, DR & Aharonovich, I 2019, 'Integrated on chip platform with quantum emitters in layered materials', Advanced Optical Materials, vol. 7, no. 23.
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Integrated quantum photonic circuitry is an emerging topic that requiresefficient coupling of quantum light sources to waveguides and opticalresonators. So far, great effort has been devoted to engineering on-chipsystems from three-dimensional crystals such as diamond or gallium arsenide. Inthis study, we demonstrate room temperature coupling of quantum emittersembedded within a layered hexagonal boron nitride to an on-chip aluminiumnitride waveguide. We achieved 1.2% light coupling efficiency of the device andrealise transmission of single photons through the waveguide. Our results serveas a foundation for the integration of layered materials with on-chipcomponents and for the realisation of integrated quantum photonic circuitry.

Kim, S, Fröch, JE, Gardner, A, Li, C, Aharonovich, I & Solntsev, AS 2019, 'Second-harmonic generation in multilayer hexagonal boron nitride flakes', Optics Letters, vol. 44, no. 23, pp. 5792-5792.
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© 2019 Optical Society of America. In this Letter, we report the second-harmonic generation (SHG) from thick hexagonal boron nitride (hBN) flakes with approximately 109–111 layers. The resulting effective second-order susceptibility is similar to previously reported few-layer experiments. This confirms that thick hBN flakes can serve as a platform for nonlinear optics, which is useful because thick flakes are easy to exfoliate while retaining a large size. We also show spatial second-harmonic maps revealing that SHG remains a useful tool for the characterization of the layer structure, even in the case of a large number of layers.

King, AT, Hiscocks, HG, Matesic, L, Bhadbhade, M, Bishop, R & Ung, AT 2019, 'Formation of an unexpected 3,3-diphenyl-3H-indazole through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate', Beilstein Journal of Organic Chemistry, vol. 15, pp. 1347-1354.
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The one-pot reaction of 2,6-bis(diphenylmethyl)-4-methoxyaniline with tert-butylnitrite, BTEAC and DABSO in the presence of CuCl2 provided an unexpected 3H-indazole product 8. The structure of the compound was determined by HRMS, IR, NMR and further confirmed by single crystal X-ray crystallography. The compound crystallises in the triclinic P-1 space group, with unit cell parameters a = 9.2107 (4), b = 10.0413 (5), c = 14.4363 (6) Å, α = 78.183 (2), β = 87.625 (2), γ = 71.975 (2)°. The formation of 8 proceeded through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate 9. The molecules of 8 are organised by edge–face Ar–H···π, face–face π···π, and bifurcated OCH2–H···N interactions. In addition to these, there are Ar–H···H–Ar close contacts, (edge–edge and surrounding inversion centres) arranged as infinite tapes along the a direction.

King, DJM, Cheung, STY, Humphry-Baker, SA, Parkin, C, Couet, A, Cortie, MB, Lumpkin, GR, Middleburgh, SC & Knowles, AJ 2019, 'High temperature, low neutron cross-section high-entropy alloys in the Nb-Ti-V-Zr system', Acta Materialia, vol. 166, pp. 435-446.
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© 2019 Acta Materialia Inc. High-entropy alloys (HEAs) with high melting points and low thermal neutron cross-section are promising new cladding materials for generation III+ and IV power reactors. In this study a recently developed high throughput computational screening tool Alloy Search and Predict (ASAP) has been used to identify the most likely candidate single-phase HEAs with low thermal neutron cross-section, from over a million four-element equimolar combinations. The selected NbTiVZr HEA was further studied by density functional theory (DFT) for moduli and lattice parameter, and by CALPHAD to predict phase formation with temperature. HEAs of NbTiVZr x (x = 0.5, 1, 2) were produced experimentally, with Zr varied as the dominant cross-section modifier. Contrary to previous experimental work, these HEAs were demonstrated to constitute a single-phase HEA system; a result obtained using a faster cooling rate following annealing at 1200 °C. However, the beta (BCC) matrix decomposed following aging at 700 °C, into a combination of nano-scale beta, alpha (HCP) and C15 Laves phases.

King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event', Microbial Ecology, vol. 77, no. 2, pp. 502-512.
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013–2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1–V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.

King, WL, Jenkins, C, Seymour, JR & Labbate, M 2019, 'Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment', Marine Environmental Research, vol. 143, pp. 124-140.
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© 2018 Elsevier Ltd Shifting environmental conditions are known to be important triggers of oyster diseases. The mechanism(s) behind these synergistic effects (interplay between host, environment and pathogen/s) are often not clear, although there is evidence that shifts in environmental conditions can affect oyster immunity, and pathogen growth and virulence. However, the impact of shifting environmental parameters on the oyster microbiome and how this affects oyster health and susceptibility to infectious pathogens remains understudied. In this review, we summarise the major diseases afflicting oysters with a focus on the role of environmental factors that can catalyse or amplify disease outbreaks. We also consider the potential role of the oyster microbiome in buffering or augmenting oyster disease outbreaks and suggest that a deeper understanding of the oyster microbiome, its links to the environment and its effect on oyster health and disease susceptibility, is required to develop new frameworks for the prevention and management of oyster diseases.

King, WL, Siboni, N, Kahlke, T, Green, TJ, Labbate, M & Seymour, JR 2019, 'A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event', Frontiers in Microbiology, vol. 10, pp. 2907-2907.
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© Copyright © 2019 King, Siboni, Kahlke, Green, Labbate and Seymour. The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.

King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O’Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease', Frontiers in Microbiology, vol. 10, no. MAR.
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Copyright © 2019 King, Siboni, Williams, Kahlke, Nguyen, Jenkins, Dove, O’Connor, Seymour and Labbate. Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or de...

Klingberg, J, Cawley, A, Shimmon, R & Fu, S 2019, 'Collision-Induced Dissociation Studies of Synthetic Opioids for Non-targeted Analysis', Frontiers in Chemistry, vol. 7.
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The continual introduction of a large number of new psychoactive substances, along with the large turnover of these substances, necessitates the development of non-targeted detection strategies to keep pace with the ever-changing drug market. The production of certified reference materials often lags behind the introduction of new substances to the market, therefore these detection strategies need to be able to function without relying on reference materials or library spectra. Synthetic opioids have recently emerged as a drug class of particular concern due to the health issues caused by their incredibly high potency. A common method which has been used for non-targeted analysis in the past involves the identification of common product ions formed as a result of the fragmentation of the parent molecule. These common fragments can then potentially be used as markers to indicate the presence of a particular class of compounds within a sample. In this study, standards of a number of different synthetic opioids, including 14 fentanyl derivatives, 7 AH series opioids, 4 U series opioids, 4 W series opioids and MT-45, were subjected to collision-induced dissociation studies to determine how the compounds fragment. The spectra obtained from these studies included a number of diagnostic fragments common to the different opioid classes that, when used in combination, show potential for use as class predictors. By using simple data processing techniques, such as extracted ion chromatograms, these diagnostic product ions identified can be applied to a non-targeted screening workflow.

Kloten, V, Neumann, MHD, Di Pasquale, F, Sprenger-Haussels, M, Shaffer, JM, Schlumpberger, M, Herdean, A, Betsou, F, Ammerlaan, W, af Hällström, T, Serkkola, E, Forsman, T, Lianidou, E, Sjöback, R, Kubista, M, Bender, S, Lampignano, R, Krahn, T & Schlange, T 2019, 'Multicenter Evaluation of Circulating Plasma MicroRNA Extraction Technologies for the Development of Clinically Feasible Reverse Transcription Quantitative PCR and Next-Generation Sequencing Analytical Work Flows', Clinical Chemistry, vol. 65, no. 9, pp. 1132-1140.
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Abstract BACKGROUND In human body fluids, microRNA (miRNA) can be found as circulating cell-free miRNA (cfmiRNA), as well as secreted into extracellular vesicles (EVmiRNA). miRNAs are being intensively evaluated as minimally invasive liquid biopsy biomarkers in patients with cancer. The growing interest in developing clinical assays for circulating miRNA necessitates careful consideration of confounding effects of preanalytical and analytical parameters. METHODS By using reverse transcription quantitative real-time PCR and next-generation sequencing (NGS), we compared extraction efficiencies of 5 different protocols for cfmiRNA and 2 protocols for EVmiRNA isolation in a multicentric manner. The efficiency of the different extraction methods was evaluated by measuring exogenously spiked cel-miR-39 and 6 targeted miRNAs in plasma from 20 healthy individuals. RESULTS There were significant differences between the tested methods. Although column-based extraction methods were highly effective for the isolation of endogenous miRNA, phenol extraction combined with column-based miRNA purification and ultracentrifugation resulted in lower quality and quantity of isolated miRNA. Among all extraction methods, the ubiquitously expressed miR-16 was represented with high abundance when compared with other targeted miRNAs. In addition, the use of miR-16 as an endogenous control for normalization of quantification cycle values resulted in a decreased variability of column-based cfmiRNA extraction methods. Cluster analysis of normalized NGS counts clearly indicated a method-dependent bias.

Knight, S, Leigh, A, Davila, YC, Martin, LJ & Krix, DW 2019, 'Calibrating assessment literacy through benchmarking tasks', Assessment & Evaluation in Higher Education, vol. 44, no. 8, pp. 1121-1132.
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© 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group. In calibration tasks students assess exemplar texts using criteria against which their own work will be assessed. Typically, these tasks are used in the context of training for peer assessment. Little research has been conducted on the benefits of calibration tasks, such as benchmarking, as learning opportunities in their own right. This paper examines a dataset from a long-running benchmarking task (∼500 students per semester, for four semesters). We investigate the relationship of benchmarking performance to other student outcomes, including ability to self-assess accurately. We show that students who complete the benchmarking perform better, that there is a relationship between benchmarking performance and self-assessment performance, and that students appreciate the support for learning that benchmarking tasks provide. We discuss implications for teaching and learning flagging the potential of calibration tasks as an under-explored tool.

Knobel, Z, Ueland, M, Nizio, KD, Patel, D & Forbes, SL 2019, 'A comparison of human and pig decomposition rates and odour profiles in an Australian environment', Australian Journal of Forensic Sciences, vol. 51, no. 5, pp. 557-572.
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© 2018, © 2018 Australian Academy of Forensic Sciences. Cadaver-detection dogs are trained to locate victim remains; however, their training is challenging owing to limited access to human remains. Animal analogues, such as pigs, are typically used as alternative training aids. This project aimed to compare the visual decomposition and volatile organic compound (VOC) profile of human and pig remains in an Australian environment, to determine the suitability of pig remains as human odour analogues for cadaver-detection dog training. Four human cadavers and four pig carcasses were placed in an outdoor environment at the Australian Facility for Taphonomic Experimental Research (AFTER) across two seasons. Decomposition was monitored progressively in summer and winter. VOCs were collected onto sorbent tubes and analysed using comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry. Visual observations highlighted the differences in decomposition rates, with pig remains progressing through all stages of decomposition, and human remains undergoing differential decomposition and mummification. Chemical and statistical analysis highlighted variations in the composition and abundance of VOCs over time between the odour profiles. This study concluded that the visual decomposition and VOC profile of pig and human remains was dissimilar. However, in cooler conditions the results from each species became more comparable, especially during the early stages of decomposition.

Kong, M, Gu, Y, Liu, Y, Shi, Y, Wu, N, Feng, W & Li, F 2019, 'Luminescence Lifetime–Based In Vivo Detection with Responsive Rare Earth–Dye Nanocomposite', Small, vol. 15, no. 46.
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AbstractFor years, luminescence lifetime imaging has served as a quantitative tool in indicating intracellular components and activities. However, very few studies involve the in vivo study of animals, especially in vivo stimuli‐responsive activities of animals, as both excitation and emission wavelengths should fall into the near‐infrared (NIR) optical transparent window (660–950 and 1000–1500 nm). Herein, this work reports a lifetime‐responsive nanocomposite with both excitation and emission in the NIR I window (800 nm) and lifetime in the microsecond region. The incorporation of Tm3+‐doped rare‐earth nanocrystals and NIR dye builds an efficient energy transfer pathway that enables a tunable luminescence lifetime range. The NaYF4:Tm nanocrystal, which absorbs and emits photons at the same energy level, is found to be 33 times brighter than optimized core–shell upconversion nanocrystals, and proved to be an effective donor for NIR luminescence resonance energy transfer (LRET). The anti‐interference capability of luminescence lifetime signals is further confirmed by luminescence and lifetime imaging. In vivo studies also verify the lifetime response upon stimulation generated in an arthritis mouse model. This work introduces an intriguing tool for luminescence lifetime–based sensing in the microsecond region.

Kravitz, ES & Carroll, RJ 2019, 'Re‐evaluating composite scores: Adaptive Lasso variable selection for non‐linear models', Stat, vol. 8, no. 1.
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In nutrition, epidemiology, and other public health fields, composite scores are a common tool used to assess a health behaviour. These composite scores compare an individual's health behaviour to an idealized standard and provide a number, often between 0 and 100, to indicate their compliance to a health behaviour. Crucially, this measure of health behaviour is applied across populations (gender, smoking status, etc.) and health outcomes (colon cancer, breast cancer, etc.) to create a single interpretable score. One such composite score is the 2005 Healthy Eating Index that breaks diet into 12 components and evaluates nutritional intake by adherence to these components. We provide a general method that can be used to reassess the importance of these 12 components using flexible non‐linear models, across populations and diseases, based on an asymptotic least squares approximation. We establish oracle properties of this variable selection technique in our context, which is different from the usual one population and one disease context. Although our methods are motivated by the Healthy Eating Index, they are broad enough to be applied to any composite score and a broad range of non‐linear models.

Kretzschmar, AL, Larsson, ME, Hoppenrath, M, Doblin, MA & Murray, SA 2019, 'Characterisation of Two Toxic Gambierdiscus spp. (Gonyaulacales, Dinophyceae) from the Great Barrier Reef (Australia): G. lewisii sp. nov. and G. holmesii sp. nov.', Protist, vol. 170, no. 6, pp. 125699-125699.
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© 2019 Elsevier GmbH Ciguatera fish poisoning (CFP) is a human illness caused via consumption of seafood contaminated with neurotoxins produced by some species from the epiphytic dinoflagellate genus Gambierdiscus. In this study, we describe two new species of Gambierdiscus isolated from Heron Island in the Southern Great Barrier Reef, Queensland, Australia. These new species were analysed using light microscopy, scanning electron microscopy, and phylogenetic analyses of nuclear encoded ribosomal ITS, SSU as well as D1-D3 and D8-D10 of the LSU gene regions. Gambierdiscus lewisii sp. nov. (Po, 3′, 0a, 7″, 6c,? s, 5‴, 0p, 2′‴) is distinguished by its strong reticulate-foveate ornamentation and is genetically distinct from its sister species, G. pacificus. Gambierdiscus holmesii sp. nov. (Po, 3′, 0a, 7″, 6c, 6s?, 5‴, 0p, 2′‴) is morphologically distinct from the genetically similar species G. silvae because of a strongly ventrally displaced apical pore complex and a characteristic fold at the anterior edge of the sulcus. Both G. lewisii and G. holmesii produce putative Maitotoxin-(44-Methylgambierone) and compounds which show ciguatoxin and maitotoxin-like activities. Identification of two new Gambierdiscus species will enable us to more accurately assess the risk of CFP in Australia and internationally.

Kretzschmar, AL, Verma, A, Kohli, G & Murray, S 2019, 'Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)', PLOS ONE, vol. 14, no. 11, pp. e0224664-e0224664.
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© 2019 Public Library of Science. All rights reserved. Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts.

Krix, DW, Phillips, ML & Murray, BR 2019, 'Relationships among leaf flammability attributes and identifying low-leaf-flammability species at the wildland–urban interface', International Journal of Wildland Fire, vol. 28, no. 4, pp. 295-295.
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Leaf flammability is a multidimensional plant functional trait with emerging importance for wildfire risk management. Understanding relationships among leaf flammability attributes not only provides information about the properties of leaves as fuels in the wildland–urban interface (WUI), it can also offer an effective way to identify low-leaf-flammability species. We examined relationships between leaf ignitibility, sustainability and combustibility among 60 plant species of the WUI of eastern Australia. We found that leaf ignitibility and sustainability worked in opposition to each other as dimensions of flammability. Species with leaves that were slow to ignite were those with leaves that sustained burning for the longest, whereas species with leaves that were fast to ignite had leaves that burned for the shortest periods of time. Low leaf combustibility was related to short leaf burning sustainability but not to ignitibility. We created an overall leaf flammability index (OLFI) to rank species on emergent properties of ignitibility, sustainability and combustibility attributes in combination. We found that low-leaf-flammability species with low OLFI values had small leaf area, high leaf mass per area and high leaf water content. Our findings have implications for species selection for green firebreaks in the WUI.

Kumar, R, Kumar, R, Sharma, N, Vyas, M, Mahajan, S, Satija, S, Singh, SK, Khursheed, R, Mehta, M, Khurana, S & Khurana, N 2019, 'Fisetin: A phytochemical with various pharmacological activities', Plant Archives, vol. 19, pp. 1012-1016.
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Flavonoids are the plant secondary metabolites which work as growth hormone as well as defence mechanism for the plants. These are well known for their antioxidant properties and are part of our daily food. Fisetin is one of the polyphenolic flavonol, present in various fruits and vegetables. Fisetin is reported to have various pharmacological properties. Strawberries have the maximum concentration of fisetin. Despite having various pharmacological properties, low oral bioavailability and high lipophilicity meared its use. In this review we tried to collect the information regarding the various pharmacological properties and its developed formulations to improve its bioavailability.

Kumar, R, Kumar, R, Sharma, N, Vyas, M, Mahajan, S, Satija, S, Singh, SK, Mehta, M & Khurana, N 2019, 'Genetics of Parkinson's disease: How close and how far we are?', Plant Archives, vol. 19, pp. 1017-1021.
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Parkinson's disease (PD) is one of the neuronal disorder in which there is continuous degeneration of the neurons occur. It is an age related disorder, so the most effected peoples are those who are 60 or above 60years of age. The main neurons involved in PD are the dopaminergic neurons, specifically present in the substantia nigra pars compacta. It is known that, at the time of diagnosis of PD or appearance of its symptoms, 80% of the dopaminergic neurons got deteriorated. The major symptoms of PD are tremors, rigidity, akinesia and postural instability. There are various etiological factors which are responsible for the development of the PD and among them, genetic factor considered to be one of main factor involved in this condition. The major genes which are involved in PD are SNCA, PARK1, PARK 2 and DJ-1. Whenever, any mutation occurs in these genes, it alters the protein expression which ultimately leads to the dysfunction of the neuronal cell organelles. There is aggregation of the α-synuclein protein occurs due to the mutation of these genes. In the present review, we reviewed the available information regarding the genetic of the PD and try to conclude about its present status.

Kumar, V, Wadhwa, R, Kumar, N & Maurya, PK 2019, 'A comparative study of chemically synthesized and Camellia sinensis leaf extract-mediated silver nanoparticles', 3 Biotech, vol. 9, no. 1.
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© 2019, King Abdulaziz City for Science and Technology. Silver nanoparticles (AgNPs) are amongst the most fascinating nanomaterials which have been extensively synthesized by chemical reduction and biological method using enzymes, microorganisms and plant extracts. In our study, an aqueous extract of green tea was used as a stabilizing and reducing agent for AgNPs synthesis. The synthesized AgNPs were characterized by dynamic light scattering, UV–visible (UV–Vis) spectroscopy and scanning electron microscopy. These AgNPs were evaluated for antimicrobial activity and photocatalytic dye degradation. The AgNPs showed antibacterial activity against E. coli, S. aureus and S. pyogenes with 6 mm, 5 mm and 8 mm zone of inhibition, respectively. Our work also focused on methylene blue degradation in aqueous solution using AgNPs as catalyst which shows 65% of dye degradation. An absorbance peak of 427–437 nm was observed using UV–Vis spectrophotometer. Our study proves that the AgNPs show potent antimicrobial activity against pathogenic bacteria. At room temperature, AgNPs possess rapid, effective and steady catalytic activity in cationic organic dye degradation. The high catalytic activity of AgNPs can be employed in industries and water purification. Our study confirmed that green-synthesized AgNPs are eco-friendly and non-toxic.

Kusuma, KD, Griffith, R, Harry, EJ, Bottomley, AL & Ung, AT 2019, 'Analysis of FtsZ Crystal Structures Towards a New Target for Antibiotics', Australian Journal of Chemistry, vol. 72, no. 3, pp. 184-193.
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The bacterial cell division protein FtsZ is conserved in most bacteria and essential for viability. There have been concerted efforts in developing inhibitors that target FtsZ as potential antibiotics. Key to this is an in-depth understanding of FtsZ structure at the molecular level across diverse bacterial species to ensure inhibitors have high affinity for the FtsZ target in a variety of clinically relevant pathogens. In this study, we show that FtsZ structures differ in three ways: (1) the H7 helix curvature; (2) the dimensions of the interdomain cleft; and (3) the opening/closing mechanism of the interdomain cleft, whereas no differences were observed in the dimensions of the nucleotide-binding pocket and T7 loop. Molecular dynamics simulation may suggest that there are two possible mechanisms for the process of opening and closing of the interdomain cleft on FtsZ structures. This discovery highlights significant differences between FtsZ structures at the molecular level and this knowledge is vital in assisting the design of potent FtsZ inhibitors.

Kusuma, KD, Payne, M, Ung, AT, Bottomley, AL & Harry, EJ 2019, 'FtsZ as an Antibacterial Target: Status and Guidelines for Progressing This Avenue', ACS Infectious Diseases, vol. 5, no. 8, pp. 1279-1294.
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© 2019 American Chemical Society. The disturbing increase in the number of bacterial pathogens that are resistant to multiple, or sometimes all, current antibiotics highlights the desperate need to pursue the discovery and development of novel classes of antibacterials. The wealth of knowledge available about the bacterial cell division machinery has aided target-driven approaches to identify new inhibitor compounds. The main division target being pursued is the highly conserved and essential protein FtsZ. Despite very active research on FtsZ inhibitors for several years, this protein is not yet targeted by any commercial antibiotic. Here, we discuss the suitability of FtsZ as an antibacterial target for drug development and review progress achieved in this area. We use hindsight to highlight the gaps that have slowed progress in FtsZ inhibitor development and to suggest guidelines for concluding that FtsZ is actually the target of these molecules, a key missing link in several studies. In moving forward, a multidisciplinary, communicative, and collaborative process, with sharing of research expertise, is critical if we are to succeed.

Kysenius, K, Hilton, JB, Paul, B, Hare, DJ & Crouch, PJ 2019, 'Anatomical redistribution of endogenous copper in embryonic mice overexpressing SOD1', Metallomics, vol. 11, no. 1, pp. 141-150.
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Detailed quantitativein situimaging of embryonic mice reveals overt Cu redistribution associated with SOD1-overexpression.

Kysenius, K, Paul, B, Hilton, JB, Liddell, JR, Hare, DJ & Crouch, PJ 2019, 'A versatile quantitative microdroplet elemental imaging method optimised for integration in biochemical workflows for low-volume samples', Analytical and Bioanalytical Chemistry, vol. 411, no. 3, pp. 603-616.
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Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) analysis of μ-droplets is becoming an attractive alternative for detecting and quantifying elements in biological samples. With minimal sample preparation required and detection limits comparable to solution nebulisation ICP-MS, μ-droplets have substantial advantages over traditional elemental detection, particularly for low volumes, such as aliquots taken from samples required for multiple independent biochemical assays, or fluids and tissues where elements of interest exist at native concentrations not suited to the necessary dilution steps required for solution nebulisation ICP-MS. However, the characteristics of μ-droplet residue deposition are heavily dependent on the matrix, and potential effects on signal suppression or enhancement have not been fully characterised. We present a validated and flexible high-throughput method for quantification of elements in μ-droplets using LA-ICP-MS imaging and matrix-matched external calibrants. Imaging the entire μ-droplet area removes analytical uncertainty arising from the often-heterogenous distribution when compared to radial or bisecting line scans that capture only a small portion of the droplet residue. We examined the effects of common matrices found in a standard biochemistry workflow, including native protein and salt contents, as well as reagents used in typical preparation steps for concurrent biochemical assays, such as total protein quantification and enzyme activity assays. We found that matrix composition results in systemic, concentration-dependent signal enhancement and suppression for carbon, whereas high sodium content has a specific space-charge-like suppression effect on high masses. We confirmed the accuracy of our method using both a certified serum standard (Seronorm™ L1) and independent measurements of analysed samples by solution nebulisation ICP-MS, then tested the specificity and reproducibility by examining spinal cord ...

Larsson, ME, Harwood, TD, Lewis, RJ, S. W. A., H & Doblin, MA 2019, 'Toxicological characterization of Fukuyoa paulensis (Dinophyceae) from temperate Australia', Phycological Research, vol. 67, no. 1, pp. 65-71.
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SUMMARYDinoflagellates of the genus Gambierdiscus are known to produce neurotoxins that cause the human illness ciguatera, a tropical and sub‐tropical fish poisoning. Some species from the Gambierdiscus genus were recently re‐classified into a new genus, Fukuyoa based on their phylogenetic and morphological divergence, however, little is known about their distribution, ecology and toxicology. Here we report the first occurrence of F. paulensis in the temperate coastal waters of eastern Australia and characterize its toxicology. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) did not detect the presence of ciguatoxins, however, a putative maitotoxin congener (MTX‐3) was present. Similarly, high maitotoxin‐like activity was detected in High Performance Liquid Chromatography (HPLC) fractionated cell extracts using a Ca2+ influx bioassay on a Fluorescent Imaging Plate Reader (FLIPR), but no ciguatoxin‐like activity was detected.

Larsson, ME, Smith, KF & Doblin, MA 2019, 'First description of the environmental niche of the epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis (Dinophyceae) from Eastern Australia', Journal of Phycology, vol. 55, no. 3, pp. 565-577.
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Environmental variables such as temperature, salinity, and irradiance are significant drivers of microalgal growth and distribution. Therefore, understanding how these variables influence fitness of potentially toxic microalgal species is particularly important. In this study, strains of the potentially harmful epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis were isolated from coastal shallow water habitats on the east coast of Australia and identified using the D1‐D3 region of the large subunit (LSU) ribosomal DNA (rDNA). To determine the environmental niche of each taxon, growth was measured across a gradient of temperature (15–30°C), salinity (20–38), and irradiance (10–200 μmol photons · m−2 · s−1). Specific growth rates of Coolia tropicalis were highest under warm temperatures (27°C), low salinities (ca. 23), and intermediate irradiance levels (150 μmol photons · m−2 · s−1), while C. malayensis showed the highest growth at moderate temperatures (24°C) and irradiance levels (150 μmol photons · m−2 · s−1) and growth rates were consistent across the range of salinity levels tested (20–38). Coolia palmyrensis had the highest growth rate of all species tested and favored moderate temperatures (24°C), oceanic salinity (35), and high irradiance (>200 μmol photons · m−2 · s−1). This is the first study to characterize the environmental niche of species from the benthic harmful algal bloom genus

Lau, A, Kong, FYS, Huston, W, Chow, EPF, Fairley, CK & Hocking, JS 2019, 'Factors associated with anorectal Chlamydia trachomatis or Neisseria gonorrhoeae test positivity in women: a systematic review and meta-analysis', Sexually Transmitted Infections, vol. 95, no. 5, pp. 361-367.
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ObjectivesThere has been considerable discussion about anorectal Chlamydia trachomatis (CT) in women, with some calling for anorectal CT screening, but little about anorectal Neisseria gonorrhoeae (NG). Given that urogenital NG is more strongly associated with pelvic inflammatory disease, this is an evidence gap. This systematic review and meta-analysis investigates the associations between anorectal CT in women and CT positivity at other sites (urogenital/oropharyngeal) and with anal intercourse, and compares these with anorectal NG within the same study populations.MethodsElectronic databases were searched for English-language studies published to October 2018 using the following terms: (“Chlamydia” OR “Chlamydia trachomatis”) AND ((“anal” OR “rect*” OR “anorect*”) OR (“extra?genital” OR “multi?site”)). Studies were included if anorectal NG data were available. Random-effects meta-analyses calculated pooled estimates; heterogeneity was investigated using meta-regression.Results25 studies were eligible. Anorectal CT positivity ranged from 0% to 17.5%, with a summary estimate of 8.0% (95% CI 7.0 to 9.1; I2=88.5%). Anorectal NG positivity ranged from 0% to 17.0%, with a summary estimate of 2.1% (95% CI 1.6 to 2.8; I2=92.7%). The association between urogenital and anorectal positivity was stronger for NG than CT (summary prevalence ratio (PR)=89.3 (95% CI 53.1 to 150.3; I2=80.1%), PR=32.2 (95% CI 25.6 to 40.7; I2=70.3%), respectively), and between oropharyngeal and anorectal positivity it was stronger for NG than CT (PR=34.8 (95% CI 10.2 to 118.2; I2=89.9%), PR=8.8 (95% CI 6.8 to 11.5; I2

Lawson, CA, Possell, M, Seymour, JR, Raina, J-B & Suggett, DJ 2019, 'Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress', Scientific Reports, vol. 9, no. 1.
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AbstractBiogenic volatile organic compounds (BVOCs) influence organism fitness by promoting stress resistance and regulating trophic interactions. Studies examining BVOC emissions have predominantly focussed on terrestrial ecosystems and atmospheric chemistry – surprisingly, highly productive marine ecosystems remain largely overlooked. Here we examined the volatilome (total BVOCs) of the microalgal endosymbionts of reef invertebrates, Symbiodiniaceae. We used GC-MS to characterise five species (Symbiodinium linucheae, Breviolum psygmophilum, Durusdinium trenchii, Effrenium voratum, Fugacium kawagutii) under steady-state growth. A diverse range of 32 BVOCs were detected (from 12 in D. trenchii to 27 in S. linucheae) with halogenated hydrocarbons, alkanes and esters the most common chemical functional groups. A thermal stress experiment on thermally-sensitive Cladocopium goreaui and thermally-tolerant D. trenchii significantly affected the volatilomes of both species. More BVOCs were detected in D. trenchii following thermal stress (32 °C), while fewer BVOCs were recorded in stressed C. goreaui. The onset of stress caused dramatic increases of dimethyl-disulfide (98.52%) in C. goreaui and nonanoic acid (99.85%) in D. trenchii. This first volatilome analysis of Symbiodiniaceae reveals that both species-specificity and environmental factors govern the composition of BVOC emissions among the Sym...

Lee, PLT, Kanodarwala, FK, Lennard, C, Spindler, X, Spikmans, V, Roux, C & Moret, S 2019, 'Latent fingermark detection using functionalised silicon oxide nanoparticles: Method optimisation and evaluation', Forensic Science International, vol. 298, pp. 372-383.
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© 2019 Elsevier B.V. The application of nanoparticles for latent fingermark detection has been reported in the literature over the past two decades. One of the nanoparticles that shows promise to become a routine technique is functionalised silicon oxide nanoparticles (SiO 2 NPs). In a recent optimisation of the technique, the use of carboxyl-functionalised SiO 2 NPs doped with luminescent ruthenium complex was proposed as a breakthrough for latent fingermark detection. In this study, the aforementioned functionalised SiO 2 NPs were extensively evaluated. Modification and optimisation of the original detection parameters were performed to enhance detection quality and improve applicability. Various detection parameters were evaluated and assessed. A lower concentration of the functionalised nanoparticles used in the colloidal dispersion was determined to offer improved detection effectiveness. A combination of increased bath temperature and reduced immersion time was found to produce good overall results. A set of modified detection parameters was suggested for the use of the functionalised SiO 2 NPs to detect latent fingermarks. Performance of the modified detection parameters was compared against that of the published detection method. Comparison experiments were carried out on fingermark specimens deposited on aluminium foil, transparent polypropylene plastic and green polyethylene plastic. Three donors (weak, average and strong) and two age intervals (ten days and three months) were considered in the comparison study. Evaluation of the results suggested that the overall performance of the modified method for latent fingermark detection was superior to that obtained using the previously published detection parameters.

Lee, U, Garcia, TP, Carroll, RJ, Gilbreath, KR & Wu, G 2019, 'Analysis of repeated measures data in nutrition research.', Front Biosci (Landmark Ed), vol. 24, no. 8, pp. 1377-1389.
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Amino acid nutrition studies often involve repeated measures data. An example is that the concentrations of plasma citrulline in steers are repeatedly measured from the same animals. The standard repeated measures ANOVA method does not detect significant time changes in the concentrations of plasma citrulline within 6 hours after steers consumed rumen-protected citrulline, while a graphical analysis indicates that there exists a time effect. Here we describe three mixed model analyses that capture the time effect in a statistically significant way, while accounting for the correlations of measurements over time from the same steers. First, we allow flexible variance-covariance structures on our model. Second, we use baseline measurements as a covariate in our model. Third, we use percent-change from baseline as a data normalization method. In our data analysis, all these three approaches can lead to meaningful statistical results that oral administration of rumen-protected citrulline enhances the concentrations of plasma citrulline over time in ruminants. This supports the notion that rumen-protected citrulline can bypass the rumen to effectively enter the blood circulation.

LEES, T, ELLIOTT, JL, GUNNING, S, NEWTON, PJ, RAI, T & LAL, S 2019, 'A systematic review of the current evidence regarding interventions for anxiety, PTSD, sleepiness and fatigue in the law enforcement workplace', Industrial Health, vol. 57, no. 6, pp. 655-667.
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© 2019 National Institute of Occupational Safety and Health. Law enforcement is inherently stressful, and police officers are particularly vulnerable to mental and physical disorders. As such, researchers are currently assessing intervention strategies that may combat or manage these psychological, physical and mental issues. To review most recent information regarding anxiety, PTSD, and sleepiness and fatigue and identify the interventions and treatments proposed to overcome work related stressors and associated mental illnesses inflicting law enforcement officers. The EMBASE, OVID MEDLINE and PsycINFO databases were canvassed for articles investigating anxiety, post-traumatic stress disorder, sleepiness, and fatigue. Initial article selections were made based on title, whilst final inclusion was informed by a full critical appraisal with respect to the primary and secondary effects. The systematic search returned 363 records, of which 183 were unique. Following screening, 43 records were included in the final review. The included literature assessed the efficacy of several interventions, and provided a number of recommendations regarding interventions, and policy. Moreover, literature indicates that police officers benefit from interventions targeting work-related stress and potential psychological disorders, if these interventions are continuous. Furthermore, larger controlled studies are required to further elucidate the benefits of psychosocial intervention in law enforcement.

Leggat, WP, Camp, EF, Suggett, DJ, Heron, SF, Fordyce, AJ, Gardner, S, Deakin, L, Turner, M, Beeching, LJ, Kuzhiumparambil, U, Eakin, CM & Ainsworth, TD 2019, 'Rapid Coral Decay Is Associated with Marine Heatwave Mortality Events on Reefs', Current Biology, vol. 29, no. 16, pp. 2723-2730.e4.
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© 2019 Elsevier Ltd Due to climate change, coral reefs are now being subjected to extreme marine heatwave (MHW) conditions. Leggat et al. show that large-scale mortality due to MHWs and microbial colonization leads to a previously undescribed rapid dissolution of the coral skeleton.

Leggio, GM, Di Marco, R, Gulisano, W, D’Ascenzo, M, Torrisi, SA, Geraci, F, Lavanco, G, Dahl, K, Giurdanella, G, Castorina, A, Aitta-aho, T, Aceto, G, Bucolo, C, Puzzo, D, Grassi, C, Korpi, ER, Drago, F & Salomone, S 2019, 'Dopaminergic-GABAergic interplay and alcohol binge drinking', Pharmacological Research, vol. 141, pp. 384-391.
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The dopamine D3 receptor (D3R), in the nucleus accumbens (NAc), plays an important role in alcohol reward mechanisms. The major neuronal type within the NAc is the GABAergic medium spiny neuron (MSN), whose activity is regulated by dopaminergic inputs. We previously reported that genetic deletion or pharmacological blockade of D3R increases GABAA α6 subunit in the ventral striatum. Here we tested the hypothesis that D3R-dependent changes in GABAA α6 subunit in the NAc affect voluntary alcohol intake, by influencing the inhibitory transmission of MSNs. We performed in vivo and ex vivo experiments in D3R knockout (D3R -/-) mice and wild type littermates (D3R +/+). Ro 15-4513, a high affinity α6-GABAA ligand was used to study α6 activity. At baseline, NAc α6 expression was negligible in D3R+/+, whereas it was robust in D3R-/-; other relevant GABAA subunits were not changed. In situ hybridization and qPCR confirmed α6 subunit mRNA expression especially in the NAc. In the drinking-in-the-dark paradigm, systemic administration of Ro 15-4513 inhibited alcohol intake in D3R+/+, but increased it in D3R-/-; this was confirmed by intra-NAc administration of Ro 15-4513 and furosemide, a selective α6-GABAA antagonist. Whole-cell patch-clamp showed peak amplitudes of miniature inhibitory postsynaptic currents in NAc medium spiny neurons higher in D3R-/- compared to D3R+/+; Ro 15-4513 reduced the peak amplitude in the NAc of D3R-/-, but not in D3R+/+. We conclude that D3R-dependent enhanced expression of α6 GABAA subunit inhibits voluntary alcohol intake by increasing GABA inhibition in the NAc.

Lehmann, DM, Krishnakumar, K, Batres, MA, Hakola-Parry, A, Cokcetin, N, Harry, E & Carter, DA 2019, 'A cost-effective colourimetric assay for quantifying hydrogen peroxide in honey', Access Microbiology, vol. 1, no. 10.
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Honey is a natural product with many beneficial properties including antimicrobial action. Production of hydrogen peroxide (H2O2) in diluted honey is central to this action. Here, we describe an optimized method for measuring levels of H2O2 in honey. This method is based on established methods, with the level of dilution, the time between dilution and reading the assay, and aeration of the samples during the assay identified as critical points for ensuring reliability and reproducibility. The method is cost-effective and easy to perform using common laboratory equipment. Using this method, we quantified the hydrogen peroxide content of five different, unprocessed polyfloral honeys collected in NC, USA. Our results show that H2O2 production by these honeys varies greatly, with some samples producing negligible levels of H2O2. We assessed the effect of colour on the assay by measuring the recovery of spiked H2O2 from light and dark honey and from serially diluted dark corn syrup, and found the amount of H2O2 that could be detected was lower in dark corn syrup and darker honey samples.

Lema, KA, Constancias, F, Rice, SA & Hadfield, MG 2019, 'High bacterial diversity in nearshore and oceanic biofilms and their influence on larval settlement by Hydroides elegans (Polychaeta)', Environmental Microbiology, vol. 21, no. 9, pp. 3472-3488.
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SummarySettlement of many benthic marine invertebrates is stimulated by bacterial biofilms, although it is not known if patterns of settlement reflect microbial communities that are specific to discrete habitats. Here, we characterized the taxonomic and functional gene diversity (16S rRNA gene amplicon and metagenomic sequencing analyses), as well as the specific bacterial abundances, in biofilms from diverse nearby and distant locations, both inshore and offshore, and tested them for their ability to induce settlement of the biofouling tubeworm Hydroides elegans, an inhabitant of bays and harbours around the world. We found that compositions of the bacterial biofilms were site specific, with the greatest differences between inshore and offshore sites. Further, biofilms were highly diverse in their taxonomic and functional compositions across inshore sites, while relatively low diversity was found at offshore sites. Hydroides elegans settled on all biofilms tested, with settlement strongly correlated with bacterial abundance. Bacterial density in biofilms was positively correlated with biofilm age. Our results suggest that the localized distribution of H. elegans is not determined by ‘selection’ to locations by specific bacteria, but it is more likely linked to the prevailing local ecology and oceanographic features that affect the development of dense biofilms and the occurrence of larvae.

Levin, LA, Bett, BJ, Gates, AR, Heimbach, P, Howe, BM, Janssen, F, McCurdy, A, Ruhl, HA, Snelgrove, P, Stocks, KI, Bailey, D, Baumann-Pickering, S, Beaverson, C, Benfield, MC, Booth, DJ, Carreiro-Silva, M, Colaço, A, Eblé, MC, Fowler, AM, Gjerde, KM, Jones, DOB, Katsumata, K, Kelley, D, Le Bris, N, Leonardi, AP, Lejzerowicz, F, Macreadie, PI, McLean, D, Meitz, F, Morato, T, Netburn, A, Pawlowski, J, Smith, CR, Sun, S, Uchida, H, Vardaro, MF, Venkatesan, R & Weller, RA 2019, 'Global Observing Needs in the Deep Ocean', Frontiers in Marine Science, vol. 6, no. May.
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© 2019 Levin, Bett, Gates, Heimbach, Howe, Janssen, McCurdy, Ruhl, Snelgrove, Stocks, Bailey, Baumann-Pickering, Beaverson, Benfield, Booth, Carreiro-Silva, Colaço, Eblé, Fowler, Gjerde, Jones, Katsumata, Kelley, Le Bris, Leonardi, Lejzerowicz, Macreadie, McLean, Meitz, Morato, Netburn, Pawlowski, Smith, Sun, Uchida, Vardaro, Venkatesan and Weller. The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth of energy, mineral, and biological resources, and represents a vast repository of biological diversity. A long history of deep-ocean exploration and observation led to the initial concept for the Deep-Ocean Observing Strategy (DOOS), under the auspices of the Global Ocean Observing System (GOOS). Here we discuss the scientific need for globally integrated deep-ocean observing, its status, and the key scientific questions and societal mandates driving observing requirements over the next decade. We consider the Essential Ocean Variables (EOVs) needed to address deep-ocean challenges within the physical, biogeochemical, and biological/ecosystem sciences according to the Framework for Ocean Observing (FOO), and map these onto scientific questions. Opportunities for new and expanded synergies among deep-ocean stakeholders are discussed, including academic-industry partnerships with the oil and gas, mining, cable and fishing industries, the ocean exploration and mapping community, and biodiversity conservation initiatives. Future deep-ocean observing will benefit from the greater integration across traditional disciplines and sectors, achieved through demonstration projects and facilitated reuse and repurposing of existing deep-sea data efforts. We highlight examples of existing and emerging deep-sea methods and technologies, noting key challenges associated with data volume, pres...

Li, A, Geyer, FC, Blecua, P, Lee, JY, Selenica, P, Brown, DN, Pareja, F, Lee, SSK, Kumar, R, Rivera, B, Bi, R, Piscuoglio, S, Wen, HY, Lozada, JR, Gularte-Mérida, R, Cavallone, L, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Balleine, R, Beesley, J, Blackburn, A, Bogwitz, M, Brown, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Campbell, I, Christian, A, Clarke, C, Cohen, P, Crook, A, Cui, J, Cummings, M, Dawson, S-J, De Fazio, A, Delatycki, M, Dobrovic, A, Dudding, T, Duijf, P, Edkins, E, Edwards, S, Farshid, G, Fellows, A, Field, M, Flanagan, J, Fong, P, Forbes, J, Forrest, L, Fox, S, French, J, Friedlander, M, Ortega, DG, Gattas, M, Giles, G, Gill, G, Gleeson, M, Greening, S, Haan, E, Harris, M, Hayward, N, Hickie, I, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kentwell, M, Kirk, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Lok, S, Macrea, F, Mann, G, Marsh, D, McLachlan, S-A, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, Pachter, N, Patterson, B, Phillips, K, Saleh, M, Salisbury, E, Saunders, C, Saunus, J, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Spigelman, A, Spurdle, M, Stone, J, Taylor, J, Thorne, H, Trainer, A, Trench, G, Tucker, K, Visvader, J, Walker, L, Wallis, M, Williams, R, Winship, I, Wu, K, Young, MA, Rezoug, Z, Nguyen-Dumont, T, Peterlongo, P, Tondini, C, Terkelsen, T, Rønlund, K, Boonen, SE, Mannerma, A, Winqvist, R, Janatova, M, Rajadurai, P, Xia, B, Norton, L, Robson, ME, Ng, P-S, Looi, L-M, Southey, MC, Weigelt, B, Soo-Hwang, T, Tischkowitz, M, Foulkes, WD & Reis-Filho, JS 2019, 'Publisher Correction: Homologous recombination DNA repair defects in PALB2-associated breast cancers', npj Breast Cancer, vol. 5, no. 1.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Li, A, Geyer, FC, Blecua, P, Lee, JY, Selenica, P, Brown, DN, Pareja, F, Lee, SSK, Kumar, R, Rivera, B, Bi, R, Piscuoglio, S, Wen, HY, Lozada, JR, Gularte-Mérida, R, Cavallone, L, Rezoug, Z, Nguyen-Dumont, T, Peterlongo, P, Tondini, C, Terkelsen, T, Rønlund, K, Boonen, SE, Mannerma, A, Winqvist, R, Janatova, M, Rajadurai, P, Xia, B, Norton, L, Robson, ME, Ng, P-S, Looi, L-M, Southey, MC, Weigelt, B, Soo-Hwang, T, Tischkowitz, M, Foulkes, WD, Reis-Filho, JS, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Balleine, R, Beesley, J, Blackburn, A, Bogwitz, M, Brown, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Campbell, I, Christian, A, Clarke, C, Cohen, P, Crook, A, Cui, J, Cummings, M, Dawson, S-J, De Fazio, A, Delatycki, M, Dobrovic, A, Dudding, T, Duijf, P, Edkins, E, Edwards, S, Farshid, G, Fellows, A, Field, M, Flanagan, J, Fong, P, Forbes, J, Forrest, L, Fox, S, French, J, Friedlander, M, Ortega, DG, Gattas, M, Giles, G, Gill, G, Gleeson, M, Greening, S, Haan, E, Harris, M, Hayward, N, Hickie, I, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kentwell, M, Kirk, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Lok, S, Macrea, F, Mann, G, Marsh, D, McLachlan, S-A, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, Pachter, N, Patterson, B, Phillips, K, Saleh, M, Salisbury, E, Saunders, C, Saunus, J, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Spigelman, A, Spurdle, M, Stone, J, Taylor, J, Thorne, H, Trainer, A, Trench, G, Tucker, K, Visvader, J, Walker, L, Wallis, M, Williams, R, Winship, I, Wu, K & Young, MA 2019, 'Homologous recombination DNA repair defects in PALB2-associated breast cancers', npj Breast Cancer, vol. 5, no. 1.
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AbstractMono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2

Li, C, Xu, Z-Q, Mendelson, N, Kianinia, M, Toth, M & Aharonovich, I 2019, 'Purification of single-photon emission from hBN using post-processing treatments', Nanophotonics, vol. 8, no. 11, pp. 2049-2055.
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Abstract Single-photon emitters (SPEs) in hexagonal boron nitride (hBN) are promising components for on-chip quantum information processing. Recently, large-area hBN films prepared by chemical vapor deposition (CVD) were found to host uniform, high densities of SPEs. However, the purity of these emitters has, to date, been low, hindering their applications in practical devices. In this work, we present two methods for post-growth processing of hBN, which significantly improve SPEs in hBN films that had been transferred from substrates used for CVD. The emitters exhibit high photon purities in excess of 90% and narrow linewidths of ~3 nm at room temperature. Our work lays a foundation for producing high-quality emitters in an ultra-compact two-dimensional material system and paves the way for deployment of hBN SPEs in scalable on-chip photonic and quantum devices.

Li, D, Roca, M, Yuecel, R & Lorenz, A 2019, 'Immediate visualization of recombination events and chromosome segregation defects in fission yeast meiosis', Chromosoma, vol. 128, no. 3, pp. 385-396.
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Li, G, Chan, YL, Nguyen, LT, Mak, C, Zaky, A, Anwer, AG, Shi, Y, Nguyen, T, Pollock, CA, Oliver, BG, Saad, S & Chen, H 2019, 'Impact of maternal e‐cigarette vapor exposure on renal health in the offspring', Annals of the New York Academy of Sciences, vol. 1452, no. 1, pp. 65-77.
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AbstractMaternal smoking during pregnancy is a significant risk factor of renal pathology in the offspring. E‐cigarettes are perceived to be a safe option and are increasingly used by pregnant women either continuously during pregnancy or as a replacement for tobacco cigarettes. This study aimed to determine the effects of replacing tobacco cigarettes with e‐cigarettes during pregnancy, and continuous e‐cigarette use during pregnancy on the offspring's kidneys. Female Balb/c mice were exposed to either air (sham) or tobacco cigarette smoke (SE) for 6 weeks prior to mating, during gestation and lactation. A subset of the “SE group” received e‐cigarette vapor (containing nicotine) after mating until pups weaned. Additional female mice were continuously exposed to e‐vapor (either with or without nicotine) for 6 weeks prior to mating until pups weaned. Kidneys and urine from the male offspring were assessed at postnatal day 1, day 20 (weaning), and 13 weeks of age (adulthood). E‐cigarette replacement was less detrimental to renal development and albuminuria than continuous SE during pregnancy. However, continuous e‐vapor exposure during pregnancy increased markers of oxidative stress, inflammation, and fibrosis in the adult offspring, independent of nicotine. E‐cigarette use during pregnancy confers future risk to the offspring's kidneys.

Li, G, Chan, YL, Sukjamnong, S, Anwer, AG, Vindin, H, Padula, M, Zakarya, R, George, J, Oliver, BG, Saad, S & Chen, H 2019, 'A Mitochondrial Specific Antioxidant Reverses Metabolic Dysfunction and Fatty Liver Induced by Maternal Cigarette Smoke in Mice', Nutrients, vol. 11, no. 7, pp. 1669-1669.
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Maternal smoking leads to glucose and lipid metabolic disorders and hepatic damage in the offspring, potentially due to mitochondrial oxidative stress. Mitoquinone mesylate (MitoQ) is a mitochondrial targeted antioxidant with high bioavailability. This study aimed to examine the impact of maternal cigarette smoke exposure (SE) on offspring’s metabolic profile and hepatic damage, and whether maternal MitoQ supplementation during gestation can affect these changes. Female Balb/c mice (eight weeks) were either exposed to air or SE for six weeks prior to mating and throughout gestation and lactation. A subset of the SE dams were supplied with MitoQ in the drinking water (500 µmol/L) during gestation and lactation. Intraperitoneal glucose tolerance test was performed in the male offspring at 12 weeks and the livers and plasma were collected at 13 weeks. Maternal SE induced glucose intolerance, hepatic steatosis, mitochondrial oxidative stress and related damage in the adult offspring. Maternal MitoQ supplementation reduced hepatic mitochondrial oxidative stress and improved markers of mitophagy and mitochondrial biogenesis. This may restore hepatic mitochondrial health and was associated with an amelioration of glucose intolerance, hepatic steatosis and pathological changes induced by maternal SE. MitoQ supplementation may potentially prevent metabolic dysfunction and hepatic pathology induced by intrauterine SE.

Li, H, Xiao, F, Hong, G, Su, J, Li, N, Cao, L, Wen, Q & Guo, W 2019, 'On the Role of Heterogeneous Nanopore Junction in Osmotic Power Generation', Chinese Journal of Chemistry, vol. 37, no. 5, pp. 469-473.
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Summary of main observation and conclusionOsmotic power generated by mixing ionic solutions of different concentration is an underutilized clean energy resource that satisfy potentially the ever‐growing energy demand. For decades, substantial efforts are made to enhance the power density. Toward this goal, we once developed a heterogeneous nanoporous membrane comprising of heterojunctions between negatively charged mesoporous carbon and positively charged macroporous alumina to harvest electric power from salinity difference and achieved outstanding performance (J. Am. Chem. Soc. 2014, 136, 12265). The heterogeneous nanopore junction effectively suppresses ion concentration polarization (ICP) at low concentration end, and consequently promotes the overall power density. However, to date, a systematic understanding of the role of the heterogeneous nanopore junction in osmotic energy conversion remains urgent and largely unexplored. Herein, we provide an in‐depth theoretical investigation on this issue with special emphasis on several influential factors, such as the ionic concentration, the surface charge density, and the geometry of heterogeneous part. To balance the suppression of ICP and maintenance of charge selectivity, we find that these influential factors in the heterogeneous part should be restricted to a specific range. These findings provide direct guidance for design and optimization of high‐performance nanofluidic power sources.

Li, J, Zhao, Y, Coleman, P, Chen, J, Ting, KK, Choi, JP, Zheng, X, Vadas, MA & Gamble, JR 2019, 'Low fluid shear stress conditions contribute to activation of cerebral cavernous malformation signalling pathways', Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, vol. 1865, no. 11, pp. 165519-165519.
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Cerebral cavernous malformations (CCMs) are vascular malformations that cause hemorrhagic stroke. CCMs can arise from loss-of-function mutations in any one of CCM1 (KRIT1), CCM2 or CCM3 (PDCD10). Despite the mutation being in all endothelial cells the CCM lesions develop primarily in the regions with low fluid shear stress (FSS). Here we investigated the role of FSS in the signalling pathways associated with loss of function of CCM genes. We performed transcriptomic analysis on CCM1 or CCM2-silenced endothelial cells subjected to various FSS. The results showed 1382 genes were deregulated under low FSS, whereas only 29 genes were deregulated under high FSS. Key CCM downstream signalling pathways, including increased KLF2/4 expression, actin cytoskeleton reorganization, TGF-β and toll-like receptor signalling pathways and also oxidative stress pathways, were all highly upregulated but only under low FSS. We also show that the key known phenotypes of CCM lesions such as disrupted endothelial cell junction, increased inflammatory response/oxidative stress and elevated RhoA-ROCK activity, are only exhibited in monolayers of CCM-silenced endothelial cells subjected to low FSS. Our data establishes that shear stress acts as a previously unappreciated but important regulator for CCM gene function and may determine the site of CCM lesion development.

Li, P, Guo, X, Wang, S, Zang, R, Li, X, Man, Z, Li, P, Liu, S, Wu, Y & Wang, G 2019, 'Two-dimensional Sb@TiO_2−x nanoplates as a high-performance anode material for sodium-ion batteries', Journal of Materials Chemistry A, vol. 7, no. 6, pp. 2553-2559.
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Two-dimensional Sb@TiO_2−x nanoplates with abundant voids deliver high reversible capacity, excellent rate capability and stable cycling performance.

Li, T, Xu, J, Wang, C, Wu, W, Su, D & Wang, G 2019, 'The latest advances in the critical factors (positive electrode, electrolytes, separators) for sodium-sulfur battery', Journal of Alloys and Compounds, vol. 792, pp. 797-817.
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© 2019 The sodium-sulfur (Na/S) batteries have caused widespread concern owing to the advantages of low cost and high energy density, these advantages make them promising in the large-scale energy storage system. But the research progress in this field is still at the beginning stage and confronts with tough challenges, for example, the low sulfur conductivity and polysulfide shuttle effect. Considering Na/S battery is a complicated system whose reaction mechanism between sulfur and sodium is different from the operating temperatures, positive electrode hosts and electrolytes, thus a comprehensive understanding about the electrochemistry of the Na/S batteries that operating in high-temperature, intermediate-temperature and room-temperature is necessary. In addition, the critical factors (positive electrodes, electrolytes, separators) associated with the development of high energy density and high performance Na/S battery, it also need to be analysed for the successful application in the near future. In this review, the working methods of high-temperature Na/S (HT-Na/S) battery, intermediate-temperature Na/S (IT-Na/S) battery and room-temperature Na/S (RT-Na/S) battery will be compared, and also focus on the latest progress of positive electrodes, electrolytes and separators in Na/S batteries. Finally, we provide an outlook on the state of the art for the production of more efficient and reliable Na/S batteries with rational technique.

Li, VWH, Toogood, H, Ryan, S & Meakin, GE 2019, 'The effects of various household cleaning methods on DNA persistence on mugs and knives', Forensic Science International: Genetics Supplement Series, vol. 7, no. 1, pp. 277-278.
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© 2019 Elsevier B.V. With the prevalence of forensic science in popular media, offenders are becoming more forensically aware and can employ precautionary methods, such as cleaning used items or rubbing away fingermarks, to reduce their traces left at a crime scene. This study examined the effects of various cleaning methods on DNA persistence on commonly encountered casework exhibits, specifically knives and mugs. Aliquots of acellular DNA were added to the knife handles or mug rims, allowed to dry, and then the substrates were either sampled directly or were cleaned and then sampled. The plastic- and wood-handled knives were cleaned with a cloth in a sink of water, diluted dish washing liquid or diluted household bleach, whereas the ceramic, glass and steel mugs were cleaned with a dry or wet cloth, or by wiping with a cloth after applying a cleaning product (dish washing liquid or household bleach spray) directly into the mug and then rinsing it with water. DNA samples were collected with wet and dry swabs, in triplicate, and extracted and quantified. In both experiments, DNA was not detected on items after cleaning with dish washing liquid or household bleach, irrespective of the differences in amounts of DNA initially deposited, substrates, and cleaning methods. Even without a cleaning product, rubbing with a dry cloth decreased DNA recovery from the mugs, regardless of the mug substrate. These results contribute to our understanding of the impact of various cleaning methods on DNA recovery at the crime scene and will help inform DNA recovery strategies.

Li, X, Wang, S, Tang, X, Zang, R, Li, P, Li, P, Man, Z, Li, C, Liu, S, Wu, Y & Wang, G 2019, 'Porous Na3V2(PO4)3/C nanoplates for high-performance sodium storage', Journal of Colloid and Interface Science, vol. 539, pp. 168-174.
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© 2018 Sodium super-ionic conductor (NASICON) structured Na3V2(PO4)3 (NVP), a promising cathode material for sodium-ion batteries (SIBs), benefits by its unique three-dimensional (3D) channel structure. However, the inherent characteristics of NVP (such as low electrical conductivity) usually lead to inferior rate and long-cycling performance, which miss the requirements of practical application in electrical energy storage systems (ESSs). Herein, we propose the synthesis of porous high-crystalline Na3V2(PO4)3/C nanoplates (NVP/C-P) via hydrothermal method and post-calcination. The porous nanoplate structure provides increased specific surface area and shortened diffusion pathway for ion/electron transport. Consequently, NVP/C-P cathodes exhibit a high specific capacity (117 mAh g−1, 0.2 C), exceptional rate performance (76.5 mAh g−1, 100 C) and long cyclic stability (10,000 cycles).

Liang, J, Mondal, AK, Wang, D & Iacopi, F 2019, 'Graphene‐Based Planar Microsupercapacitors: Recent Advances and Future Challenges', Advanced Materials Technologies, vol. 4, no. 1, pp. 1800200-1800200.
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AbstractThe continuous development of integrated electronics such as maintenance‐free biosensors, remote and mobile environmental sensors, wearable personal electronics, nanorobotics etc. and their continued miniaturization has led to an increasing demand for miniaturized energy storage units. Microsupercapacitors with graphene electrodes hold great promise as miniaturized, integrated power sources thanks to their fast charge/discharge rates, superior power performance, and long cycling stability. In addition, planar interdigitated electrodes also have the capability to reduce ion diffusion distances leading to a greatly improved electrochemical performance. Either as standalone power sources or complementing energy harvesting units, it is expected that graphene‐based microsupercapacitors will play a key role as miniaturized power sources in electronic microsystems. This review highlights the recent development, challenges, and perspectives in this area, with an emphasis on the link between material and geometry design of planar graphene‐based electrodes and their electrochemical performance and integrability.

Liang, L, Ma, Y & Carroll, RJ 2019, 'A semiparametric efficient estimator in case-control studies for gene–environment independent models', Journal of Multivariate Analysis, vol. 173, pp. 38-50.
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© 2019 Elsevier Inc. Case-controls studies are popular epidemiological designs for detecting gene–environment interactions in the etiology of complex diseases, where the genetic susceptibility and environmental exposures may often be reasonably assumed independent in the source population. Various papers have presented analytical methods exploiting gene–environment independence to achieve better efficiency, all of which require either a rare disease assumption or a distributional assumption on the genetic variables. We relax both assumptions. We construct a semiparametric estimator in case-control studies exploiting gene–environment independence, while the distributions of genetic susceptibility and environmental exposures are both unspecified and the disease rate is assumed unknown and is not required to be close to zero. The resulting estimator is semiparametric efficient and its superiority over prospective logistic regression, the usual analysis in case-control studies, is demonstrated in various numerical illustrations.

Lim, CED, Ng, RWC, Cheng, NCL, Zhang, GS & Chen, H 2019, 'Acupuncture for polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, vol. 2019, no. 7, p. CD007689.
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© 2019 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. Background Polycystic ovarian syndrome (PCOS) is characterised by the clinical signs of oligo-amenorrhoea, infertility and hirsutism. Conventional treatment of PCOS includes a range of oral pharmacological agents, lifestyle changes and surgical modalities. Beta-endorphin is present in the follicular fluid of both normal and polycystic ovaries. It was demonstrated that the beta-endorphin levels in ovarian follicular fluid of otherwise healthy women who were undergoing ovulation were much higher than the levels measured in plasma. Given that acupuncture impacts on beta-endorphin production, which may affect gonadotropin-releasing hormone (GnRH) secretion, it is postulated that acupuncture may have a role in ovulation induction via increased beta-endorphin production effecting GnRH secretion. This is an update of our previous review published in 2016. Objectives To assess the effectiveness and safety of acupuncture treatment for oligo/anovulatory women with polycystic ovarian syndrome (PCOS) for both fertility and symptom control. Search methods We identified relevant studies from databases including the Gynaecology and Fertility Group Specialised Register, CENTRAL, MED-LINE, Embase, PsycINFO, CNKI, CBM and VIP. We also searched trial registries and reference lists from relevant papers. CENTRAL, MEDLINE, Embase, PsycINFO, CNKI and VIP searches are current to May 2018. CBM database search is to November 2015. Selection criteria We included randomised controlled trials (RCTs) that studied the efficacy of acupuncture treatment for oligo/anovulatory women with PCOS. We excluded quasi-or pseudo-RCTs. Data collection and analysis Two review authors independently selected the studies, extracted data and assessed risk of bias. We calculated risk ratios (RR), mean difference (MD), standardised mean difference (SMD) and 95% confidence intervals (CIs). Primary outcomes were live birth rate, multi...

Lin, Y, Ghazanfar, S, Wang, KYX, Gagnon-Bartsch, JA, Lo, KK, Su, X, Han, Z-G, Ormerod, JT, Speed, TP, Yang, P & Yang, JYH 2019, 'scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets', Proceedings of the National Academy of Sciences, vol. 116, no. 20, pp. 9775-9784.
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Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.

Lin, Y, He, P, Hu, P, Chen, H, Chen, Y & McGowan, E 2019, 'Low level of centromere-associated protein E promotes growth of hepatocellular carcinoma and is associated with adverse clinical features', Annals of Oncology, vol. 30, pp. iv9-iv9.
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Lin, Y, Yin, H, An, H, Zhou, C, Zhou, L, Chen, S & McGowan, E 2019, 'Chemokine receptor CCR2b expressing anti-Tn-MUC1 CAR-T cells enhanced anti-breast cancer activity', Annals of Oncology, vol. 30, no. Supplement 11, pp. xi12-xi12.
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Background: Enhanced anti-tumour activity is required for eradication of solid tumours by CART cells. One possibility of enhancing anti-tumour activity is by programming CART cells to express chemokine receptors that match chemokines produced either by the tumours or tumour-associated cells, thereby improving the infiltrating capacity of the CART cells. In this study, we engineered CCR2b expressing anti-Tn-MUC1 CAR T cells for the treatment of breast cancer. Methods: Anti-Tn-MUC1-CARs were constructed using the SM3 scFv. Following lenti-MUC1 CAR retroviral transduction, efficiency of transgenic expression was assessed by flow cytometry. CCR2b expressing anti-Tn-MUC1 CAR T cells were prepared using PLV-CAR-5E5-CCR2b lentivirus. The susceptibility of MCF-7 cells to either anti-MUC1 CART or CCR2b expressing anti-MUC1 CART cell-mediated lysis was assessed using in vitro killing assays. For cytolytic analysis, CART-cells were cocultured 10:1 (effector:target) ratio with MCF-7 cells. The effects of CCR2b expressing CART cells on anti-tumour activity and infiltration were also assessed in an in vivo murine xenograft model. Results: Activated T cells co-modified with both CCR2b and anti-MUC1-CAR had greater anti-tumour activity both in vivo and in vitro. When the effector / target cell ratio was 10, the killing rates of CART and CART-CCR2b were 56.9% and 83.9%, respectively. Tumour size was significantly smaller (P < 0.001) in the CAR-CCR2b group compared to the CAR alone group. At day 7 post-injection of CART cells, the infiltrated T cells was significantly increased (~2 folds) in the CAR-CCR2b group compared with the CART only group. Conclusions: Our data demonstrated that the anti-tumour activity of the CCR2b expressing anti-Tn-MUC1 CART cells is 1.5 times more potent than CART cells without CCR2b. Augmentation of tumour suppression was also demonstrated in vivo in a murine xenograft model. These pre-clinical results show translational potential to the clinic for tr...

Liu, DL, Wang, B, Evans, J, Ji, F, Waters, C, Macadam, I, Yang, X & Beyer, K 2019, 'Propagation of climate model biases to biophysical modelling can complicate assessments of climate change impact in agricultural systems', International Journal of Climatology, vol. 39, no. 1, pp. 424-444.
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Regional climate model (RCM) simulations are being increasingly used for climate change impact assessments, but their application is challenging due to considerable biases inherited from global climate model (GCM) simulations and generated from dynamical downscaling processes. This study assesses the biases in NARCliM (NSW and ACT regional climate modelling) simulations and quantifies the consequence of the climate biases in the downstream assessment of climate change impact on wheat crop system, using the Agricultural Production System sIMulator (APSIM). Results showed that post‐processing bias‐corrected temperature and rainfall data from NARCliM had small annual mean biases but large biases in the crop growing season (CGS). During the CGS, the mean bias error of rainfall was generally positive for rainfall probability and negative for intensity, which subsequently resulted in APSIM simulating negative biases for runoff and deep drainage and positive bias in soil evaporation. Bias in soil water balance and water availability resulted in less plant transpiration and less N uptake, ultimately, leading to large negative biases in crop yields. A simple bias correction of the simulated crop yield driven by RCMs could result in a largely consistent distribution with those generated with APSIM simulations forced by observed climate. Our results showed that RCM simulation biases could confound with the climate change signal and produced an unreliable estimate of the effects of the changes in climate and farm management variables on crop yields. The results suggested that RCM simulations with the current bias correction on the RCM‐simulated outputs applied on an annual basis were inadequate for climate change assessments which involve biophysical models. Our study highlights the need for improved RCM simulations by eliminating the systemic biases associated with rainfall characteristics, although suitable post‐processing bias correction on a seasonal or...

Liu, F, Nattestad, A, Naficy, S, Han, R, Casillas, G, Angeloski, A, Sun, X & Huang, Z 2019, 'Fluorescent Carbon‐ and Oxygen‐Doped Hexagonal Boron Nitride Powders as Printing Ink for Anticounterfeit Applications', Advanced Optical Materials, vol. 7, no. 24, pp. 1901380-1901380.
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AbstractIncreasing demands for optical anticounterfeiting technology require the development of versatile luminescent materials with tunable photoluminescence properties. Herein, a number of fluorescent carbon‐ and oxygen‐doped hexagonal boron nitride (denoted as BCNO) phosphors are found to offer a such high‐tech anticounterfeiting solution. These multicolor BCNO powders, developed in a two‐step process with controlled annealing and oxidation, feature rod‐like particle shape, with varied luminescence properties. Studies of the optical properties of BCNO, along with other characterization, provide insight into this underexplored material. Anticounterfeiting applications are demonstrated with printed patterns which are indistinguishable to the naked eye under visible light but become highly discernible under UV irradiation. The fabricated patterns are demonstrated to be both chemically stable in corrosive environments and physically robust in mechanical bending testing. These properties render BCNO as promising and versatile anticounterfeiting material a wide variety of environments.

Liu, G, Cooley, MA, Jarnicki, AG, Borghuis, T, Nair, PM, Tjin, G, Hsu, AC, Haw, TJ, Fricker, M, Harrison, CL, Jones, B, Hansbro, NG, Wark, PA, Horvat, JC, Argraves, WS, Oliver, BG, Knight, DA, Burgess, JK & Hansbro, PM 2019, 'Fibulin-1c regulates transforming growth factor–β activation in pulmonary tissue fibrosis', JCI Insight, vol. 4, no. 16.
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Copyright: © 2019, American Society for Clinical Investigation. Tissue remodeling/fibrosis is a major feature of all fibrotic diseases, including idiopathic pulmonary fibrosis (IPF). It is underpinned by accumulating extracellular matrix (ECM) proteins. Fibulin-1c (Fbln1c) is a matricellular ECM protein associated with lung fibrosis in both humans and mice and stabilizes collagen formation. Here we discovered that Fbln1c was increased in the lung tissues of patients with IPF and experimental bleomycin-induced pulmonary fibrosis. Fbln1c-deficient (Fbln1c–/–) mice had reduced pulmonary remodeling/fibrosis and improved lung function after bleomycin challenge. Fbln1c interacted with fibronectin, periostin, and tenascin-C in collagen deposits following bleomycin challenge. In a potentially novel mechanism of fibrosis, Fbln1c bound to latent TGF-β–binding protein 1 (LTBP1) to induce TGF-β activation and mediated downstream Smad3 phosphorylation/signaling. This process increased myofibroblast numbers and collagen deposition. Fbln1c and LTBP1 colocalized in lung tissues from patients with IPF. Thus, Fbln1c may be a novel driver of TGF-β–induced fibrosis involving LTBP1 and may be an upstream therapeutic target.

Liu, G, Mateer, SW, Hsu, A, Goggins, BJ, Tay, H, Mathe, A, Fan, K, Neal, R, Bruce, J, Burns, G, Minahan, K, Maltby, S, Fricker, M, Foster, PS, Wark, PAB, Hansbro, PM & Keely, S 2019, 'Platelet activating factor receptor regulates colitis-induced pulmonary inflammation through the NLRP3 inflammasome', Mucosal Immunology, vol. 12, no. 4, pp. 862-873.
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© 2019, Society for Mucosal Immunology. Extra-intestinal manifestations (EIM) are common in inflammatory bowel disease (IBD). One such EIM is sub-clinical pulmonary inflammation, which occurs in up to 50% of IBD patients. In animal models of colitis, pulmonary inflammation is driven by neutrophilic infiltrations, primarily in response to the systemic bacteraemia and increased bacterial load in the lungs. Platelet activating factor receptor (PAFR) plays a critical role in regulating pulmonary responses to infection in conditions, such as chronic obstructive pulmonary disease and asthma. We investigated the role of PAFR in pulmonary EIMs of IBD, using dextran sulfate sodium (DSS) and anti-CD40 murine models of colitis. Both models induced neutrophilic inflammation, with increased TNF and IL-1β levels, bacterial load and PAFR protein expression in mouse lungs. Antagonism of PAFR decreased lung neutrophilia, TNF, and IL-1β in an NLRP3 inflammasome-dependent manner. Lipopolysaccharide from phosphorylcholine (ChoP)-positive bacteria induced NLRP3 and caspase-1 proteins in human alveolar epithelial cells, however antagonism of PAFR prevented NLRP3 activation by ChoP. Amoxicillin reduced bacterial populations in the lungs and reduced NLRP3 inflammasome protein levels, but did not reduce PAFR. These data suggest a role for PAFR in microbial pattern recognition and NLRP3 inflammasome signaling in the lung.

Liu, L, Zhang, X, Liu, Y, Zhang, L, Zheng, J, Wang, J, Hansbro, PM, Wang, L, Wang, G & Hsu, AC-Y 2019, 'Chitinase-like protein YKL-40 correlates with inflammatory phenotypes, anti-asthma responsiveness and future exacerbations', Respiratory Research, vol. 20, no. 1, p. 95.
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© 2019 The Author(s). Background: Asthma is a heterogeneous chronic airway disease, which may be classified into different phenotypes. YKL-40 is a chitin-binding glycoprotein with unclear functions, but its expression is associated with inflammation and tissue remodeling. However, few studies have explored whether YKL-40 is associated with inflammatory phenotypes of asthma. Methods: The study had two parts. Study I (n = 115) was a one-year prospective cohort designed to explore the relationship of serum YKL-40 levels with inflammatory phenotypes of asthma at baseline, and during exacerbations. Study II (n = 62) was a four-week prospective cohort designed to define whether serum YKL-40 levels could predict responses to a fixed anti-asthma regimen. YKL-40, IL-6 and CCL22 levels were detected using ELISA, and a sputum inflammatory panel (including IL-1β, IL-5, IL-8 and TNF-α) was assessed using Luminex-based MILLIPLEX assay. Results: Study I: Serum YKL-40 levels in non-eosinophilic asthma (NEA) i.e. neutrophilic (47.77 [29.59, 74.97] ng/mL, n = 40) and paucigranulocytic (47.36 [28.81, 61.68] ng/mL, n = 31) were significantly elevated compared with eosinophilic asthma (31.05 [22.41, 51.10] ng/mL, n = 44) (P = 0.015). Serum YKL-40levels positively correlated with blood neutrophils, sputum IL-1β and plasma IL-6 but negatively correlated with serum IgE and blood eosinophils (all P ≤ 0.05). Baseline YKL-40 levels predicted moderate to severe exacerbations within a one-year period (aOR = 4.13, 95% CI = [1.08, 15.83]). Study II: Serum YKL-40 was an independent biomarker of negative responses to anti-asthma regimens (adjusted Odds Ratio [aOR] = 0.82, 95% CI = [0.71, 0.96]. Conclusions: These studies show that YKL-40 is a non-type 2 inflammatory signature for NEA, which could predict responsiveness or insensitivity to anti-asthma medications and more exacerbations. Further studies are needed to assess whether monitoring YKL-40 levels could provide potential implica...

Liu, P & Separovic, F 2019, 'Membrane biophysics session', Biophysical Reviews, vol. 11, no. 3, pp. 283-284.
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Liu, T, Zhang, W, Ye, L, Ueland, M, Forbes, SL & Su, SW 2019, 'A novel multi-odour identification by electronic nose using non-parametric modelling-based feature extraction and time-series classification', Sensors and Actuators B: Chemical, vol. 298, pp. 126690-126690.
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© 2019 Elsevier B.V. The electronic nose (e-nose) is an olfaction system that consists of an array of chemical sensors and effective machine learning algorithms for the detection of various target odours. Feature extraction and classification methods are of great importance in improving the performance of the e-nose system. In this paper, a novel odour identification method is presented. Firstly, we use the kernel-based system modelling approach to extract odour features. Its solution is a series of finite impulse responses which containing discriminant information of different odours. In addition, a parameter optimisation method based on normalised mean square error and information entropy is proposed to optimise the kernel function. The entropy is effective in preventing the finite impulse responses from overfitting. Multi-odour classification is achieved based on Gaussian mixture density hidden Markov model (GMM-HMM) considering the characteristic of the extracted features. Also, parameter selection for GMM-HMM is realised according to BIC index and cross-validation. Then, we validate the performance of the proposed feature extraction method in resistance to noise and compare it with other existed features. The modelling-based feature reached the highest performance even without applying any filtering or smoothing techniques. Finally, we compare the proposed combination of feature extraction and classification algorithms with other approaches. The proposed method outperformed other approaches reaching 93.56% in sensitivity and 98.71% in specificity. The results demonstrate that the proposed method is applicable in e-nose-based odour identification.

Liu, X, Liu, L, Ji, Y, Li, C, Wei, T, Yang, X, Zhang, Y, Cai, X, Gao, Y, Xu, W, Rao, S, Jin, D, Lou, W, Qiu, Z & Wang, X 2019, 'Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer', EBioMedicine, vol. 41, pp. 345-356.
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Lockwood, TE, Talebi, M, Minett, A, Mills, S, Doble, PA & Bishop, DP 2019, 'Micro solid-phase extraction for the analysis of per- and polyfluoroalkyl substances in environmental waters', Journal of Chromatography A, vol. 1604, pp. 460495-460495.
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© 2019 Growing concern over the environmental and health impacts of per- and polyfluoroalkyl substances (PFASs) has led to the development of increasingly stringent regulatory guidelines. To meet these guidelines for the determination of PFASs in surface-water, solid-phase extraction (SPE) is commonly implemented for clean-up and pre-concentration of samples. In this paper a micro-SPE method for the clean-up and pre-concentration of PFASs from surface-water was developed. A micro-SPE packing phase was created to retain 13 long and short chain PFAS after examining combinations of four 3 µm particle size sorbents, with the optimal phase consisting of a 50:50 mixture of C18 and aminopropyl silica. Micro-SPE achieved similar results to conventional SPE methods while reducing sample preparation time to 5 min and using only 2 mL of sample. The method was validated using spiked recoveries (100 ng L−1) from PFAS contaminated surface-water samples with recoveries ranging from 86% to 111% and relative standard deviations below 18%. Concentrations of the PFASs in the samples ranged from below the limit of quantification to 898 ± 15 ng L−1. Automation of sample preparation, including the micro-SPE extraction, was also demonstrated. These results show the potential for automated micro-SPE to replace conventional SPE, with the decreases in sample preparation time, sample and solvent volumes crucial for incorporation into routine analyses in commercial laboratories.

Loering, S, Cameron, GJM, Starkey, MR & Hansbro, PM 2019, 'Lung development and emerging roles for type 2 immunity', The Journal of Pathology, vol. 247, no. 5, pp. 686-696.
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AbstractLung development is a complex process mediated through the interaction of multiple cell types, factors and mediators. In mice, it starts as early as embryonic day 9 and continues into early adulthood. The process can be separated into five different developmental stages: embryonic, pseudoglandular, canalicular, saccular, and alveolar. Whilst lung bud formation and branching morphogenesis have been studied extensively, the mechanisms of alveolarisation are incompletely understood. Aberrant lung development can lead to deleterious consequences for respiratory health such as bronchopulmonary dysplasia (BPD), a disease primarily affecting preterm neonates, which is characterised by increased pulmonary inflammation and disturbed alveolarisation. While the deleterious effects of type 1‐mediated inflammatory responses on lung development have been well established, the role of type 2 responses in postnatal lung development remains poorly understood. Recent studies indicate that type 2‐associated immune cells, such as group 2 innate lymphoid cells and alveolar macrophages, are increased in number during postnatal alveolarisation. Here, we present the current state of understanding of the postnatal stages of lung development and the key cell types and mediators known to be involved. We also provide an overview of how stem cells are involved in lung development and regeneration, and the negative influences of respiratory infections. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Lohr, KE, Camp, EF, Kuzhiumparambil, U, Lutz, A, Leggat, W, Patterson, JT & Suggett, DJ 2019, 'Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling', Journal of Experimental Biology, vol. 222, no. 8.
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Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.

Lohr, KE, Khattri, RB, Guingab-Cagmat, J, Camp, EF, Merritt, ME, Garrett, TJ & Patterson, JT 2019, 'Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral', Scientific Reports, vol. 9, no. 1.
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AbstractGlobal threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.

López-Campos, G, Bonner, E & McClements, L 2019, 'An Integrative Biomedical Informatics Approach to Elucidate the Similarities Between Pre-Eclampsia and Hypertension.', MedInfo, vol. 264, pp. 988-992.
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© 2019 International Medical Informatics Association (IMIA) and IOS Press. Pre-eclampsia is a pregnancy condition affecting 5-10% of pregnancies, and it is the leading cause of death in pregnancy associated with increased risk of cardiovascular disease later in life. Despite research, the pathogenesis of pre-eclampsia is still poorly understood. In this paper, we investigate the overlapping pathogenic mechanisms between pre-eclampsia and adult hypertension using an integrative biomedical informatics strategy that combined text mining techniques to identify genes and proteins, with geneset analyses, generating knowledge on the pathways and mechanisms involved in these conditions. We identified several overlapping pathogenic pathways/systems including metabolic pathways, developmental biology pathways, immune system, haemostasis, tyrosine kinase pathways, extracellular matrix and oxidative stress pathways. This bioinformatics approach could be applied for investigating mechanistic pathways of other disorders.

Lu, J, Cokcetin, NN, Burke, CM, Turnbull, L, Liu, M, Carter, DA, Whitchurch, CB & Harry, EJ 2019, 'Honey can inhibit and eliminate biofilms produced by Pseudomonas aeruginosa', Scientific Reports, vol. 9, no. 1.
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AbstractChronic wound treatment is becoming increasingly difficult and costly, further exacerbated when wounds become infected. Bacterial biofilms cause most chronic wound infections and are notoriously resistant to antibiotic treatments. The need for new approaches to combat polymicrobial biofilms in chronic wounds combined with the growing antimicrobial resistance crisis means that honey is being revisited as a treatment option due to its broad-spectrum antimicrobial activity and low propensity for bacterial resistance. We assessed four well-characterised New Zealand honeys, quantified for their key antibacterial components, methylglyoxal, hydrogen peroxide and sugar, for their capacity to prevent and eradicate biofilms produced by the common wound pathogen Pseudomonas aeruginosa. We demonstrate that: (1) honey used at substantially lower concentrations compared to those found in honey-based wound dressings inhibited P. aeruginosa biofilm formation and significantly reduced established biofilms; (2) the anti-biofilm effect of honey was largely driven by its sugar component; (3) cells recovered from biofilms treated with sub-inhibitory honey concentrations had slightly increased tolerance to honey; and (4) honey used at clinically obtainable concentrations completely eradicated established P. aeruginosa biofilms. These results, together with their broad antimicrobial spectrum, demonstrate that manuka honey-based wound dressings are a promising treatment for infected chronic wounds, including those with P. aeruginosa biofilms.

Luo, C-Q, Ling, FC-C, Rahman, MA, Phillips, M, Ton-That, C, Liao, C, Shih, K, Lin, J, Tam, HW, Djurišić, AB & Wang, S-P 2019, 'Surface polarity control in ZnO films deposited by pulsed laser deposition', Applied Surface Science, vol. 483, pp. 1129-1135.
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© 2019 Elsevier B.V. We demonstrate a simple and inexpensive method of surface polarity control of ZnO grown by pulsed laser deposition (PLD). The polarity control is achieved in a straightforward way by changing the thickness of MgO buffer layer. The Zn- and O-polar ZnO films possess very distinct growth rate, electron concentration and mobility as well as different defect structures. These different structural and electronic properties result in significant differences in surface reactivity and device performance. For example, Pd Schottky diodes fabricated onto the O-polar ZnO film exhibit lower barrier height and ideality factor compared with the equivalent Zn-polar devices, while methylammonium lead iodide perovskite films are readily formed on O-terminated and rapidly decompose on Zn-terminated surfaces. This can be attributed to higher photocatalytic activity of Zn-terminated surface, as well as higher surface coverage of adsorbed hydroxyl groups. Consequently, our results indicate that polarity engineering to obtain favorable O-terminated surface can result in improved performance of ZnO-containing optoelectronic devices, while Zn-terminated surfaces could be of interest for photocatalytic and sensing applications.

Luo, Z, Neville, SL, Campbell, R, Morey, JR, Menon, S, Thomas, M, Eijkelkamp, BA, Ween, MP, Huston, WM, Kobe, B & McDevitt, CA 2019, 'Structure and Metal Binding Properties of Chlamydia trachomatis YtgA', Journal of Bacteriology, vol. 202, no. 1.
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Chlamydia trachomatis is the most common bacterial sexually transmitted infection in developed countries, with an estimated global prevalence of 4.2% in the 15- to 49-year age group. Although infection is asymptomatic in more than 80% of infected women, about 10% of cases result in serious disease. Infection by C. trachomatis is dependent on the ability to acquire essential nutrients, such as the transition metal iron, from host cells. In this study, we show that iron is the most abundant transition metal in C. trachomatis and report the structural and biochemical properties of the iron-recruiting protein YtgA. Knowledge of the high-resolution structure of YtgA will provide a platform for future structure-based antimicrobial design approaches.

Luu, LDW 2019, 'Pathogen adaptation to vaccination: the Australian Bordetella pertussis story', Microbiology Australia, vol. 40, no. 4, pp. 177-180.
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Whooping cough (pertussis) is a highly contagious vaccine preventable respiratory disease caused by the Gram-negative bacterium Bordetella pertussis. Despite high level vaccination coverage over the past 20 years, Australia has one of the highest per capita burdens of pertussis globally. Oneof theprimaryfactors associated withthere-emergence of pertussis is pathogen adaptation of B. pertussis to the current acellular vaccines used. This article will focusonthe genomic and proteomic changes that have occurred in the Australian B. pertussis population, the significance of these adaptive changes on fitness in a vaccinated environment and what we can do to reduce the significant burden of pertussis in the future.

Lyu, X, Wang, X & Leslie, LM 2019, 'The Dependence of Northwest Pacific Tropical Cyclone Intensification Rates on Environmental Factors', Advances in Meteorology, vol. 2019, pp. 1-18.
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The Northwest Pacific tropical cyclone (TC) intensification is classified into rapid intensification (RI), normal intensification (NI), and slow intensification (SI) categories. The initial location and intensity, the preceding intensity change, the motion direction, the occurrence month, and the intensification duration time are all found to differ for RI cases compared with NI and SI cases. The dependence of RI, NI, and SI on environmental conditions is further examined statistically by using the intensification rates of named TCs, for the 21-year period 1995–2015, obtained from JTWC best track data, and the environmental conditions derived from the ERA-Interim reanalysis data and GODAS high-resolution global ocean analysis data. It was found that deep-layer and upper-mid vertical wind shear (VWS), upper-level outflow, sea surface temperature (SST), and ocean heat content (OHC) are statistically different among RI, NI, and SI both before and during intensification. RI is enhanced by weaker and decreasing VWS, warmer oceans, and stronger and increasing outflow. In contrast, SI typically occurs with larger and increasing VWS, cooler oceans, and weaker, static outflow. The impacts of low-level VWS and net moisture inflow are only significantly different between RI and SI and between NI and SI, but not between RI and NI. Another key finding is that increased upper-level outflow and decreased VWS are important precursors and hence are possible predictors, of RI onset. The direction of upper-level outflow affects TC intensification, with NW and NE outflow being more favorable for TC RI than SE and SW outflow.

Ma, B, Huang, Y, Nie, Z, Qiu, X, Su, D, Wang, G, Yuan, J, Xie, X & Wu, Z 2019, 'Facile synthesis of Camellia oleifera shell-derived hard carbon as an anode material for lithium-ion batteries', RSC Advances, vol. 9, no. 35, pp. 20424-20431.
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Bio-waste Camellia oleifera shells (COS) are converted into porous carbon by a two-step method.

Ma, K, Liu, G-J, Yan, L, Wen, S, Xu, B, Tian, W, Goldys, EM & Liu, G 2019, 'AIEgen based poly(L-lactic-co-glycolic acid) magnetic nanoparticles to localize cytokine VEGF for early cancer diagnosis and photothermal therapy', Nanomedicine, vol. 14, no. 9, pp. 1191-1201.
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Aim: We demonstrated a novel theranostic system for simultaneous photothermal therapy and magnetic resonance imaging applicable to early diagnostics and treatment of cancer cells. Materials & methods: Oleic acid-Fe3O4 and triphenylamine-divinylanthracene-dicyano were loaded to the poly(L-lactic-co-glycolic acid) nanoparticles (NPs) on which anti-VEGF antibodies were modified to form anti-VEGF/OA-Fe3O4/triphenylamine-divinylanthracene-dicyano@poly(L-lactic-co-glycolic acid) NPs. The 1H nuclear magnetic resonance (NMR), mass spectra, fluorescence, UV absorption, dynamic light scattering, transmission electron microscope and inductively coupled plasma mass spectrometry tests were used to characterize the NPs, and the bioimaging was illustrated by confocal laser scanning microscope (CLSM) and in vivo MRI animal experiment. Results: This system was capable to recognize the overexpressed VEGF-A as low as 68 pg/ml in different cell lines with good selectivity and photothermal therapy effect. Conclusion: These ultrasensitive theranostic NPs were able to identify tumor cells by fluorescence imaging and MRI, and destroy tumors under near infrared illumination.

Ma, S, Zhu, L, Zhang, Z, Tsai, C-L & Carroll, RJ 2019, 'A robust and efficient approach to causal inference based on sparse sufficient dimension reduction', The Annals of Statistics, vol. 47, no. 3, pp. 1505-1535.
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© Institute of Mathematical Statistics, 2019. A fundamental assumption used in causal inference with observational data is that treatment assignment is ignorable given measured confounding variables. This assumption of no missing confounders is plausible if a large number of baseline covariates are included in the analysis, as we often have no prior knowledge of which variables can be important confounders. Thus, estimation of treatment effects with a large number of covariates has received considerable attention in recent years. Most existing methods require specifying certain parametric models involving the outcome, treatment and confounding variables, and employ a variable selection procedure to identify confounders. However, selection of a proper set of confounders depends on correct specification of the working models. The bias due to model misspecification and incorrect selection of confounding variables can yield misleading results. We propose a robust and efficient approach for inference about the average treatment effect via a flexible modeling strategy incorporating penalized variable selection. Specifically, we consider an estimator constructed based on an efficient influence function that involves a propensity score and an outcome regression. We then propose a new sparse sufficient dimension reduction method to estimate these two functions without making restrictive parametric modeling assumptions. The proposed estimator of the average treatment effect is asymptotically normal and semiparametrically efficient without the need for variable selection consistency. The proposed methods are illustrated via simulation studies and a biomedical application.

Ma, X, Huete, A & Tran, NN 2019, 'Interaction of Seasonal Sun-Angle and Savanna Phenology Observed and Modelled using MODIS', Remote Sensing, vol. 11, no. 12, pp. 1398-1398.
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Remote sensing of phenology usually works at the regional and global scales, which imposes considerable variations in the solar zenith angle (SZA) across space and time. Variations in SZA alters the shape and profile of the surface reflectance and vegetation index (VI) time series, but this effect on remote-sensing-derived vegetation phenology has not been adequately evaluated. The objective of this study is to understand the behaviour of VIs response to SZA, and to further improve the interpretation of satellite observed vegetation dynamics, across space and time. In this study, the sensitivity of two widely used VIs—the normalised difference vegetation index (NDVI) and the enhanced vegetation index (EVI)—to SZA was investigated at four northern Australian savanna sites, over a latitudinal distance of 9.8° (~1100 km). Complete time series of surface reflectances, as acquired with different SZA configurations, were simulated using Bidirectional Reflectance Distribution Function (BRDF) parameters provided by MODerate Resolution Imaging Spectroradiometer (MODIS). The sun-angle dependency of the four phenological transition dates were assessed. Results showed that while NDVI was very sensitive to SZA, such sensitivity was nearly absent for EVI. A negative correlation was also observed between NDVI sensitivity to SZA and vegetation cover, with sensitivity declining to the same level as EVI when vegetation cover was high. Different sun-angle configurations resulted in considerable variations in the shape and magnitude of the phenological profiles. The sensitivity of VIs to SZA was generally greater during the dry season (with only active trees present) than in the wet season (with both active trees and grasses), thus, the sun-angle effect on VIs was phenophase-dependent. The sun-angle effect on NDVI time series resulted in considerable differences in the phenological metrics across different sun-angle configurations. Across four sites, the sun-angle ...

Macha, IJ, Ben-Nissan, B, Vilchevskaya, EN, Morozova, AS, Abali, BE, Müller, WH & Rickert, W 2019, 'Drug Delivery From Polymer-Based Nanopharmaceuticals—An Experimental Study Complemented by Simulations of Selected Diffusion Processes', Frontiers in Bioengineering and Biotechnology, vol. 7.
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The success of medical therapy depends on the correct amount and the appropriate delivery of the required drugs for treatment. By using biodegradable polymers a drug delivery over a time span of weeks or even months is made possible. This opens up a variety of strategies for better medication. The drug is embedded in a biodegradable polymer (the "carrier") and injected in a particular position of the human body. As a consequence of the interplay between the diffusion process and the degrading polymer the drug is released in a controlled manner. In this work we study the controlled release of medication experimentally by measuring the delivered amount of drug within a cylindrical shell over a long time interval into the body fluid. Moreover, a simple continuum model of the Fickean type is initially proposed and solved in closed-form. It is used for simulating some of the observed release processes for this type of carrier and takes the geometry of the drug container explicitly into account. By comparing the measurement data and the model predictions diffusion coefficients are obtained. It turns out that within this simple model the coefficients change over time. This contradicts the idea that diffusion coefficients are constants independent of the considered geometry. The model is therefore extended by taking an additional absorption term into account leading to a concentration dependent diffusion coefficient. This could now be used for further predictions of drug release in carriers of different shape. For a better understanding of the complex diffusion and degradation phenomena the underlying physics is discussed in detail and even more sophisticated models involving different degradation and mass transport phenomena are proposed for future work and study.

Macha, IJ, Karacan, I, Ben-Nissan, B, Cazalbou, S & Müller, WH 2019, 'Development of antimicrobial composite coatings for drug release in dental, orthopaedic and neural prostheses applications', SN Applied Sciences, vol. 1, no. 1.
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While one of the major clinical and scientific challenges in the management of implant-related infections and post-operative complications after surgery is the application of new techniques, a new approach is pertinent in the design of medical implants to reduce bacterial infections. We have designed and tested antibiotic-containing biocomposite thin films of polylactic acid (PLA), and coralline-derived hydroxyapatite (HAp) as controlled drug delivery systems for the treatment of dental, orthopaedic and neural implant-related post-operative infections. These films can be applied to complicated designs of dental, miniaturized neural devices, cochlear or total hip replacement (THR) implants by spray or dip-coating techniques. Current results reveal that the devices could release antibiotic in a controlled manner to prevent significantly bacterial growth and biofilm production. Hydroxyapatite within the composites controls the release rate and also supplies minerals, such as calcium Ca2+ and phosphate PO42− ions, which are essential minerals for bone tissue regeneration. It is concluded from the physical, mechanical and biological properties that these coatings and devices could easily be utilized in a wide range of biomedical applications.

Maciuca, IE, Cummins, ML, Cozma, AP, Rimbu, CM, Guguianu, E, Panzaru, C, Licker, M, Szekely, E, Flonta, M, Djordjevic, SP & Timofte, D 2019, 'Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry', Frontiers in Microbiology, vol. 10, p. 2267.
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© Copyright © 2019 Maciuca, Cummins, Cozma, Rimbu, Guguianu, Panzaru, Licker, Szekely, Flonta, Djordjevic and Timofte. Colistin is a last resort antibiotic used for the treatment of human infections associated with carbapenemase-producing Enterobacteriales. Here, we evaluated the occurrence of mcr-1 and -2 plasmid-mediated colistin resistance in colistin and/or carbapenem resistant human clinical Enterobacteriales and other gram-negative bacteria (n = 543) as well as third generation cephalosporin-resistant (3GCR) Escherichia coli isolates from poultry abattoir workers (n = 15) and poultry fecal samples (n = 92) collected from two geographically separate abattoirs in Romania. which revealed that mcr-1 was present within four sequence types (STs): ST744 (n = 7), ST57 (n = 7), ST156 (n = 2), and ST10 (n = 1). Within STs, serotypes were conserved and, notably, all except one of the mcr-1-positive isolates were found to exhibit fluoroquinolone-resistance (FQR) associated SNPs in both gyrA and parC. While there were variations in genotypes, all isolates belonging to ST744, ST57, and ST156 were rich in resistance determinants, carrying aminoglycoside-modifying enzymes genes, sulfonamide resistance gene blaTEM–1 as well as blaCMY–2 AmpC β-lactamase resistance genes. They also exhibited high similarity in carriage of virulence genes; ST10, however, only carried the mcr-1 gene. Whole genome sequencing (WGS) analysis also revealed that although the mcr-1 gene was identified in a diverse population of E. coli, two STs (ST57 and ST744) predominated and interestingly, were found in isolates across both abattoirs providing evidence for clonal transmission. Also, two main genomic contexts of mcr-1 isolates were revealed with all ST57 isolates harboring the mcr-1 gene between two copies of ISApl1 (or the Tn6330 transposon) whilst a common mcr-1 containing scaffold, highly similar to IncX type mcr-1-bearing plasmids (pWI2-mcr, Accession number: LT838201), was present am...

Macreadie, PI, Atwood, TB, Seymour, JR, Fontes, MLS, Sanderman, J, Nielsen, DA & Connolly, RM 2019, 'Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen', Science of The Total Environment, vol. 686, pp. 264-275.
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© 2019 Seagrass meadows store globally-significant quantities of organic ‘blue’ carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000 yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2 yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered ‘thermally recalcitrant’, and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34–38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation.

Mahmood, A, Li, S, Ali, Z, Tabassum, H, Zhu, B, Liang, Z, Meng, W, Aftab, W, Guo, W, Zhang, H, Yousaf, M, Gao, S, Zou, R & Zhao, Y 2019, 'Ultrafast Sodium/Potassium‐Ion Intercalation into Hierarchically Porous Thin Carbon Shells', Advanced Materials, vol. 31, no. 2, pp. 1805430-1805430.
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AbstractThe large‐scale application of sodium/potassium‐ion batteries is severely limited by the low and slow charge storage dynamics of electrode materials. The crystalline carbons exhibit poor insertion capability of large Na+/K+ ions, which limits the storage capability of Na/K batteries. Herein, porous S and N co‐doped thin carbon (S/N@C) with shell‐like (shell size ≈20–30 nm, shell wall ≈8–10 nm) morphology for enhanced Na+/K+ storage is presented. Thanks to the hollow structure and thin shell‐wall, S/N@C exhibits an excellent Na+/K+ storage capability with fast mass transport at higher current densities, leading to limited compromise over charge storage at high charge/discharge rates. The S/N@C delivers a high reversible capacity of 448 mAh g‐1 for Na battery, at the current density of 100 mA g‐1 and maintains a discharge capacity up to 337 mAh g‐1 at 1000 mA g‐1. Owing to shortened diffusion pathways, S/N@C delivers an unprecedented discharge capacity of 204 and 169 mAh g‐1 at extremely high current densities of 16 000 and 32 000 mA g‐1, respectively, with excellent reversible capacity for 4500 cycles. Moreover, S/N@C exhibits high K+ storage capability (320 mAh g‐1 at current density of 50 mA g‐1) and excellent cyclic life.

Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2019, 'A strategic impact assessment of hydropower plants in alpine and non-alpine areas of Europe', Applied Energy, vol. 250, pp. 198-214.
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Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2019, 'Techno-Economic Operation and Environmental Life-Cycle Assessment of a Solar PV-Driven Islanded Microgrid', IEEE Access, vol. 7, pp. 111828-111839.
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Mai, HT, Tran, TS, Ho-Le, TP, Center, JR, Eisman, JA & Nguyen, TV 2019, 'Two-Thirds of All Fractures Are Not Attributable to Osteoporosis and Advancing Age: Implications for Fracture Prevention', The Journal of Clinical Endocrinology & Metabolism, vol. 104, no. 8, pp. 3514-3520.
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Abstract Context Although bone mineral density (BMD) is strongly associated with fracture and postfracture mortality, the burden of fractures attributable to low BMD has not been investigated. Objectives We sought to estimate the population attributable fraction of fractures and fracture-related mortality that can be attributed to low BMD. Design and Setting This study is a part of an ongoing population-based prospective cohort study, the Dubbo Osteoporosis Epidemiology study. In total, 3700 participants aged ≥50 years participated in the study. Low-trauma fracture was ascertained by X-ray reports, and mortality was ascertained from the Birth, Death and Marriage Registry. Results Overall, 21% of women and 11% of men had osteoporotic BMD. In univariable analysis, 21% and 16% of total fractures in women and men, respectively, were attributable to osteoporosis. Osteoporosis combined with advancing age (>70 years) accounted for 34% and 35% of fractures in women and men, respectively. However, these two factors accounted for ∼60% of hip fractures. About 99% and 66% of postfracture mortality in women and men, respectively, were attributable to advancing age, osteoporosis, and fracture; however, most of the attributable proportion was accounted for by advancing age. Conclusions A substantial health care burden of fracture is ...

Maitre, M, Chadwick, S, Kirkbride, KP, Gassner, A-L, Weyermann, C, Beavis, A & Roux, C 2019, 'An investigation on the secondary transfer of organic gunshot residues', Science & Justice, vol. 59, no. 3, pp. 248-255.
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Gunshot residues (GSR) are an important forensic trace in firearm-related events. Currently, routine GSR analyses focus on the detection and characterisation of the inorganic components (IGSR). The increasing prevalence of heavy metal-free ammunition challenges these current protocols and there is an increasing interest in how the organic components of GSR (OGSR) can provide complementary information. Similar to the situation with IGSR, OGSR compounds originally deposited on the shooter during the firing process may further be transferred onto another individual or surface. Hence, the aim of this study was to provide additional information regarding the risk of a secondary transfer of OGSR. Two scenarios were investigated, the first one related to the arrest process and the possibilities of a secondary transfer arising between a shooter onto a non-shooter (e.g. between a police officer and a person of interest (POI)). The second scenario concerned the transfer of OGSR onto the non-shooter after handling a firearm for few minutes without discharging it. One calibre was chosen, the .40 S&W calibre, used by several Australian State police forces. A secondary transfer was observed in all cases for the two scenarios investigated, for three compounds of interest: ethylcentralite (EC), diphenylamine (DPA), N-nitrosodiphenylamine (N-nDPA). The firearm handling scenario resulted in a larger secondary transfer to that of the arrest scenario. Overall, the amounts of OGSR detected on the non-shooter were generally lower than that detected on the shooter and controls after the arrest scenario. The results of this study provide complementary knowledge about OGSR, which can be further used to improve the current practice and the interpretation of OGSR evidence. In particular, it highlights that the secondary transfer proposition must be considered during the interpretation of forensic findings, especially when small amounts of OGSR target compounds are detected.

Maity, AK, Carroll, RJ & Mallick, BK 2019, 'Integration of Survival and Binary Data for Variable Selection and Prediction: A Bayesian Approach', Journal of the Royal Statistical Society Series C: Applied Statistics, vol. 68, no. 5, pp. 1577-1595.
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SummaryWe consider the problem where the data consist of a survival time and a binary outcome measurement for each individual, as well as corresponding predictors. The goal is to select the common set of predictors which affect both the responses, and not just one of them. In addition, we develop a survival prediction model based on data integration. The paper is motivated by the Cancer Genomic Atlas databank, which is currently the largest genomics and transcriptomics database. The data contain cancer survival information along with cancer stages for each patient. Furthermore, it contains reverse phase protein array measurements for each individual, which are the predictors associated with these responses. The biological motivation is to identify the major actionable proteins associated with both survival outcomes and cancer stages. We develop a Bayesian hierarchical model to model jointly the survival time and the classification of the cancer stages. Moreover, to deal with the high dimensionality of the reverse phase protein array measurements, we use a shrinkage prior to identify significant proteins. Simulations and Cancer Genomic Atlas data analysis show that the joint integrated modelling approach improves survival prediction.

Man, Z, Li, P, Zhou, D, Zang, R, Wang, S, Li, P, Liu, S, Li, X, Wu, Y, Liang, X & Wang, G 2019, 'High-performance lithium–organic batteries by achieving 16 lithium storage in poly(imine-anthraquinone)', Journal of Materials Chemistry A, vol. 7, no. 5, pp. 2368-2375.
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The Li/PIAQ cell exhibits excellent electrochemical performances with a 16 Li-storage mechanism based on DFT calculations and experimental investigations.

Maniam, S, Higginbotham, HF, Bell, TDM & Langford, SJ 2019, 'Frontispiece: Harnessing Brightness in Naphthalene Diimides', Chemistry – A European Journal, vol. 25, no. 29.
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Maniam, S, Higginbotham, HF, Bell, TDM & Langford, SJ 2019, 'Harnessing Brightness in Naphthalene Diimides', Chemistry – A European Journal, vol. 25, no. 29, pp. 7044-7057.
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AbstractThe development of brightly emissive compounds is of great research and commercial interest, with established and emerging applications across chemistry, biology, physics, medicine and engineering. Among the many types of molecules available, naphthalene diimides have been widely used for both fundamental photophysical studies and in practical applications that utilise fluorescence as an information readout. The monomeric naphthalene diimide is weakly fluorescent, however through various methods of core‐derivatisation, it can be developed to be highly fluorescent and further functionalised to add utility. In this review, we highlight recent advances made in naphthalene diimide chemistry that have led to development of molecules with improved optical properties, and the design strategies utilised to produce bright fluorescence emission as small molecules or in supramolecular architectures.

Mantri, VA, Ganesan, M, Gupta, V, Krishnan, P & Siddhanta, AK 2019, 'An overview on agarophyte trade in India and need for policy interventions', Journal of Applied Phycology, vol. 31, no. 5, pp. 3011-3023.
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Marino, G, Solntsev, AS, Xu, L, Gili, VF, Carletti, L, Poddubny, AN, Rahmani, M, Smirnova, DA, Chen, H, Lemaître, A, Zhang, G, Zayats, AV, Angelis, CD, Leo, G, Sukhorukov, AA & Neshev, DN 2019, 'Spontaneous photon-pair generation at the nanoscale', Optica, vol. 6, no. 11, pp. 1416-1422.
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Optical nanoantennas have shown a great capacity for efficient extraction ofphotons from the near to the far-field, enabling directional emission fromnanoscale single-photon sources. However, their potential for the generationand extraction of multi-photon quantum states remains unexplored. Here wedemonstrate experimentally the nanoscale generation of two-photon quantumstates at telecommunication wavelengths based on spontaneous parametricdown-conversion in an optical nanoantenna. The antenna is a crystalline AlGaAsnanocylinder, possessing Mie-type resonances at both the pump and the bi-photonwavelengths and when excited by a pump beam generates photonpairs with a rateof 35 Hz. Normalized to the pump energy stored by the nanoantenna, this ratecorresponds to 1.4 GHz/Wm, being one order of magnitude higher thanconventional on-chip or bulk photon-pair sources. Our experiments open the wayfor multiplexing several antennas for coherent generation of multi-photonquantum states with complex spatial-mode entanglement and applications infree-space quantum communications and sensing.

Marlton, F, Checchia, S & Daniels, J 2019, 'Revealing phase boundaries by weighted parametric structural refinement', Journal of Synchrotron Radiation, vol. 26, no. 5, pp. 1638-1643.
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Parametric Rietveld refinement from powder diffraction data has been utilized in a variety of situations to understand structural phase transitions of materials in situ. However, when analysing data from lower-resolution two-dimensional detectors or from samples with overlapping Bragg peaks, such transitions become difficult to observe. In this study, a weighted parametric method is demonstrated whereby the scale factor is restrained via an inverse tan function, making the phase boundary composition a refinable parameter. This is demonstrated using compositionally graded samples within the lead-free piezoelectric (BiFeO3) x (Bi0.5K0.5TiO3) y (Bi0.5Na0.5TiO3)1–x–y and (Bi0.5Na0.5TiO3) x (BaTiO3)1–x systems. This has proven to be an effective method for diffraction experiments with relatively low resolution, weak peak splitting or compositionally complex multiphase samples.

Marlton, F, Ivashko, O, Zimmerman, MV, Gutowski, O, Dippel, A-C & Jørgensen, MRV 2019, 'A simple correction for the parallax effect in X-ray pair distribution function measurements', Journal of Applied Crystallography, vol. 52, no. 5, pp. 1072-1076.
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Total scattering and pair distribution function (PDF) analysis has created new insights that traditional powder diffraction methods have been unable to achieve in understanding the local structures of materials exhibiting disorder or complex nanostructures. Care must be taken in such analyses as subtle and discrete features in the PDF can easily be artefacts generated in the measurement process, which can result in unphysical models and interpretation. The focus of this study is an artefact called the parallax effect, which can occur in area detectors with thick detection layers during the collection of X-ray PDF data. This effect results in high-Qpeak offsets, which subsequently cause anr-dependent shift in the PDF peak positions in real space. Such effects should be accounted for if a truly accurate model is to be achieved, and a simple correction that can be conducted via a Rietveld refinement against the reference data is proposed.

Marsh, DJ & Dickson, K-A 2019, 'Writing Histone Monoubiquitination in Human Malignancy—The Role of RING Finger E3 Ubiquitin Ligases', Genes, vol. 10, no. 1, pp. 67-67.
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There is growing evidence highlighting the importance of monoubiquitination as part of the histone code. Monoubiquitination, the covalent attachment of a single ubiquitin molecule at specific lysines of histone tails, has been associated with transcriptional elongation and the DNA damage response. Sites function as scaffolds or docking platforms for proteins involved in transcription or DNA repair; however, not all sites are equal, with some sites resulting in actively transcribed chromatin and others associated with gene silencing. All events are written by E3 ubiquitin ligases, predominantly of the RING (really interesting new gene) finger type. One of the most well-studied events is monoubiquitination of histone H2B at lysine 120 (H2Bub1), written predominantly by the RING finger complex RNF20-RNF40 and generally associated with active transcription. Monoubiquitination of histone H2A at lysine 119 (H2AK119ub1) is also well-studied, its E3 ubiquitin ligase constituting part of thePolycomb Repressor Complex 1 (PRC1), RING1B-BMI1, associated with transcriptional silencing. Both modifications are activated as part of the DNA damage response. Histone monoubiquitination is a key epigenomic event shaping the chromatin landscape of malignancy and influencing how cells respond to DNA damage. This review discusses a number of these sites and the E3 RING finger ubiquitin ligases that write them.

Marsh, JW, Hayward, RJ, Shetty, A, Mahurkar, A, Humphrys, MS & Myers, GSA 2019, 'Dual RNA-Seq of Chlamydia and Host Cells', Methods in Molecular Biology, vol. 2042, pp. 123-135.
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During the infection of a host cell by a bacterial pathogen, a cascading series of gene expression changes occurs as each organism manipulates or responds to the other via defense or survival strategies. Unraveling this complex interplay is key for our understanding of bacterial virulence and host response pathways for the development of novel therapeutics. Dual RNA sequencing (dual RNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. Leveraging the sensitivity and resolution allowed by RNA-seq, dual RNA-Seq can be applied to any bacteria-eukaryotic host interaction. We pioneered dual RNA-Seq to simultaneously capture Chlamydia and host expression profiles during an in vitro infection as proof of principle. Here we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on Chlamydia as the organism of interest.

Marsh-Wakefield, F, Kruzins, A, McGuire, HM, Yang, S, Bryant, C, Fazekas de St. Groth, B, Nassif, N, Byrne, SN, Gibson, J, Brown, C, Larsen, S, McCulloch, D, Boyle, R, Clark, G, Joshua, D, Ho, PJ & Vuckovic, S 2019, 'Mass Cytometry Discovers Two Discrete Subsets of CD39−Treg Which Discriminate MGUS From Multiple Myeloma', Frontiers in Immunology, vol. 10, no. AUG, p. 1596.
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© 2019 Marsh-Wakefield, Kruzins, McGuire, Yang, Bryant, Fazekas de St. Groth, Nassif, Byrne, Gibson, Brown, Larsen, McCulloch, Boyle, Clark, Joshua, Ho and Vuckovic. Multiple Myeloma (MM) is preceded by the clinically stable condition monoclonal gammopathy of undetermined significance (MGUS). Critical immune events that discriminate MGUS from newly diagnosed MM (ND)MM patients remain unknown, but may involve changes in the regulatory T cell (Treg) compartment that favor myeloma growth. To address this possibility, we used mass cytometry and the unsupervised clustering algorithm Flow self-organizing map (FlowSOM) to interrogate the distribution of multiple subsets within CD25+ CD127low/neg Treg in matched bone marrow (BM) and peripheral blood (PB) of MGUS and NDMM patients. Both mass cytometry and flow cytometry confirmed a trend toward prevalence of CD39− Treg within the Treg compartment in BM and PB of NDMM patients compared to CD39− Treg in MGUS patients. FlowSOM clustering displayed a phenotypic organization of Treg into 25 metaclusters that confirmed Treg heterogeneity. It identified two subsets which emerged within CD39− Treg of NDMM patients that were negligible or absent in CD39− Treg of MGUS patients. One subset was found in both BM and PB which phenotypically resembled activated Treg based on CD45RO, CD49d, and CD62L expression; another subset resembled BM-resident Treg based on its tissue-resident CD69+ CD62L− CD49d− phenotype and restricted location within the BM. Both subsets co-expressed PD-1 and TIGIT, but PD-1 was expressed at higher levels on BM-resident Treg than on activated Treg. Within BM, both subsets had limited Perforin and Granzyme B production, whilst activated Treg in PB acquired high Perforin and Granzyme B production. In conclusion, the use of mass cytometry and FlowSOM clustering discovered two discrete subsets of CD39− Treg which are discordant in MGUS and NDMM patients and may be permissive of myeloma growth which warrants...

Mazraani, R, Timms, P, Hill, PC, Suaalii-Sauni, T, Niupulusu, T, Temese, SVA, Iosefa-Siitia, L, Auvaa, L, Tapelu, SA, Motu, MF, Righarts, A, Walsh, MS, Rombauts, L, Allan, JA, Horner, P & Huston, WM 2019, 'Evaluation of a PGP3 ELISA for surveillance of the burden of Chlamydia infection in women from Australia and Samoa', Pathogens and Disease, vol. 77, no. 3.
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ABSTRACT Serological assays can be used to investigate the population burden of infection and potentially sequelae from Chlamydia. We investigated the PGP3 ELISA as a sero-epidemiological tool for infection or sub-fertility in Australian and Samoan women. The PGP3 ELISA absorbance levels were compared between groups of women with infertility, fertile, and current chlamydial infections. In the Australian groups, women with chlamydial tubal factor infertility had significantly higher absorbance levels in the PGP3 ELISA compared to fertile women (P &lt; 0.0001), but not when compared to women with current chlamydial infection (P = 0.44). In the Samoan study, where the prevalence of chlamydial infections is much higher there were significant differences in the PGP3 ELISA absorbance levels between chlamydial sub-fertile women and fertile women (P = 0.003). There was no difference between chlamydial sub-fertile women and women with a current infection (P = 0.829). The results support that the PGP3 assay is effective for sero-epidemiological analysis of burden of infection, but not for evaluation of chlamydial pathological sequelae such as infertility.

McAlinden, KD, Deshpande, DA, Ghavami, S, Xenaki, D, Sohal, SS, Oliver, BG, Haghi, M & Sharma, P 2019, 'Autophagy Activation in Asthma Airways Remodeling', American Journal of Respiratory Cell and Molecular Biology, vol. 60, no. 5, pp. 541-553.
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Copyright © 2019 by the American Thoracic Society Current asthma therapies fail to target airway remodeling that correlates with asthma severity driving disease progression that ultimately leads to loss of lung function. Macroautophagy (hereinafter “autophagy”) is a fundamental cell-recycling mechanism in all eukaryotic cells; emerging evidence suggests that it is dysregulated in asthma. We investigated the interrelationship between autophagy and airway remodeling and assessed preclinical efficacy of a known autophagy inhibitor in murine models of asthma. Human asthmatic and nonasthmatic lung tissues were histologically evaluated and were immunostained for key autophagy markers. The percentage area of positive staining was quantified in the epithelium and airway smooth muscle bundles using ImageJ software. Furthermore, the autophagy inhibitor chloroquine was tested intranasally in prophylactic (3 wk) and treatment (5 wk) models of allergic asthma in mice. Human asthmatic tissues showed greater tissue inflammation and demonstrated hallmark features of airway remodeling, displaying thickened epithelium (P, 0.001) and reticular basement membrane (P, 0.0001), greater lamina propria depth (P, 0.005), and increased airway smooth muscle bundles (P, 0.001) with higher expression of Beclin-1 (P, 0.01) and ATG5 (autophagy-related gene 5) (P, 0.05) together with reduced p62 (P, 0.05) compared with nonasthmatic control tissues. Beclin-1 expression was significantly higher in asthmatic epithelium and ciliated cells (P, 0.05), suggesting a potential role of ciliophagy in asthma. Murine asthma models demonstrated effective preclinical efficacy (reduced key features of allergic asthma: airway inflammation, airway hyperresponsiveness, and airway remodeling) of the autophagy inhibitor chloroquine. Our data demonstrate cell context–dependent and selective activation of autophagy in structural cells in asthma. Furthermore, this pathway can be effectively targeted to amelio...

McAllum, EJ & Hare, DJ 2019, 'From niche methods to necessary tools: The growing importance of analytical atomic spectrometry in metal imaging in neuroscience', Spectrochimica Acta Part B: Atomic Spectroscopy, vol. 156, pp. 20-32.
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© 2019 Visualizing the highly compartmentalized distribution of metals in the brain has grown from a handful of analytical method development laboratories to now being an integral part of contemporary neuroscience and medical research. The burgeoning interest in mapping metals in the brain has been spurred on by an increasing appreciation of the role minor and trace elements play in normal neural function, ageing, neuroinflammation, and as a potential causative factor in a range of neurological disorders. Advances in technology, development of versatile imaging protocols, and an array of data analysis resources have all contributed to the current status of quantitative metal imaging as an invaluable, and often envied tool in the modern neuroscience laboratory. Atomic mass spectrometry and emission spectroscopy methods cover a broad range of applications that span macro, micro, and nanoscale imaging. Most importantly, increasing awareness of the capabilities of metal imaging has gradually captured the attention of neuroscientists, resulting in a shift in focus from traditional method development and optimization to use as a routine analytical technique in broader studies of brain function and disease. We reflect on the history and growth of metal imaging within the neurosciences, discuss how it has contributed to recent advances in our understanding of the brain and neurological disorders, appraise the challenges and limitations that remain unaddressed, and speculate on the future roles metal imaging will have in neuroscience research over the next decade.

McCabe, MJ, Gauthier, M-EA, Chan, C-L, Thompson, TJ, De Sousa, SMC, Puttick, C, Grady, JP, Gayevskiy, V, Tao, J, Ying, K, Cipponi, A, Deng, N, Swarbrick, A, Thomas, ML, Lord, RV, Johns, AL, Kohonen-Corish, M, O’Toole, SA, Clark, J, Mueller, SA, Gupta, R, McCormack, AI, Dinger, ME, Cowley, MJ, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Armitage, S, Arnold, L, Balleine, R, Bastick, P, Beesley, J, Beilby, J, Bennett, I, Blackburn, A, Bogwitz, M, Botes, L, Brennan, M, Brown, M, Buckley, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Callen, D, Campbell, I, Chauhan, D, Chauhan, M, Chenevix-Trench, G, Christian, A, Clarke, C, Cohen, P, Colley, A, Crook, A, Cui, J, Culling, B, Cummings, M, Dawson, S-J, deFazio, A, Delatycki, M, Dickson, R, Dixon, J, Dobrovic, A, Dudding, T, Edkins, T, Edwards, S, Eisenbruch, M, Farshid, G, Fellows, A, Fenton, G, Field, M, Flanagan, J, Fong, P, Forrest, L, Fox, S, French, J, Friedlander, M, Gaff, C, Ortega, DG, Gattas, M, George, P, Giles, G, Gill, G, Greening, S, Haan, E, Harris, M, Hart, S, Hayward, N, Heiniger, L, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kidd, A, Kirk, J, Koehler, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Mann, G, Marsh, D, McLachaln, SA, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, O’Sullivan, S, Pachter, N, Patterson, B, Phillips, K, Pieper, E, Rickard, E, Robinson, B, Saleh, M, Salisbury, E, Sambrook, J, Saunders, C, Saunus, J, Scott, E, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Southey, M, Spurdle, A, Taylor, J, Thorne, H, Trainer, A, Tucker, K, Visvader, J, Walker, L, Williams, R, Winship, I & Young, M-A 2019, 'Development and validation of a targeted gene sequencing panel for application to disparate cancers', Scientific Reports, vol. 9, no. 1.
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AbstractNext generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.

McCambridge, AB, Zaslawski, C & Bradnam, LV 2019, 'Investigating the mechanisms of acupuncture on neural excitability in healthy adults', NeuroReport, vol. 30, no. 2, pp. 71-76.
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Acupuncture is gaining interest as a potential treatment modality for various neurological conditions. Yet, the underlying mechanisms and efficacy on brain function are not well understood. Therefore, this study investigated the previously proposed hypothesis that acupuncture suppresses motor cortex excitability using transcranial magnetic stimulation (TMS) in healthy adults. The study was randomised, sham-controlled, and double-blinded. Single and paired-pulse TMS was delivered before, during, immediately after, and 30 min after removal of the needle. Acupuncture to the right Hegu acupoint (LI-4) of the hand was delivered by an experienced acupuncturist using standardised manipulations. A disposable (0.22×30 mm, Hwato) needle was used for verum stimulation (penetrating) and a Park retractable needle for sham (nonpenetrating). The peak-to-peak amplitude of TMS-induced motor-evoked potentials was recorded from two intrinsic hand muscles. Needling sensations were quantified using the Massachusett's acupuncture sensation scale. Participant needling sensations were not different between verum or sham acupuncture (P>0.54). Corticomotor excitability, intracortical inhibition, and intracortical facilitation were not modulated by verum or sham acupuncture during, immediately after, or 30 min after, recorded from a local or distant hand muscle to the needling site (all P>0.075). Contrary to previous studies, manual acupuncture did not affect motor cortex excitability in healthy adults. Because of the increasing popularity of acupuncture therapy, further research using patient populations should be considered.

McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2019, 'Corrigendum to “Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)” [Algal Res. 35 (November 2018) 586–594]', Algal Research, vol. 40, pp. 101478-101478.
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© 2019 Elsevier B.V. The authors wish to make the following corrigendum. Venus Shell Systems (VSS) provided the Ulva sp. used in this study. They are listed under the author affiliations, as well as in the Methods Section 2.1 as having provided the samples. To further clarify the involvement of the company we wish to make the following changes to the Conflicts of interest section. The company Venus Shell Systems (VSS), listed in the author affiliations, provided the cultivated Ulva sp. used in this study, obtained using a proprietary culture system. The authors declare that there was no significant financial support that could have influenced the outcome of the project. The research is free of bias and was conducted ethically in accord with the University of Wollongong's policy on external research collaboration. The authors would like to apologise for any inconvenience caused.

McClements, L, Annett, S, Yakkundi, A, O’Rourke, M, Valentine, A, Moustafa, N, Alqudah, A, Simões, BM, Furlong, F, Short, A, McIntosh, SA, McCarthy, HO, Clarke, RB & Robson, T 2019, 'FKBPL and its peptide derivatives inhibit endocrine therapy resistant cancer stem cells and breast cancer metastasis by downregulating DLL4 and Notch4', BMC Cancer, vol. 19, no. 1, p. 351.
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© 2019 The Author(s). Background: Optimising breast cancer treatment remains a challenge. Resistance to therapy is a major problem in both ER- and ER+ breast cancer. Tumour recurrence after chemotherapy and/or targeted therapy leads to more aggressive tumours with enhanced metastatic ability. Self-renewing cancer stem cells (CSCs) have been implicated in treatment resistance, recurrence and the development of metastatic disease. Methods: In this study, we utilised in vitro, in vivo and ex vivo breast cancer models using ER+ MCF-7 and ER- MDA-MB-231 cells, as well as solid and metastatic breast cancer patient samples, to interrogate the effects of FKBPL and its peptide therapeutics on metastasis, endocrine therapy resistant CSCs and DLL4 and Notch4 expression. The effects of FKBPL overexpression or peptide treatment were assessed using a t-test or one-way ANOVA with Dunnett's multiple comparison test. Results: We demonstrated that FKBPL overexpression or treatment with FKBPL-based therapeutics (AD-01, pre-clinical peptide /ALM201, clinical peptide) inhibit i) CSCs in both ER+ and ER- breast cancer, ii) cancer metastasis in a triple negative breast cancer metastasis model and iii) endocrine therapy resistant CSCs in ER+ breast cancer, via modulation of the DLL4 and Notch4 protein and/or mRNA expression. AD-01 was effective at reducing triple negative MDA-MB-231 breast cancer cell migration (n ≥ 3, p < 0.05) and invasion (n ≥ 3, p < 0.001) and this was translated in vivo where AD-01 inhibited breast cancer metastasis in MDA-MB-231-lucD3H1 in vivo model (p < 0.05). In ER+ MCF-7 cells and primary breast tumour samples, we demonstrated that ALM201 inhibits endocrine therapy resistant mammospheres, representative of CSC content (n ≥ 3, p < 0.05). Whilst an in vivo limiting dilution assay, using SCID mice, demonstrated that ALM201 alone or in combination with tamoxifen was very effective at delaying tumour recurrence by 12 (p < 0.05) or 21 days (p < 0.001), res...

McInnes, AS, Laczka, OF, Baker, KG, Larsson, ME, Robinson, CM, Clark, JS, Laiolo, L, Alvarez, M, Laverock, B, Kremer, CT, van Sebille, E & Doblin, MA 2019, 'Live cell analysis at sea reveals divergent thermal performance between photosynthetic ocean microbial eukaryote populations', The ISME Journal, vol. 13, no. 5, pp. 1374-1378.
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Abstract Experimentation at sea provides insight into which traits of ocean microbes are linked to performance in situ. Here we show distinct patterns in thermal tolerance of microbial phototrophs from adjacent water masses sampled in the south-west Pacific Ocean, determined using a fluorescent marker for reactive oxygen species (ROS). ROS content of pico-eukaryotes was assessed after 1, 5 and 25 h of incubation along a temperature gradient (15.6–32.1 °C). Pico-eukaryotes from the East Australian Current (EAC) had relatively constant ROS and showed greatest mortality after 25 h at 7 °C below ambient, whereas those from the Tasman Sea had elevated ROS in both warm and cool temperature extremes and greatest mortality at temperatures 6–10 °C above ambient, interpreted as the outcome of thermal stress. Tracking of water masses within an oceanographic circulation model showed populations had distinct thermal histories, with EAC pico-eukaryotes experiencing higher average temperatures for at least 1 week prior to sampling. While acclimatization and community assembly could both influence biological responses, this study clearly demonstrates that phenotypic divergence occurs along planktonic drift trajectories.

McLean, MW & Wand, MP 2019, 'Variational Message Passing for Elaborate Response Regression Models', Bayesian Analysis, vol. 14, no. 2, pp. 371-398.
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© 2019 International Society for Bayesian Analysis. We build on recent work concerning message passing approaches to approximate fitting and inference for arbitrarily large regression models. The focus is on regression models where the response variable is modeled to have an elaborate distribution, which is loosely defined to mean a distribution that is more complicated than common distributions such as those in the Bernoulli, Poisson and Normal families. Examples of elaborate response families considered here are the Negative Binomial and t families. Variational message passing is more challenging due to some of the conjugate exponential families being non-standard and numerical integration being needed. Nevertheless, a factor graph fragment approach means the requisite calculations only need to be done once for a particular elaborate response distribution family. Computer code can be compartmentalized, including that involving numerical integration. A major finding of this work is that the modularity of variational message passing extends to elaborate response regression models.

McNevin, D 2019, 'Response to: Biedermann & Hicks (2019), Commentary on “Dennis McNevin, Bayesian interpretation of discrete class characteristics, Forensic Science International, 292 (2018) 125–130”', Forensic Science International, vol. 298, pp. e1-e2.
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McNevin, D, Wright, K, Chaseling, J & Barash, M 2019, 'Commentary on: Bright et al. (2018) Internal validation of STRmix™ – a multi laboratory response to PCAST, Forensic Science International: Genetics, 34: 11–24', Forensic Science International: Genetics, vol. 41, pp. e14-e17.
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Mehta, M, Deeksha, Sharma, N, Vyas, M, Khurana, N, Maurya, PK, Singh, H, Andreoli de Jesus, TP, Dureja, H, Chellappan, DK, Gupta, G, Wadhwa, R, Collet, T, Hansbro, PM, Dua, K & Satija, S 2019, 'Interactions with the macrophages: An emerging targeted approach using novel drug delivery systems in respiratory diseases', Chemico-Biological Interactions, vol. 304, pp. 10-19.
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© 2019 Macrophages are considered as the most flexible cells of the hematopoietic system that are distributed in the tissues to act against pathogens and foreign particles. Macrophages are essential in maintaining homeostatic tissue processes, repair and immunity. Also, play important role in cytokine secretion and signal transduction of the infection so as to develop acquired immunity. Accounting to their involvement in pathogenesis, macrophages present a therapeutic target for the treatment of inflammatory respiratory diseases. This review focuses on novel drug delivery systems (NDDS) including nanoparticles, liposomes, dendrimers, microspheres etc that can target alveolar macrophage associated with inflammation, intracellular infection and lung cancer. The physiochemical properties and functional moieties of the NDDS attributes to enhanced macrophage targeting and uptake. The NDDS are promising for sustained drug delivery, reduced therapeutic dose, improved patient compliance and reduce drug toxicity. Further, the review also discuss about modified NDDS for specificity to the target and molecular targeting via anti-microbial peptides, kinases, NRF-2 and phosphodiesterase.

Mehta, M, Deeksha, Tewari, D, Gupta, G, Awasthi, R, Singh, H, Pandey, P, Chellappan, DK, Wadhwa, R, Collet, T, Hansbro, PM, Kumar, SR, Thangavelu, L, Negi, P, Dua, K & Satija, S 2019, 'Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases', Chemico-Biological Interactions, vol. 308, pp. 206-215.
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© 2019 Elsevier B.V. Oligonucleotide-based therapies are advanced novel interventions used in the management of various respiratory diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). These agents primarily act by gene silencing or RNA interference. Better methodologies and techniques are the need of the hour that can deliver these agents to tissues and cells in a target specific manner by which their maximum potential can be reached in the management of chronic inflammatory diseases. Nanoparticles play an important role in the target-specific delivery of drugs. In addition, oligonucleotides also are extensively used for gene transfer in the form of polymeric, liposomal and inorganic carrier materials. Therefore, the current review focuses on various novel dosage forms like nanoparticles, liposomes that can be used efficiently for the delivery of various oligonucleotides such as siRNA and miRNA. We also discuss the future perspectives and targets for oligonucleotides in the management of respiratory diseases.

Mendelson, N, Xu, Z-Q, Tran, TT, Kianinia, M, Scott, J, Bradac, C, Aharonovich, I & Toth, M 2019, 'Engineering and Tuning of Quantum Emitters in Few-Layer Hexagonal Boron Nitride', ACS Nano, vol. 13, no. 3, pp. 3132-3140.
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© 2019 American Chemical Society. Quantum technologies require robust and photostable single photon emitters (SPEs). Hexagonal boron nitride (hBN) has recently emerged as a promising candidate to host bright and optically stable SPEs operating at room temperature. However, the emission wavelength of the fluorescent defects in hBN has, to date, been shown to be uncontrolled, with a widespread of zero phonon line (ZPL) energies spanning a broad spectral range (hundreds of nanometers), which hinders the potential development of hBN-based devices and applications. Here we demonstrate chemical vapor deposition growth of large-area, few-layer hBN films that host large quantities of SPEs: -100-200 per 10 × 10 μm 2 . More than 85% of the emitters have a ZPL at (580 ± 10) nm, a distribution that is an order of magnitude narrower than reported previously. Furthermore, we demonstrate tuning of the ZPL wavelength using ionic liquid devices over a spectral range of up to 15 nm-the largest obtained to date from any solid-state SPE. The fabricated devices illustrate the potential of hBN for the development of hybrid quantum nanophotonic and optoelectronic devices based on two-dimensional materials.

Menictas, M, Nolan, TH, Simpson, DG & Wand, MP 2019, 'Streamlined Variational Inference for Higher Level Group-Specific Curve Models', Statistical Modelling: An International Journal.
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A two-level group-specific curve model is such that the mean response of eachmember of a group is a separate smooth function of a predictor of interest. Thethree-level extension is such that one grouping variable is nested withinanother one, and higher level extensions are analogous. Streamlined variationalinference for higher level group-specific curve models is a challengingproblem. We confront it by systematically working through two-level and thenthree-level cases and making use of the higher level sparse matrixinfrastructure laid down in Nolan and Wand (2018). A motivation is analysis ofdata from ultrasound technology for which three-level group-specific curvemodels are appropriate. Whilst extension to the number of levels exceedingthree is not covered explicitly, the pattern established by our systematicapproach sheds light on what is required for even higher level group-specificcurve models.

Metzen, D, Sheridan, GJ, Benyon, RG, Bolstad, PV, Griebel, A & Lane, PNJ 2019, 'Spatio-temporal transpiration patterns reflect vegetation structure in complex upland terrain', Science of The Total Environment, vol. 694, pp. 133551-133551.
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Topography exerts control on eco-hydrologic processes via alteration of energy inputs due to slope angle and orientation. Further, water availability varies with drainage position in response to topographic water redistribution and the catena effect on soil depth and thus soil water storage capacity. Our understanding of the spatio-temporal dynamics and drivers of transpiration patterns in complex terrain is still limited by lacking knowledge of how systematic interactions of energy and moisture patterns shape ecosystem state and water fluxes and adaptation of the vegetation to these patterns. To untangle the effects of slope orientation and hillslope position on forest structure and transpiration patterns, we measured forest structure, sap flux, soil moisture, throughfall and incoming shortwave radiation along two downslope transects in a forested head water catchment in south-east Australia. Our plot locations controlled for three systematically varying drainage position levels (topographic wetness index: 5.0, 6.5 and 8.0) and two levels of energy input (aridity index: 1.2 and 1.8). Vegetation patterns were generally stronger related to drainage position than slope orientation, whereas sap velocity variations were less pronounced. However, in combination with stand sapwood area, consistent spatio-temporal transpiration patterns emerged in relation to landscape position, where slope orientation was the primary and drainage position the secondary controlling factor. On short temporal scales, radiation and vapor pressure deficit were most important in regulating transpiration rates, whereas soil water limitation only occurred on shallow soils during summer. The importance of stand structural parameters increased on longer time scales, indicating optimization of vegetation in response to the long-term hydro-climatic conditions at a given landscape position. Thus, vegetation patterns can be conceptualized as a 'time-integrated' predictor variable that captures large...

Meunier, V, Bonnet, S, Pernice, M, Benavides, M, Lorrain, A, Grosso, O, Lambert, C & Houlbrèque, F 2019, 'Bleaching forces coral’s heterotrophy on diazotrophs and Synechococcus', The ISME Journal, vol. 13, no. 11, pp. 2882-2886.
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Abstract Coral reefs are threatened by global warming, which disrupts the symbiosis between corals and their photosynthetic symbionts (Symbiodiniaceae), leading to mass coral bleaching. Planktonic diazotrophs or dinitrogen (N2)-fixing prokaryotes are abundant in coral lagoon waters and could be an alternative nutrient source for corals. Here we incubated untreated and bleached coral colonies of Stylophora pistillata with a 15N2-pre-labelled natural plankton assemblage containing diazotrophs. 15N2 assimilation rates in Symbiodiniaceae cells and tissues of bleached corals were 5- and 30-fold higher, respectively, than those measured in untreated corals, demonstrating that corals incorporate more nitrogen derived from planktonic diazotrophs under bleaching conditions. Bleached corals also preferentially fed on Synechococcus, nitrogen-rich picophytoplanktonic cells, instead of Prochlorococcus and picoeukaryotes, which have a lower cellular nitrogen content. By providing an alternative source of bioavailable nitrogen, both the incorporation of nitrogen derived from planktonic diazotrophs and the ingestion of Synechococcus may have profound consequences for coral bleaching recovery, especially for the many coral reef ecosystems characterized by high abundance and activity of planktonic diazotrophs.

Meyer, S, Clarke, C, dos Santos, RO, Bishop, D, Krieger, MA & Blanes, L 2019, 'Developing self-generated calibration curves using a capillary-driven wax-polyester lab on a chip device and thermal gates', Microchemical Journal, vol. 146, pp. 708-712.
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© 2019 Elsevier B.V. Here we describe the development of a capillary-driven wax-polyester lab on a chip device and the concept of thermal gates to create self-generated calibration curves. The devices were fabricated by printing a wax pattern on a polyester film, and laminating two mirrored layers together. Victoria Blue R and a diluent of methanol/water (1:1) were placed in separate wells, and capillary forces drove the reagents through three additional mixing wells, resulting in respective dilutions of 50%, 25% and 12.5% of the original dye concentration (100%). A photo was taken after the capillary action ceased, and the color brightness of the four different concentrations was used for the creation of a calibration curve, resulting in a coefficient of determination of 0.99. The chip was readily adapted to include an additional channel to perform chemical reactions with KOH to increase the available detection options. The chip designs required up to three reagents to be simultaneously added, with any discrepancies in the synchronization of reagent addition leading to irreproducible results. To overcome these synchronization discrepancies, thermal gates were added by printing 0.15 mm wax barriers across the channel inlets to prevent liquid movement. These gates were simultaneously opened to allow the solutions to flow by applying heat, controlled by an Arduino-based instrument controller, through bent copper filaments positioned adjacent to the barriers for 380 milliseconds.

Mi, C, Zhou, J, Wang, F & Jin, D 2019, 'Thermally enhanced NIR–NIR anti-Stokes emission in rare earth doped nanocrystals', Nanoscale, vol. 11, no. 26, pp. 12547-12552.
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Surface phonons enhancing the one-photon anti-Stokes fluorescence has been demonstrated in rare earth doped nanocrystals.

Mi, C, Zhou, J, Wang, F, Lin, G & Jin, D 2019, 'Ultrasensitive Ratiometric Nanothermometer with Large Dynamic Range and Photostability', Chemistry of Materials, vol. 31, no. 22, pp. 9480-9487.
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Copyright © 2019 American Chemical Society. Thermally responsive fluorescent nanoparticles can be constructed to allow robust, rapid, and noninvasive temperature measurements. Furthermore, due to their tiny size, they can be used to detect temperature changes at the nanoscale. In this way, such sensors are ideally suited to emerging applications including intracellular temperature sensing and microelectronics failure diagnostics. Despite their potential, current nanothermometers still suffer from limited sensitivity, dynamic range, and stability. By introducing thermal enhanced anti-Stokes emission from a pair of lanthanide ions, ytterbium and neodymium, we show an increase of more than 1 order of magnitude in both the sensitivity and the dynamic range when compared to conventional ytterbium and erbium-codoped nanothermometers. Here, we report heterogeneous temperature-responsive nanoparticles with a new record of sensitivity (9.6%/K at room temperature and above 2.3%/K at elevated temperatures up to 413 K) that can be used for ratiometric thermometry. The heterogeneous nanostructure design shows that the thermal responses can be fine-tuned by the controlled growth of nanoparticles. The stability of the ultrasensitive nanothermometers has enabled long-term noncontact monitoring of local heat dissipation of a microelectronic device.

Mohd Yusop, AY, Xiao, L & Fu, S 2019, 'Data on the optimisation and validation of a liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to establish the presence of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes', Data in Brief, vol. 25, pp. 104234-104234.
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This paper presents the data on the optimisation and validation of a liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to establish the presence of phosphodiesterase 5 (PDE5) inhibitors and their analogues as adulterants in instant coffee premixes. The method development data covered chromatographic optimisation for better analyte separation and isomeric resolution, mass spectrometry optimisation for high sensitivity and sample preparation optimisation for high extraction recovery (RE) and low matrix effect (ME). The validation data covered specificity, linearity, range, accuracy, limit of detection, limit of quantification, precisions, ME, and RE. The optimisation and validation data presented here is related to the article: "Determination of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes using liquid chromatography-high-resolution mass spectrometry (LC-HRMS)" Mohd Yusop et al., 2019.

Mohd Yusop, AY, Xiao, L & Fu, S 2019, 'Determination of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes using liquid chromatography-high-resolution mass spectrometry (LC-HRMS)', Talanta, vol. 204, pp. 36-43.
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As a widely consumed beverage, coffee tends to be a target for intentional adulteration. This study describes the application of modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) coupled to liquid chromatography-high-resolution mass spectrometry (LC-HRMS) for simultaneous screening, identification, and quantification of undeclared phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes (ICPs). The mass spectrometer was operated in auto MS/MS acquisition for simultaneous MS and MS/MS experiments. Qualitative establishments from the suspected-target screening and targeted identification processes led to an unambiguous analyte assignment from the protonated molecule ([M+H]+) precursor ion which is subsequently used for quantification of 23 targeted PDE5 inhibitors. The analytical method validation covered specificity, linearity, range, accuracy, limit of detection (LOD), limit of quantification (LOQ), precisions, matrix effect (ME), and extraction recovery (RE). The specificity was established using the optimised chromatographic separation as well as the distinguishable [M+H]+ precursor ion. The linearity of each target analyte was demonstrated with a coefficient of determination (r2) of >0.9960 over the expected range of sample concentrations. The accuracy ranged from 88.1%–119.3% with LOD and LOQ of <70 ng/mL and 80 ng/mL, respectively. Excellent precisions were established within 0.4%–9.1% of the relative standard deviation. An insignificant ME within −5.2% to +8.7% was achieved using three different strategies of chromatography, sample extraction, and sample dilution. The RE was good for all target analytes within 84.7%–123.5% except for N-desethylacetildenafil at low (53.8%) and medium (65.1%) quality control levels. The method was successfully applied to 25 samples of ICPs where 17 of them were found to be adulterated with PDE5 inhibitors and their analogues. Further quantification revealed the total amount of these adulterants range...

Monahan, LG, DeMaere, MZ, Cummins, ML, Djordjevic, SP, Roy Chowdhury, P & Darling, AE 2019, 'High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei', Gut Pathogens, vol. 11, no. 1.
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© 2019 The Author(s). Background: Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies. Results: Here we used both short- and long-read methods to sequence the genome of a multidrug-resistant hospital isolate (C15117), which we identified as E. hormaechei. Hybrid assembly generated a complete circular chromosome of 4,739,272 bp and a fully resolved plasmid of 339,920 bp containing several antibiotic resistance genes. The strain also harboured a 34,857 bp repeat encoding copper resistance, which was present in both the chromosome and plasmid. Long reads that unambiguously spanned this repeat were required to resolve the chromosome and plasmid into separate replicons. Conclusion: This study provides important insights into the evolution and potential spread of antimicrobial resistance in a nosocomial E. hormaechei strain. More broadly, it further exemplifies the power of long-read sequencing technologies, particularly the Oxford Nanopore platform, for the characterisation of bacteria with complex resistance loci and large repeat elements.

Monterroso, B, Zorrilla, S, Sobrinos-Sanguino, M, Robles-Ramos, MÁ, Alfonso, C, Söderström, B, Meiresonne, NY, Verheul, J, den Blaauwen, T & Rivas, G 2019, 'The Bacterial DNA Binding Protein MatP Involved in Linking the Nucleoid Terminal Domain to the Divisome at Midcell Interacts with Lipid Membranes', mBio, vol. 10, no. 3.
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The division of an E. coli cell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integrated in vivo and in vitro analysis provides evidence that MatP can interact with lipid membranes reproducing the phospholipid mixture in the E. coli inner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.

Moodley, YP, Corte, TJ, Oliver, BG, Glaspole, IN, Livk, A, Ito, J, Peters, K, Lipscombe, R, Casey, T & Tan, DBA 2019, 'Analysis by proteomics reveals unique circulatory proteins in idiopathic pulmonary fibrosis', Respirology, vol. 24, no. 11, pp. 1111-1114.
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ABSTRACTBackground and objectiveIdiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease that has a poor 3‐year median survival rate with unclear pathophysiology. Radiological features include bibasal, subpleural fibrosis and honeycombing while its pathology is characterized by fibroblastic foci and honeycombing. Proteomic analysis of circulating molecules in plasma may identify factors that characterize IPF and may assist in the diagnosis, prognostication and determination of pathogenic pathways in this condition.MethodsTwo independent quantitative proteomic techniques were used, isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM), to identify differentially expressed plasma proteins in a group of IPF patients in comparison to healthy controls with normal lung function matched for age and gender.ResultsFive proteins were identified to be differentially expressed in IPF compared to healthy controls (upregulation of platelet basic protein and downregulation of actin, cytoplasmic 2, antithrombin‐III, extracellular matrix protein‐1 and fibronectin).ConclusionThis study further validates the combinational use of non‐targeted discovery proteomics (iTRAQ) with targeted quantitation by mass spectrometry (MRM) of soluble biomarkers to identify potentially important molecules and pathways for pulmonary diseases such as IPF.

Moore, LR, Huang, T, Ostrowski, M, Mazard, S, Kumar, SS, Gamage, HKAH, Brown, MV, Messer, LF, Seymour, JR & Paulsen, IT 2019, 'Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia’s Northern Oceanic Ecoregions', Frontiers in Microbiology, vol. 9, no. JAN.
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© 2019 Moore, Huang, Ostrowski, Mazard, Kumar, Gamage, Brown, Messer, Seymour and Paulsen. The tropical marine environments of northern Australia encompasses a diverse range of geomorphological and oceanographic conditions and high levels of productivity and nitrogen fixation. However, efforts to characterize phytoplankton assemblages in these waters have been restricted to studies using microscopic and pigment analyses, leading to the current consensus that this region is dominated by large diatoms, dinoflagellates, and the marine cyanobacterium Trichodesmium. During an oceanographic transect from the Arafura Sea through the Torres Strait to the Coral Sea, we characterized prokaryotic and eukaryotic phytoplankton communities in surface waters using a combination of flow cytometry and Illumina based 16S and 18S ribosomal RNA amplicon sequencing. Similar to observations in other marine regions around Australian, phytoplankton assemblages throughout this entire region were rich in unicellular picocyanobacterial primary producers while picoeukaryotic phytoplankton formed a consistent, though smaller proportion of the photosynthetic biomass. Major taxonomic groups displayed distinct biogeographic patterns linked to oceanographic and nutrient conditions. Unicellular picocyanobacteria dominated in both flow cytometric abundance and carbon biomass, with members of the Synechococcus genus dominating in the shallower Arafura Sea and Torres Strait where chlorophyll a was relatively higher (averaging 0.4 ± 0.2 mg m-3), and Prochlorococcus dominating in the oligotrophic Coral Sea where chlorophyll a averaged 0.13 ± 0.07 mg m-3. Consistent with previous microscopic and pigment-based observations, we found from sequence analysis that a variety of diatoms (Bacillariophyceae) exhibited high relative abundance in the Arafura Sea and Torres Strait, while dinoflagellates (Dinophyceae) and prymnesiophytes (Prymnesiophyceae) were more abundant in the Coral Sea. Ordination a...

Moret, S, Lee, PLT, de la Hunty, M, Spindler, X, Lennard, C & Roux, C 2019, 'Single metal deposition versus physical developer: A comparison between two advanced fingermark detection techniques', Forensic Science International, vol. 294, pp. 103-112.
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© 2018 Elsevier B.V. Single metal deposition (SMD II) is a fingermark detection technique based on the use of colloidal gold. The technique has been simplified and optimised over the years to become more reliable, sensitive and user-friendly. Physical developer (PD) is a well-established detection method based on silver deposition from a redox solution. This study presents an extensive comparison of SMD II against PD for fingermark detection on porous substrates. The two techniques were compared as (i) standalone methods, (ii) in sequence after the application of routine amino acids reagents (1,2-indanedione/zinc followed by ninhydrin), and (iii) after the substrates have been wet. More than 1000 fingermark specimens were processed. Overall, the performance of SMD II was judged to be inferior to that of PD; therefore, SMD II cannot be recommended as a valid replacement for fingermark detection on porous substrates. Indanedione/zinc and ninhydrin application negatively impacts on SMD II performance and the technique gave inconsistent results across the selected range of porous substrates. Moreover, the detected fingermarks lacked contrast making their visualisation difficult. However, even if PD remains the technique of choice, SMD II showed significant potential. It proved to be less affected by donor variability and it can be applied on both porous and non-porous substrates. It did not lead to uncontrolled background staining that commonly occurs with PD. If contrast and consistency issues can be addressed in future research, SMD II may become a viable alternative to PD.

Mote, S, Schönberg, CHL, Samaai, T, Gupta, V & Ingole, B 2019, 'A new clionaid sponge infests live corals on the west coast of India (Porifera, Demospongiae, Clionaida)', Systematics and Biodiversity, vol. 17, no. 2, pp. 190-206.
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Mowe, MAD, Song, Y, Sim, DZH, Lu, J, Mitrovic, SM, Tan, HTW & Yeo, DCJ 2019, 'Comparative study of six emergent macrophyte species for controlling cyanobacterial blooms in a tropical reservoir', Ecological Engineering, vol. 129, pp. 11-21.
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© 2019 Elsevier B.V. Interactions between macrophytes and phytoplankton have been studied extensively in temperate water bodies, but far less attention has been paid to those for emergent macrophytes in the tropics. We investigated the effects of six emergent macrophyte species (Brachiaria mutica, Ipomoea aquatica, Sphagneticola trilobata, Ludwigia adscendens, Pandanus amaryllifolius and Persicaria barbata) on the phytoplankton community of a tropical reservoir using ex situ experiments with multiple planting densities (Treatment 1: 0.108, Treatment 2: 0.24, Treatment 3: 0.40, Treatment 4: 0.58 g dry weight L −1 ) in 100-L mesocosms. Chlorophyll a (as a proxy of total phytoplankton biomass) and phytoplankton community structure were examined. The initial phytoplankton community (average chlorophyll a: 20.36 ± 0.69 µg L −1 ) was dominated by cyanobacteria: Planktolyngybya, Pseudanabaena and Cylindrospermopsis (average relative biovolume 0.68 ± 0.03). Over four weeks, L. adscendens (Treatments 3 and 4) and P. barbata (Treatments 2 to 4) significantly reduced chlorophyll a concentrations by 3.29–6.69 µg L −1 compared to the controls. Comparing species effects over four weeks for Treatment 4, P. barbata significantly lowered chlorophyll a concentrations compared to I. aquatica while there were no significant differences between all other species. All treatments of L. adscendens and P. barbata significantly reduced the relative biovolume of cyanobacteria in the phytoplankton communities by 0.19–0.39 compared to the controls. The highest-density treatments of all six macrophyte species led to significant shifts in the phytoplankton community structure by reducing the relative abundance of filamentous cyanobacteria (Planktolyngbya, Pseudanabaena) and/or increasing the relative abundance of cryptomonads (Chroomonas, Rhodomonas). This study shows the potential of emergent macrophyte species, especially L. adscendens and P. barbata, to reduce total phytoplankton biomass a...

Müller, S, Zavřel, T & Červený, J 2019, 'Towards a quantitative assessment of inorganic carbon cycling in photosynthetic microorganisms', Engineering in Life Sciences, vol. 19, no. 12, pp. 955-967.
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AbstractPhotosynthetic organisms developed various strategies to mitigate high light stress. For instance, aquatic organisms are able to spend excessive energy by exchanging dissolved CO2 (dCO2) and bicarbonate () with the environment. Simultaneous uptake and excretion of the two carbon species is referred to as inorganic carbon cycling. Often, inorganic carbon cycling is indicated by displacements of the extracellular dCO2 signal from the equilibrium value after changing the light conditions. In this work, we additionally use (i) the extracellular pH signal, which requires non‐ or weakly‐buffered medium, and (ii) a dynamic model of carbonate chemistry in the aquatic environment to detect and quantitatively describe inorganic carbon cycling. Based on simulations and experiments in precisely controlled photobioreactors, we show that the magnitude of the observed dCO2 displacement crucially depends on extracellular pH level and buffer concentration. Moreover, we find that the dCO2 displacement can also be caused by simultaneous uptake of both dCO2 and (no inorganic carbon cycling). In a next step, the dynamic model of carbonate chemistry allows for a quantitative assessment of cellular dCO2, , and H+ exchange rates from the measur...

Murray, SA, Ruvindy, R, Kohli, GS, Anderson, DM & Brosnahan, ML 2019, 'Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1', Scientific Reports, vol. 9, no. 1, p. 14532.
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AbstractAlexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L−1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.

Nader, CP, Cidem, A, Verrills, NM & Ammit, AJ 2019, 'Protein phosphatase 2A (PP2A): a key phosphatase in the progression of chronic obstructive pulmonary disease (COPD) to lung cancer', Respiratory Research, vol. 20, no. 1, p. 222.
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AbstractLung cancer (LC) has the highest relative risk of development as a comorbidity of chronic obstructive pulmonary disease (COPD). The molecular mechanisms that mediate chronic inflammation and lung function impairment in COPD have been identified in LC. This suggests the two diseases are more linked than once thought. Emerging data in relation to a key phosphatase, protein phosphatase 2A (PP2A), and its regulatory role in inflammatory and tumour suppression in both disease settings suggests that it may be critical in the progression of COPD to LC. In this review, we uncover the importance of the functional and active PP2A holoenzyme in the context of both diseases. We describe PP2A inactivation via direct and indirect means and explore the actions of two key PP2A endogenous inhibitors, cancerous inhibitor of PP2A (CIP2A) and inhibitor 2 of PP2A (SET), and the role they play in COPD and LC. We explain how dysregulation of PP2A in COPD creates a favourable inflammatory micro-environment and promotes the initiation and progression of tumour pathogenesis. Finally, we highlight PP2A as a druggable target in the treatment of COPD and LC and demonstrate the potential of PP2A re-activation as a strategy to halt COPD disease progression to LC. Although further studies are required to elucidate if PP2A activity in COPD is a causal link for LC progression, studies focused on the potential of PP2A reactivating agents to reduce the risk of LC formation in COPD patients will be pivotal in improving clinical outcomes for both COPD and LC patients in the future.

Nair, PM, Starkey, MR, Haw, TJ, Liu, G, Collison, AM, Mattes, J, Wark, PA, Morris, JC, Verrills, NM, Clark, AR, Ammit, AJ & Hansbro, PM 2019, 'Enhancing tristetraprolin activity reduces the severity of cigarette smoke‐induced experimental chronic obstructive pulmonary disease', Clinical & Translational Immunology, vol. 8, no. 10.
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AbstractObjectiveChronic obstructive pulmonary disease (COPD) is a progressive disease that causes significant mortality and morbidity worldwide and is primarily caused by the inhalation of cigarette smoke (CS). Lack of effective treatments for COPD means there is an urgent need to identify new therapeutic strategies for the underlying mechanisms of pathogenesis. Tristetraprolin (TTP) encoded by the Zfp36 gene is an anti‐inflammatory protein that induces mRNA decay, especially of transcripts encoding inflammatory cytokines, including those implicated in COPD.MethodsHere, we identify a novel protective role for TTP in CS‐induced experimental COPD using Zfp36aa/aa mice, a genetically modified mouse strain in which endogenous TTP cannot be phosphorylated, rendering it constitutively active as an mRNA‐destabilising factor. TTP wild‐type (Zfp36+/+) and Zfp36aa/aa active C57BL/6J mice were exposed to CS for four days or eight weeks, and the impact on acute inflammatory responses or chronic features of COPD, respectively, was assessed.ResultsAfter four days of CS exposure, Zfp36aa/aa mice had reduced numbers of airway neutrophils and lymphocytes and mRNA expression levels of cytokines compared to wild‐type controls. After eight weeks, Zfp36aa/aa mice had reduced pulmonary inflammation, airway remodelling and emphysema‐like alveolar enlargement, and lung function was improved. We then used pharmacological treatments in vivo (protein phosphatase 2A activator, AAL(S)

Naser, IB, Hoque, MM, Faruque, SN, Kamruzzaman, M, Yamasaki, S & Faruque, SM 2019, 'Vibrio cholerae strains with inactivated cqsS gene overproduce autoinducer-2 which enhances resuscitation of dormant environmental V. cholerae', PLOS ONE, vol. 14, no. 10, pp. e0223226-e0223226.
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BACKGROUND: Toxigenic Vibrio cholerae resides in aquatic reservoirs of cholera-endemic areas mostly in a dormant form known as conditionally viable environmental cells (CVEC) in which the bacteria remain embedded in an exopolysaccharide matrix, and fail to grow in routine bacteriological culture. The CVEC can be resuscitated by supplementing culture media with either of two autoinducers CAI-1 and AI-2, which are signal molecules controlling quorum sensing, a regulatory network of bacterial gene expression dependent on cell density. This study investigated possible existence of variant strains that overproduce AIs, sufficient to resuscitate CVEC in environmental waters. METHODS: Environmental V. cholerae isolates and Tn insertion mutants of a V. cholerae strain C6706 were screened for production of AIs using bioluminescent reporter strains. Relevant mutations in environmental strains which overproduced AI-2 were characterized by nucleotide sequencing and genetic complementation studies. Effect of AIs produced in culture supernatants of relevant strains on reactivation of CVEC in water was determined by resuscitation assays. RESULTS: Two of 54 environmental V. cholerae isolates were found to overproduce AI-2. Screening of a Tn-insertion library of V. cholerae strain C6706, identified a mutant which overproduced AI-2, and carried Tn insertion in the cqsS gene. Nucleotide sequencing also revealed mutations inactivating the cqsS gene in environmental isolates which overproduced AI-2, and this property was reversed when complemented with a wild type cqsS gene. Culture of river water samples supplemented with spent medium of these mutants resuscitated dormant V. cholerae cells in water. SIGNIFICANCE: V. cholerae strains with inactivated cqsS gene may offer a convenient source of AI-2 in enhanced assays for monitoring bacteriological quality of water. The results also suggest a potential role of naturally occurring cqsS mutants in the environmental biology of V...

Nasiri, N, Jin, D & Tricoli, A 2019, 'Nanoarchitechtonics of Visible‐Blind Ultraviolet Photodetector Materials: Critical Features and Nano‐Microfabrication', Advanced Optical Materials, vol. 7, no. 2, pp. 1800580-1800580.
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AbstractAccurate measurement of ultraviolet radiation is key to many technologies including wearable devices for skin cancer prevention, optical communication systems, and missile launch detection. Nanostructuring of wide bandgap semiconductors, such as GaN, ZnO, and SiC, promises some benefits over established commercial solutions relying on n–p type Si‐homojunction technology. In the past decade, a variety of carefully nanostructured architectures have been demonstrated as efficient designs for visible‐blind UV photodetectors featuring superior detectivity, thermal stability, robust radiation hardness, and very low operation bias and power consumption. Here, a comprehensive review of the latest achievements on ultraviolet photodetector materials is presented, with focus on the multiscale engineering of composition and nano‐microscale morphology. The review concludes with a critical assessment and comparison of state‐of‐the‐art devices aiming to provide guidelines and research directions for the next generation of UV photodetector materials.

Nelz, R, Radtke, M, Slablab, A, Kianinia, M, Li, C, Xu, Z-Q, Bradac, C, Aharonovich, I & Neu, E 2019, 'Near-field energy transfer between a luminescent 2D material and color centers in diamond', Advanced Quantum Technologies, vol. 3, no. 2.
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Energy transfer between fluorescent probes lies at the heart of manyapplications ranging from bio-sensing and -imaging to enhanced photo-detectionand light harvesting. In this work, we study F\'orster resonance energytransfer (FRET) between shallow defects in diamond --- nitrogen-vacancy (NV)centers --- and atomically-thin, two-dimensional materials --- tungstendiselenide (WSe$_2$). By means of fluorescence lifetime imaging, we demonstratethe occurrence of FRET in the WSe$_2$/NV system. Further, we show that in thecoupled system, NV centers provide an additional excitation pathway for WSe$_2$photoluminescence. Our results constitute the first step towards therealization of hybrid quantum systems involving single-crystal diamond andtwo-dimensional materials that may lead to new strategies for studying andcontrolling spin transfer phenomena and spin valley physics.

Ng, SW, Chan, Y, Chellappan, DK, Madheswaran, T, Zeeshan, F, Chan, YL, Collet, T, Gupta, G, Oliver, BG, Wark, P, Hansbro, N, Hsu, A, Hansbro, PM, Dua, K & Panneerselvam, J 2019, 'Molecular modulators of celastrol as the keystones for its diverse pharmacological activities', Biomedicine & Pharmacotherapy, vol. 109, pp. 1785-1792.
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© 2018 The Authors In the recent years, much attention has been focused on identifying bioactive compounds from medicinal plants that could be employed in therapeutics, which is attributed to their potent pharmacological actions and better toxicological profile. One such example that has come into the light with considerable interest is the pentacyclic triterpenoid, celastrol, which has been found to provide substantial therapeutic properties in a variety of diseases. In an effort to further accelerate its potential to be utilized in clinical practice in the future; along with advancing technologies in the field of drug discovery and development, different researchers have been investigating on the various mechanisms and immunological targets of celastrol that underlie its broad spectrum of pharmacological properties. In this review, we have collated the various research findings related to the molecular modulators responsible for different pharmacological activities shown by celastrol. Our review will be of interest to the herbal, biological, molecular scientist and by providing a quick snapshot about celastrol giving a new direction in the area of herbal drug discovery and development.

Nguyen, L, Mak, C, Chen, H, Zaky, A, Wong, M, Pollock, C & Saad, S 2019, 'SIRT1 Attenuates Kidney Disorders in Male Offspring Due to Maternal High-Fat Diet', Nutrients, vol. 11, no. 1, pp. 146-146.
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Maternal obesity has been associated with kidney disorders in male offspring. Our previous studies have demonstrated that Sirtuin (SIRT)1, an essential regulator of metabolic stress responses, is suppressed in the offspring as the result of maternal high-fat diet (HFD) consumption, which is likely to underpin the adverse metabolic and renal outcomes. To examine if SIRT1 overexpression or activation early in life can protect the offspring kidney, wild-type (WT) and transgenic (Tg) offspring were born to the same diet-induced obese female C57BL/6 mice through breeding with hemizygous SIRT1-transgenic (Tg) male mice and examined for renal pathological changes. In separate experiments, SIRT1 activator SRT1720 (25 mg/kg/2 days i.p) was administrated in WT offspring over 6 weeks of postnatal high-fat diet exposure. The results show that offspring born to obese dams have increased kidney weight, higher levels of renal triglycerides, and increased expression of oxidative stress, inflammatory, and fibrotic markers, as well as increased albuminuria compared to offspring of control dams. Both SIRT1 overexpression and SRT1720 treatment attenuated renal lipid contents and expression of lipogenesis, oxidative stress, and inflammatory markers; however, fibrosis was modestly reduced and albuminuria was not affected. The findings suggest that SIRT1 therapy can ameliorate some pathological mechanisms of kidney programming due to maternal obesity but may not be sufficient to prevent the resulting chronic kidney injury.

Nguyen, LT, Chen, H, Zaky, A, Pollock, C & Saad, S 2019, 'SIRT1 overexpression attenuates offspring metabolic and liver disorders as a result of maternal high‐fat feeding', The Journal of Physiology, vol. 597, no. 2, pp. 467-480.
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Key pointsMaternal high‐fat diet (MHF) consumption led to metabolic and liver disorders in male offspring, which are associated with reduced sirtuin (SIRT)1 expression and activity in the offspring liverSIRT1 overexpression in MHF offspring reduced their body weight and adiposity and normalized lipid metabolic markers in epididymal and retroperitoneal adipose tissuesSIRT1 overexpression in MHF offspring improved glucose tolerance, as well as systemic and hepatic insulin sensitivitySIRT1 overexpression ameliorated MHF‐induced lipogenesis, oxidative stress and fibrogenesis in the liver of offspring.AbstractMaternal obesity can increase the risk of metabolic disorders in the offspring. However, the underlying mechanism responsible for this is not clearly understood. Previous evidence implied that sirtuin (SIRT)1, a potent regulator of energy metabolism and stress responses, may play an important role. In the present study, we have shown, in C57BL/6 mice, that maternal high‐fat diet (HFD) consumption can induce a pre‐diabetic and non‐alcoholic fatty liver disease phenotype in the offspring, associated with reduced SIRT1 expression in the hypothalamus, white adipose tissues (WAT) and liver. Importantly, the overexpression of SIRT1 in these offspring significantly attenuated the excessive accumulation of epididymal (Epi) white adipose tissue (WAT) and retroperitoneal (Rp)WAT (P < 0.001), glucose intolerance and insulin resistance (both P < 0.05) at weaning age. These changes were associated with the suppression of peroxisome proliferator‐activated recept...

Nguyen, M, Nikolay, N, Bradac, C, Kianinia, M, Ekimov, EA, Mendelson, N, Benson, O & Aharonovich, I 2019, 'Photodynamics and quantum efficiency of germanium vacancy color centers in diamond', Advanced Photonics, vol. 1, no. 06, pp. 1-1.
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Color centers in diamond-especially group IV defects-have been advanced as a viable solid-state platform for quantum photonics and information technologies. We investigate the photodynamics and characteristics of germanium-vacancy (GeV) centers hosted in high-pressure high-temperature diamond nanocrystals. Through back-focal plane imaging, we analyze the far-field radiation pattern of the investigated emitters and derive a crossed-dipole emission, which is strongly aligned along one axis. We use this information in combination with lifetime measurements to extract the decay rate statistics of the GeV emitters and determine their quantum efficiency, which we estimated to be ∼ (22 ± 2) %. Our results offer further insight into the photodynamic properties of the GeV center in nanodiamonds and confirm its suitability as a desirable system for quantum technologies.

Nguyen, T, Li, GE, Chen, H, Cranfield, CG, McGrath, KC & Gorrie, CA 2019, 'Neurological Effects in the Offspring After Switching From Tobacco Cigarettes to E-Cigarettes During Pregnancy in a Mouse Model', Toxicological Sciences, vol. 172, no. 1, pp. 191-200.
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Abstract Maternal smoking is currently a public health concern and has been associated with a number of complications in the offspring. E-cigarettes are gaining popularity as a “safer” alternative to tobacco cigarettes during pregnancy, however, there are a limited number of studies to suggest that it is actually “safe.” Balb/C female mice were exposed to ambient air (n = 8; Sham), or tobacco cigarette smoke (n = 8; SE) before gestation, during gestation and lactation. A third group was exposed to cigarette smoke before gestation followed by e-cigarette aerosols during gestation and lactation (n = 8; Switch). Male offspring (12-week old, n = 10–14/group) underwent behavioral assessments to investigate short-term memory, anxiety, and activity using the novel object recognition and elevated plus maze tests. Brains were collected at postnatal day (P)1, P20, and Week 13 for global DNA methylation, epigenetic gene expression, and neuronal cell counts. The offspring from mothers switching to e-cigarettes exhibited no change in exploration/activity but showed a decrease in global DNA methylation, Aurora Kinase (Aurk) A and AurkB gene expression and a reduction in neuronal cell numbers in the cornu ammonis 1 region of the dorsal hippocampus compared with the SE group. Continuous tobacco cigarette smoke exposure during pregnancy resulted in marked neurological deficits in the offspring. Switching to e-cigarettes during pregnancy reduced these neurological deficits compared with cigarette smoke exposure. However, neurological changes were still observed, so we therefore conclude that e-cigarette use during pregnancy is not advised.

Nikolay, N, Mendelson, N, Özelci, E, Sontheimer, B, Böhm, F, Kewes, G, Toth, M, Aharonovich, I & Benson, O 2019, 'Direct measurement of quantum efficiency of single-photon emitters in hexagonal boron nitride', Optica, vol. 6, no. 8, pp. 1084-1084.
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© 2019 Optical Society of America. Single-photon emitters (SPEs) in two-dimensional materials are promising candidates for the future generation of quantum photonic technologies. In this work, we experimentally determine the quantum efficiency (QE) of SPEs in few-layer hexagonal boron nitride (h-BN). We employ a metal hemisphere that is attached to the tip of an atomic force microscope to directly measure the lifetime variation of the SPEs as the tip approaches the h-BN. This technique enables nondestructive, yet direct and absolute measurement of the QE of SPEs. We find that the emitters exhibit very high QEs approaching (87 ± 7)% at wavelengths of ≈580 nm, which is among the highest QEs recorded for a solid-state SPE.

Nixon, B, Johnston, SD, Skerrett-Byrne, DA, Anderson, AL, Stanger, SJ, Bromfield, EG, Martin, JH, Hansbro, PM & Dun, MD 2019, 'Modification of Crocodile Spermatozoa Refutes the Tenet That Post-testicular Sperm Maturation Is Restricted To Mammals*', Molecular & Cellular Proteomics, vol. 18, pp. S58-S76.
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© 2019 Nixon et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc. Competition to achieve paternity has contributed to the development of a multitude of elaborate male reproductive strategies. In one of the most well-studied examples, the spermatozoa of all mammalian species must undergo a series of physiological changes, termed capacitation, in the female reproductive tract before realizing their potential to fertilize an ovum. However, the evolutionary origin and adaptive advantage afforded by capacitation remains obscure. Here, we report the use of comparative and quantitative proteomics to explore the biological significance of capacitation in an ancient reptilian species, the Australian saltwater crocodile (Crocodylus porosus). Our data reveal that exposure of crocodile spermatozoa to capacitation stimuli elicits a cascade of physiological responses that are analogous to those implicated in the functional activation of their mammalian counterparts. Indeed, among a total of 1119 proteins identified in this study, we detected 126 that were differentially phosphorylated ( 1.2 fold-change) in capacitated versus noncapacitated crocodile spermatozoa. Notably, this subset of phosphorylated proteins shared substantial evolutionary overlap with those documented in mammalian spermatozoa, and included key elements of signal transduction, metabolic and cellular remodeling pathways. Unlike mammalian sperm, however, we noted a distinct bias for differential phosphorylation of serine (as opposed to tyrosine) residues, with this amino acid featuring as the target for 80% of all changes detected in capacitated spermatozoa. Overall, these results indicate that the phenomenon of sperm capacitation is unlikely to be restricted to mammals and provide a framework for understanding the molecular changes in sperm physiology necessary for fertilization.

Nolan, LM, Turnbull, L, Katrib, M, Osvath, SR, Losa, D, Lazenby, JJ & Whitchurch, CB 2019, 'Pseudomonas aeruginosa is capable of natural transformation in biofilms'.
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AbstractNatural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologs of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa.

Nolan, M & Fronzi, M 2019, 'Activation of CO2 at chromia-nanocluster-modified rutile and anatase TiO2', Catalysis Today, vol. 326, pp. 68-74.
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© 2018 Elsevier B.V. Converting CO2 to fuels is required to enable the production of sustainable fuels and to contribute to alleviating CO2 emissions. In considering conversion of CO2, the initial step of adsorption and activation by the catalyst is crucial. In addressing this difficult problem, we have examined how nanoclusters of reducible metal oxides supported on TiO2 can promote CO2 activation. In this paper we present density functional theory (DFT) simulations of CO2 activation on heterostructures composed of clean or hydroxylated extended rutile and anatase TiO2 surfaces modified with chromia nanoclusters. The heterostructures show non-bulk Cr and O sites in the nanoclusters and an upshifted valence band edge that is dominated by Cr 3d- O 2p interactions. We show that the supported chromia nanoclusters can adsorb and activate CO2 and that activation of CO2 is promoted whether the TiO2 support is oxidised or hydroxylated. Reduced heterostructures, formed by removal of oxygen from the chromia nanocluster, also promote CO2 activation. In the strong CO2 adsorption modes, the molecule bends giving O–C–O angles of 127 - 132° and elongation of C–O distances up to 1.30 Å; no carbonates are formed. The electronic properties show a strong CO2–Cr–O interaction that drives the interaction of CO2 with the nanocluster and induces the structural distortions. These results highlight that a metal oxide support modified with reducible metal oxide nanoclusters can activate CO2, thus helping to overcome difficulties associated with the difficult first step in CO2 conversion.

Nolan, TH, Menictas, M & Wand, MP 2019, 'Streamlined Computing for Variational Inference with Higher Level Random Effects', Journal of Machine Learning Research, vol. 21, pp. 1-62.
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We derive and present explicit algorithms to facilitate streamlined computingfor variational inference for models containing higher level random effects.Existing literature, such as Lee and Wand (2016), is such that streamlinedvariational inference is restricted to mean field variational Bayes algorithmsfor two-level random effects models. Here we provide the following extensions:(1) explicit Gaussian response mean field variational Bayes algorithms forthree-level models, (2) explicit algorithms for the alternative variationalmessage passing approach in the case of two-level and three-level models, and(3) an explanation of how arbitrarily high levels of nesting can be handledbased on the recently published matrix algebraic results of the authors. Apay-off from (2) is simple extension to non-Gaussian response models. Insummary, we remove barriers for streamlining variational inference algorithmsbased on either the mean field variational Bayes approach or the variationalmessage passing approach when higher level random effects are present.

O’Rourke, MB, Town, SEL, Dalla, PV, Bicknell, F, Koh Belic, N, Violi, JP, Steele, JR & Padula, MP 2019, 'What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows', Proteomes, vol. 7, no. 3, pp. 29-29.
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The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process.

Obeidat, M, Faiz, A, Li, X, van den Berge, M, Hansel, NN, Joubert, P, Hao, K, Brandsma, C-A, Rafaels, N, Mathias, R, Ruczinski, I, Beaty, TH, Barnes, KC, Man, SFP, Paré, PD & Sin, DD 2019, 'The pharmacogenomics of inhaled corticosteroids and lung function decline in COPD', European Respiratory Journal, vol. 54, no. 6, pp. 1900521-1900521.
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Inhaled corticosteroids (ICS) are widely prescribed for patients with chronic obstructive pulmonary disease (COPD), yet have variable outcomes and adverse reactions, which may be genetically determined. The primary aim of the study was to identify the genetic determinants for forced expiratory volume in 1 s (FEV1) changes related to ICS therapy.In the Lung Health Study (LHS)-2, 1116 COPD patients were randomised to the ICS triamcinolone acetonide (n=559) or placebo (n=557) with spirometry performed every 6 months for 3 years. We performed a pharmacogenomic genome-wide association study for the genotype-by-ICS treatment effect on 3 years of FEV1 changes (estimated as slope) in 802 genotyped LHS-2 participants. Replication was performed in 199 COPD patients randomised to the ICS, fluticasone or placebo.A total of five loci showed genotype-by-ICS interaction at p<5×10−6; of these, single nucleotide polymorphism (SNP) rs111720447 on chromosome 7 was replicated (discovery p=4.8×10−6, replication p=5.9×10−5) with the same direction of interaction effect. ENCODE (Encyclopedia of DNA Elements) data revealed that in glucocorticoid-treated (dexamethasone) A549 alveolar cell line, glucocorticoid receptor binding sites were located near SNP rs111720447. In stratified analyses of LHS-2, genotype at SNP rs111720447 was significantly associated with rate of FEV1 decline in patients taking ICS (C allele β 56.36 mL·year−1, 95% CI 29.96–82.76 mL·year−1) and in patients who were assigned to placebo, although the relationship was weaker and in the opposite direction to that in the ICS group (C allele β −27.57 mL·year−1, 95% CI −53.27– −1.87 mL·year−1).The study uncovered genetic factors associated with FEV...

Ockelford, A, Woodcock, S & Haynes, H 2019, 'The impact of inter‐flood duration on non‐cohesive sediment bed stability', Earth Surface Processes and Landforms, vol. 44, no. 14, pp. 2861-2871.
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AbstractLimited field and flume data suggests that both uniform and graded beds appear to progressively stabilize when subjected to inter‐flood flows as characterized by the absence of active bedload transport. Previous work has shown that the degree of bed stabilization scales with duration of inter‐flood flow, however, the sensitivity of this response to bed surface grain size distribution has not been explored. This article presents the first detailed comparison of the dependence of graded bed stability on inter‐flood flow duration. Sixty discrete experiments, including repetitions, were undertaken using three grain size distributions of identical D50 (4.8 mm); near‐uniform (σg = 1.13), unimodal (σg = 1.63) and bimodal (σg = 2.08). Each bed was conditioned for between 0 (benchmark) and 960 minutes by an antecedent shear stress below the entrainment threshold of the bed (τ*c50). The degree of bed stabilization was determined by measuring changes to critical entrainment thresholds and bedload flux characteristics.Results show that (i) increasing inter‐flood duration from 0 to 960 minutes increases the average threshold shear stress of the D50 by up to 18%; (ii) bedload transport rates were reduced by up to 90% as inter‐flood duration increased from 0 to 960 minutes; (iii) the rate of response to changes in inter‐flood duration in both critical shear stress and bedload transport rate is non‐linear and is inversely proportional to antecedent duration; (iv) there is a grade dependent response to changes in critical shear stress where the magnitude of response in uniform beds is up to twice that of the graded beds; and (v) t...

Oliver, B, Tonga, K, Darley, D, Rutting, S, Zhang, X, Chen, H & Wang, G 2019, 'COPD treatment choices based on blood eosinophils: are we there yet?', Breathe, vol. 15, no. 4, pp. 318-323.
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Eosinophils are increasingly being recognised as an important characteristic feature of COPD. Patients with COPD and eosinophilic inflammation tend to respond to steroid therapy; however, many questions remain regarding the optimum measurement. Eosinophilic inflammation may be defined based on various sampling techniques, including eosinophil levels in blood, sputum, bronchoalveolar lavage or biopsy, which leads to inconsistencies in its definition. Blood eosinophils may increase in conjunction with sputum eosinophils during COPD exacerbations and therefore may be a good surrogate marker of airway eosinophilic inflammation. However, the timing of the blood eosinophil measurement, the stability of the eosinophil count and the threshold used in different studies are variable. The use of blood eosinophil count to direct biological therapies in COPD has also had variable outcomes. Eosinophilic inflammation has an important role in COPD management; however, its use as the optimum biomarker still needs further investigation.Key pointsEosinophilia may play a significant role in the pathogenesis of COPD.Eosinophilic inflammation in COPD can be steroid responsive; however, eosinophilic inflammation is variable, and caution needs to be taken with measurements and the thresholds used.The long-term effects of reducing eosinophil levels in COPD is unclear.Educational aimsTo explore current knowledge of eosinophils in COPD.To explore the relationship between eosinophilia and corticosteroid use.To understand the limitations of asses...

Ong, J, Faiz, A, Timens, W, van den Berge, M, Terpstra, MM, Kok, K, van den Berg, A, Kluiver, J & Brandsma, CA 2019, 'Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts', Scientific Reports, vol. 9, no. 1.
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AbstractCOPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.

Ong, J, van den Berg, A, Faiz, A, Boudewijn, I, Timens, W, Vermeulen, C, Oliver, B, Kok, K, Terpstra, M, van den Berge, M, Brandsma, C-A & Kluiver, J 2019, 'Current Smoking is Associated with Decreased Expression of miR-335-5p in Parenchymal Lung Fibroblasts', International Journal of Molecular Sciences, vol. 20, no. 20, pp. 5176-5176.
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Cigarette smoking causes lung inflammation and tissue damage. Lung fibroblasts play a major role in tissue repair. Previous studies have reported smoking-associated changes in fibroblast responses and methylation patterns. Our aim was to identify the effect of current smoking on miRNA expression in primary lung fibroblasts. Small RNA sequencing was performed on lung fibroblasts from nine current and six ex-smokers with normal lung function. MiR-335-5p and miR-335-3p were significantly downregulated in lung fibroblasts from current compared to ex-smokers (false discovery rate (FDR) <0.05). Differential miR-335-5p expression was validated with RT-qPCR (p-value = 0.01). The results were validated in lung tissue from current and ex-smokers and in bronchial biopsies from non-diseased smokers and never-smokers (p-value <0.05). The methylation pattern of the miR-335 host gene, determined by methylation-specific qPCR, did not differ between current and ex-smokers. To obtain insights into the genes regulated by miR-335-5p in fibroblasts, we overlapped all proven miR-335-5p targets with our previously published miRNA targetome data in lung fibroblasts. This revealed Rb1, CARF, and SGK3 as likely targets of miR-335-5p in lung fibroblasts. Our study indicates that miR-335-5p downregulation due to current smoking may affect its function in lung fibroblasts by targeting Rb1, CARF and SGK3.

Ong, M, Cheng, J, Jin, X, Lao, W, Johnson, M, Tan, Y & Qu, X 2019, 'Paeoniflorin extract reverses dexamethasone-induced testosterone over-secretion through downregulation of cytochrome P450 17A1 expression in primary murine theca cells', Journal of Ethnopharmacology, vol. 229, pp. 97-103.
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© 2018 Elsevier B.V. Ethnopharmacological relevance: Polycystic Ovarian Syndrome (PCOS) is a complex endocrine and reproductive disorder. A main hallmark includes increased androgen production. The root of Paeonia lactiflora Pall. (Bai Shao) is used in Chinese herbal medicine for reproductive disorders, however its effects and mechanisms on ovarian theca cells has not yet been fully elucidated. Aim of the study: The aim of this study was to evaluate effect of paeoniflorin extract (PFE), the main constituents of Bai Shao, on androgen production in ovarian theca cells. Materials and methods: Primary murine theca cells were treated with concentrations of PFE (1–100 µg/mL) in the presence of dexamethasone (10 µM) with media-only treated cells used as the control. After 24 h, culture media was collected for biochemistry assays of testosterone and progesterone. Expression of key steroidogenic enzymes, cholesterol side-chain cleavage (CYP11A1) and 17α-hydroxylase (CYP17A1) was characterized using immunofluorescence staining, immunoblotting and qRT-PCR. Results: Dexamethasone significantly enhanced testosterone secretion (P < 0.05 vs. the control cells). PFE reversed over-production of testosterone induced by dexamethasone in a dose-dependent manner. The treatment with PFE also normalized production of progesterone in dexamethasone-treated cells. Expression of CYP11A1 and CYP17A1 in the theca cells were visualised by immunofluorescence staining. All doses of PFE significantly inhibited CYP17A1 expression detected by immunoblotting, but only 100 µg/mL of PFE downregulated CYP11A1 expression and reduced CYP11A1 significantly in dexamethasone-treated theca cells. Conclusions: PFE may reduce over-secretion of testosterone in theca cells through downregulation of CYP17A1 and CYP11A1. These findings provide scientific evidence to treat ovarian hyperandrogenism with the root of Paeonia lactiflora Pall.

O'Rourke, MB & Padula, MP 2019, 'An Inexpensive, simple calibration method for MALDI TOF/TOF systems', Journal of Mass Spectrometry, vol. 54, no. 12, pp. 1003-1007.
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AbstractThe array of analytes that can be measured by MADLI MS has created an equally vast range of calibration mixtures. The inherent problem with this is that acquiring all of them at commercial rates can be prohibitively expensive. With this in mind, we have created a low‐cost alternative to the most commonly used peptide calibrants.We were able to achieve an overall 78 ppm mass accuracy across a mass range of 900 to 2500 Da which was comparable to the mass accuracy achievable with commercial peptide mixes and hence has become a viable alternative.

O'Rourke, MB, Smith, CC, De La Monte, SM, Sutherland, GT & Padula, MP 2019, 'Higher Mass Accuracy MALDI‐TOF/TOF Lipid Imaging of Human Brain Tissue in Alzheimer's Disease', Current Protocols in Molecular Biology, vol. 126, no. 1, pp. e86-e86.
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AbstractMatrix‐assisted laser desorption/ionization imaging mass spectrometry (MALDI‐IMS) is a well‐established technique for elucidating the location and relative abundance of a range of biomolecules. More recently, research into this technique has shifted from simple discovery and demonstration of utility to application in biomedical research. Here, we describe a protocol utilizing MALDI‐IMS for the spatial mapping of lipids in brain tissue from normal human brains and brains from patients with Alzheimer's disease, in the context of Alzheimer's disease. Improved accuracy calibration of the instrument from the tissue surface is emphasized, as this allows for significantly improved mass determination in time of flight (TOF)‐based instruments enabling more confident preliminary lipid identification. This improved initial result allows MALDI‐IMS data to be complemented with additional instrumentation, such as liquid chromatography mass spectrometry workflows or specialized non‐TOF systems such as Fourier transform cyclotron resonance instruments. This method is not limited to human tissue and can be applied to virtually any lipid‐rich formalin‐fixed tissue. © 2019 by John Wiley & Sons, Inc.

O'Rourke, MB, Smith, CC, Tse, BCY, Sutherland, GT, Crossett, B & Padula, MP 2019, '‘What did I do wrong?’ An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging', Future Science OA, vol. 5, no. 4.
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Aim: This guide aims to broaden the uptake of MALDI-MSI biomedical research by removing the initial ‘lag phase’ associated with empirical determination in sample preparation and data analysis. Methods: Samples from several tissue types were prepared for lipid, protein and peptide MSI analysis. Broadly, samples were cryo sectioned, mounted onto conductive MALDI slides and sublimed with an analyte specific matrix, recrystallised and analyzed in a Bruker UltrafleXtreme MALDI TOF/TOF. Results/conclusion: Here we present a general guide that serves as the first comprehensive, explanatory index for curation and verification of both sample preparation and data generation during the MALDI-MSI process.

Paijmans, KC, Booth, DJ & Wong, MYL 2019, 'Towards an ultimate explanation for mixed‐species shoaling', Fish and Fisheries, vol. 20, no. 5, pp. 921-933.
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AbstractThe formation of social groups has important impacts on fitness for many animal species, with differences in group compositions resulting in a range of fitness outcomes for individuals. Recent interest in mixed‐species grouping, which extends from a large body of literature invested in understanding single‐species grouping, highlights novel complexities of group formation which relate to phenotypic, behavioural and physiological differences that naturally exist between species. Among fishes, mixed‐species shoaling is a common form of social grouping behaviour displayed across a range of marine and freshwater ecosystems. Research explaining mixed‐species shoaling shows some overlap with explanations for single‐species shoaling; however, it also demonstrates that distinct differences between species give rise to unique cost‐benefit trade‐offs which need to be incorporated into conceptual models of mixed‐species shoaling behaviour. Unique predation related trade‐offs may arise from inefficiency of the confusion effect, variation in vigilance between species and unequal species‐preferences shown by predators, whilst unique foraging‐related trade‐offs may arise from diet partitioning, variations in foraging behaviour and differences in competitive abilities between species. We review the literature on fitness outcomes associated with mixed‐species shoaling and present a new theoretical framework to explain the cost‐benefit trade‐offs for individuals within mixed‐species shoals. The framework incorporates both trade‐offs arising from differences between species and those arising from group size, the former having been largely ignored due to a focus on single‐species shoaling. Our framework is designed to inform future research striving to explain mixed‐species shoaling behaviour.

Palmer, SR, Ren, Z, Hwang, G, Liu, Y, Combs, A, Söderström, B, Lara Vasquez, P, Khosravi, Y, Brady, LJ, Koo, H & Stoodley, P 2019, 'Streptococcus mutans yidC1 and yidC2 Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties', Journal of Bacteriology, vol. 201, no. 1.
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YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen Streptococcus mutans are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either yidC results in changes to the structure and physical properties of the EPS matrix produced by S. mutans , ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial yidC orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.

Pamphlett, R, Kum Jew, S, Doble, PA & Bishop, DP 2019, 'Elemental Analysis of Aging Human Pituitary Glands Implicates Mercury as a Contributor to the Somatopause', Frontiers in Endocrinology, vol. 10, no. JUN.
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Copyright © 2019 Pamphlett, Kum Jew, Doble and Bishop. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Background: Growth hormone levels often decline on aging, and this “somatopause” is associated with muscle and bone loss, visceral adiposity and impaired cardiovascular function. Mercury has been detected in human pituitary glands, so to see if mercury could play a part in the somatopause we measured the proportion of people at different ages who had mercury in their anterior pituitary cells. Materials and methods: Paraffin sections of pituitary glands taken at autopsy from 94 people between the ages of 2 and 99 years were stained for inorganic mercury using autometallography. Pituitary mercury content was classified as none, low (<30% of cells) or high (>30% of cells) in increasing two-decade age groups. Autometallography combined with immunohistochemistry determined which hormone-producing cells contained mercury. Laser ablation-inductively coupled plasma-mass spectrometry was used to confirm the presence of mercury. Results: The proportion of people with low-content pituitary mercury remained between 33 and 42% at all ages. The proportion of people with high-content mercury increased with increasing age, from 0% of people in the 2-20 year group to a peak of 50% of people in the 61-80 years group, followed by a fall to 35% of people in the 81-99 years group. Mercury, when present, was found always in somatotrophs, occasionally in corticotrophs, rarely in thyrotrophs and gonadotrophs, and never in lactotrophs. Laser ablation-inductively coupled plasma-mass s...

Panigrahi, R, Oh, H, Sharma, V, Lee, KWK, Rice, SA, Cohn, D & Ramanujan, RV 2019, 'Remote control of biofouling by heating PDMS/MnZn ferrite nanocomposites with an alternating magnetic field', Journal of Chemical Technology & Biotechnology, vol. 94, no. 8, pp. 2713-2720.
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AbstractBACKGROUNDThe accumulation of unwanted microorganisms on wetted surfaces, leading to surface damage and contamination, is a common and significant global issue.RESULTSHerein, we report a novel technique where the growth of microorganisms can be readily controlled by coating the surfaces with a polydimethylsiloxane (PDMS)/Mn0.8Zn0.2Fe2O4 (manganese‐zinc ferrite) nanocomposite followed by applying alternating magnetic field (AMF). The PDMS/MnZn ferrite nanocomposite is light weight and thermally stable (up to ∼ 330 °C) that can form a flexible coating. PDMS also provides hydrophobicity, which is further enhanced by the addition of Mn and Zn. The improved hydrophobicity makes the coated surface less susceptible to biofilm formation. When external AMF was applied to nanocomposites containing various MnZn ferrite nanoparticle loads of 10%, 20% and 30%, the temperature of the surface of nanocomposites reached to 80, 120 and 160 °C, respectively. Successful biofilm deactivation was achieved by heating the nanocomposites via AMF application, as shown in the biofilm test where up to ∼ 70% of the Pseudomonas aeruginosa PAO1 biofilm cells were killed when the AMF was applied for 20 min to the nanocomposites containing 30% nanoparticles.CONCLUSIONCoating the surface with PDMS/MnZn ferrite nanocomposites followed by applying external AMF can be an effective way to remove biofilm remotely in a wide range of applications. © 2019 Society of Chemical Industry

Parameshwaran, K, Sharma, P, Rajendra, S, Stelzer-Braid, S, Xuan, W & Rawlinson, WD 2019, 'Circulating human papillomavirus DNA detection in Barrett's dysplasia and esophageal adenocarcinoma', Diseases of the Esophagus, vol. 32, no. 12, pp. 1-6.
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SUMMARY There is evidence to suggest that human papillomaviruses (HPV) are associated with Barrett's dysplasia and esophageal adenocarcinoma. In other HPV-linked cancers such as cervical and oropharyngeal cancer, circulating HPV DNA is a potential biomarker to assist in tumor diagnosis and management. This study aimed to determine whether circulating HPV DNA was detectable in patients with Barrett's dysplasia and esophageal adenocarcinoma, and if so, whether there is any correlation with esophageal tissue HPV status. Plasma from 138 patients representing esophageal adenocarcinoma (N = 41), Barrett's dysplasia (N = 48) and hospital controls (N = 49) were analyzed for the presence of circulating HPV DNA using droplet-digital PCR targeting the E7 gene of HPV types 16 and 18. Circulating HPV DNA was detected in 11/138 (8.0%) study subjects including 1/49 (2.0%) hospital controls, 4/48 (8.3%) Barrett's dysplasia patients, and 6/41 (14.6%) esophageal adenocarcinoma patients. Detection of circulating HPV DNA was higher in patients with HPV-positive esophageal tissue (6/35, 17.1%) compared to those with HPV-negative specimens (5/103; 4.9%) (OR = 4.06; 95% CI 1.15–14.25; P = 0.020). The highest rates of detection occurred in esophageal adenocarcinoma patients, particularly those with invasive tumors that had breached the esophageal submucosa, had regional lymph node involvement or metastatic disease. Circulating HPV DNA was detectable in a subset of Barrett's dysplasia and esophageal adenocarcinoma patients. Detection was associated with tissue HPV positivity and possibly disease severity.

Park, S-H, Park, S-H, Howe, ENW, Hyun, JY, Chen, L-J, Hwang, I, Vargas-Zuñiga, G, Busschaert, N, Gale, PA, Sessler, JL & Shin, I 2019, 'Determinants of Ion-Transporter Cancer Cell Death', Chem, vol. 5, no. 8, pp. 2079-2098.
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Parvez Mahmud, MA, Hossain, MJ, Nizami, MSH, Rahman, MS, Farjana, SH, Huda, N & Lang, C 2019, 'Advanced power routing framework for optimal economic operation and control of solar photovoltaic‐based islanded microgrid', IET Smart Grid, vol. 2, no. 2, pp. 242-249.
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© 2019 Institution of Engineering and Technology. All rights reserved. Energy sharing through a microgrid (MG) is essential for islanded communities to maximise the use of distributed energy resources (DERs) and battery energy storage systems (BESSs). Proper energy management and control strategies of such MGs can offer revenue to prosumers (active consumers with DERs) by routing excess energy to their neighbours and maintaining grid constraints at the same time. This paper proposes an advanced power-routing framework for a solarphotovoltaic (PV)-based islanded MG with a central storage system (CSS). An optimisation-based economic operation for the MG is developed that determines the power routing and energy sharing in the MG in the day-ahead stage. A modified droop controller-based real-time control strategy has been established that maintains the voltage constraints of the MG. The proposed power-routing framework is verified via a case study for a typical islanded MG. The outcome of the optimal economic operation and a controller verification of the proposed framework are presented to demonstrate the effectiveness of the proposed powerrouting framework. Results reveal that the proposed framework performs a stable control operation and provides a profit of 57 AU$/day at optimal conditions.

Paull, NJ, Irga, PJ & Torpy, FR 2019, 'Active botanical biofiltration of air pollutants using Australian native plants', Air Quality, Atmosphere & Health, vol. 12, no. 12, pp. 1427-1439.
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© 2019, Springer Nature B.V. Air pollutants are of public concern due to their adverse health effects. Biological air filters have shown great promise for the bioremediation of air pollutants. Different plant species have previously been shown to significantly influence pollutant removal capacities, although the number of species tested to date is small. The aims of this paper were to determine the pollutant removal capacity of different Australian native species for their effect on active biowall particulate matter, volatile organic compounds and carbon dioxide removal, and to compare removal rates with previously tested ornamental species. The single-pass removal efficiency for PM and VOCs of native planted biofilters was determined with a flow-through chamber. CO2 removal was tested by a static chamber pull down study. The results indicated that the native species were not effective for CO2 removal likely due to their high light level requirements in conjunction with substrate respiration. Additionally, the native species had lower PM removal efficiencies compared to ornamental species, with this potentially being due to the ornamental species possessing advantageous leaf traits for increased PM accumulation. Lastly, the native species were found to have similar benzene removal efficiencies to ornamental species. As such, whilst the native species showed a capacity to phytoremediate air pollutants, ornamental species have a comparatively greater capacity to do so and are more appropriate for air filtration purposes in indoor circumstances. However, as Australian native plants have structural and metabolic adaptations that enhance their ability to tolerate harsh environments, they may find use in botanical biofilters in situations where common ornamental plants may be suitable, especially in the outdoor environment.

Pavasini, R, Serenelli, M, Celis-Morales, CA, Gray, SR, Izawa, KP, Watanabe, S, Colin-Ramirez, E, Castillo-Martínez, L, Izumiya, Y, Hanatani, S, Onoue, Y, Tsujita, K, Macdonald, PS, Jha, SR, Roger, VL, Manemann, SM, Sanchis, J, Ruiz, V, Bugani, G, Tonet, E, Ferrari, R, Volpato, S & Campo, G 2019, 'Grip strength predicts cardiac adverse events in patients with cardiac disorders: an individual patient pooled meta-analysis', Heart, vol. 105, no. 11, pp. 834-841.
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ObjectiveGrip strength is a well-characterised measure of weakness and of poor muscle performance, but there is a lack of consensus on its prognostic implications in terms of cardiac adverse events in patients with cardiac disorders.MethodsArticles were searched in PubMed, Cochrane Library, BioMed Central and EMBASE. The main inclusion criteria were patients with cardiac disorders (ischaemic heart disease, heart failure (HF), cardiomyopathies, valvulopathies, arrhythmias); evaluation of grip strength by handheld dynamometer; and relation between grip strength and outcomes. The endpoints of the study were cardiac death, all-cause mortality, hospital admission for HF, cerebrovascular accident (CVA) and myocardial infarction (MI). Data of interest were retrieved from the articles and after contact with authors, and then pooled in an individual patient meta-analysis. Univariate and multivariate logistic regression was performed to define predictors of outcomes.ResultsOverall, 23 480 patients were included from 7 studies. The mean age was 62.3±6.9 years and 70% were male. The mean follow-up was 2.82±1.7 years. After multivariate analysis grip strength (difference of 5 kg, 5× kg) emerged as an independent predictor of cardiac death (OR 0.84, 95% CI 0.79 to 0.89, p<0.0001), all-cause death (OR 0.87, 95% CI 0.85 to 0.89, p<0.0001) and hospital admission for HF (OR 0.88, 95% CI 0.84 to 0.92, p<0.0001). On the contrary, we did not find any relationship between grip strength and occurrence of MI or CVA.ConclusionIn patients with cardiac disorders, grip strength predicted cardiac death, all-cause death and hospital admission for HF.Trial registration numberCRD4201502...

Pavlov, D, Gurbatov, S, Kudryashov, SI, Danilov, PA, Porfirev, AP, Khonina, SN, Vitrik, OB, Kulinich, SA, Lapine, M & Kuchmizhak, AA 2019, '10-million-elements-per-second printing of infrared-resonant plasmonic arrays by multiplexed laser pulses', Optics Letters, vol. 44, no. 2, pp. 283-283.
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© 2019 Optical Society of America. We report on high-quality infrared (IR)-resonant plasmonic nanoantenna arrays fabricated on a thin gold film by tightly focused femtosecond (fs) laser pulses coming at submegahertz repetition rates at a printing rate of 10 million elements per second. To achieve this, the laser pulses were spatially multiplexed by fused silica diffractive optical elements into 51 identical submicrometer-sized laser spots arranged into a linear array at periodicity down to 1 μm. The demonstrated high-throughput nanopatterning modality indicates fs laser maskless microablation as an emerging robust, flexible, and competitive lithographic tool for advanced fabrication of IR-range plasmonic sensors for environmental sensing, chemosensing, and biosensing.

Pavlov, D, Syubaev, S, Kuchmizhak, A, Gurbatov, S, Vitrik, O, Modin, E, Kudryashov, S, Wang, X, Juodkazis, S & Lapine, M 2019, 'Direct laser printing of tunable IR resonant nanoantenna arrays', Applied Surface Science, vol. 469, pp. 514-520.
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© 2018 We report on the application of direct femtosecond laser printing for manufacturing periodic nanoantenna structures with various geometry and period, printed on pure or alloyed noble metal films over a silica substrate. By varying applied pulse energy, we have realised a wide range of possible morphologies, from smooth nano-bumps to protruding nanojets with up to 1 μm height, and finally to through microholes. Using several pulse energy levels, we have printed periodic nanojet arrays with periods from 1.75 to 4 μm, and measured their IR reflection spectra. The resonance frequency and magnitude of the resulting absorbance were found to essentially depend on both the periodicity of the arrays and nanojet geometry. We explain these observations by considering nanojet-assisted plasmon excitation running along the nanojets and along the surface, and found a convincing agreement to the experiments. To this end, we have shown that the reported approach is suitable for designing structures with distinct IR resonances, tunable over a range of at least 2–6 μm. Finally, we have also applied direct laser printing to a variety of noble metal alloys, involving gold, silver and palladium in various combinations and compositions, and showed that nanojets can be reliably printed for such alloys, preserving their chemical composition and its homogeneous volumetric distribution.

Pearse, R, Hitchcock, JN & Keane, H 2019, 'Gender, inter/disciplinarity and marginality in the social sciences and humanities: A comparison of six disciplines', Women's Studies International Forum, vol. 72, pp. 109-126.
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Peel, R, Ren, S, Hure, A, Evans, T, D'Este, CA, Abhayaratna, WP, Tonkin, AM, Hopper, I, Thrift, AG, Levi, CR, Sturm, J, Durrheim, D, Hung, J, Briffa, TG, Chew, DP, Anderson, P, Moon, L, McEvoy, M, Hansbro, PM, Newby, DA & Attia, JR 2019, 'Evaluating recruitment strategies for AUSPICE , a large Australian community‐based randomised controlled trial', Medical Journal of Australia, vol. 210, no. 9, pp. 409-415.
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© 2019 AMPCo Pty Ltd Objectives: To examine the effectiveness of different strategies for recruiting participants for a large Australian randomised controlled trial (RCT), the Australian Study for the Prevention through Immunisation of Cardiovascular Events (AUSPICE). Design, setting, participants: Men and women aged 55–60 years with at least two cardiovascular risk factors (hypertension, hypercholesterolaemia, overweight/obesity) were recruited for a multicentre placebo-controlled RCT assessing the effectiveness of 23-valent pneumococcal polysaccharide vaccine (23vPPV) for preventing cardiovascular events. Methods: Invitations were mailed by the Australian Department of Human Services to people in the Medicare database aged 55–60 years; reminders were sent 2 weeks later. Invitees could respond in hard copy or electronically. Direct recruitment was supplemented by asking invitees to extend the invitation to friends and family (snowball sampling) and by Facebook advertising. Main outcome: Proportions of invitees completing screening questionnaire and recruited for participation in the RCT. Results: 21 526 of 154 992 invited people (14%) responded by completing the screening questionnaire, of whom 4725 people were eligible and recruited for the study. Despite the minimal study burden (one questionnaire, one clinic visit), the overall participation rate was 3%, or an estimated 10% of eligible persons. Only 16% of eventual participants had responded within 2 weeks of the initial invitation letter (early responders); early and late responders did not differ in their demographic or medical characteristics. Socio-economic disadvantage did not markedly influence response rates. Facebook advertising and snowball sampling did not increase recruitment. Conclusions: Trial participation rates are low, and multiple concurrent methods are needed to maximise recruitment. Social media strategies may not be successful in older age groups. Trial registration: Australian N...

Pelegri, NG, Gorrie, CA & Santos, J 2019, 'Rat Hippocampal Neural Stem Cell Modulation Using PDGF, VEGF, PDGF/VEGF, and BDNF', Stem Cells International, vol. 2019, pp. 1-12.
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Neural stem cells have become the focus of many studies as they have the potential to differentiate into all three neural lineages. This may be utilised to develop new and novel ways to treat neurological conditions such as spinal cord and brain injuries, especially if the stem cells can be modulated in vivo without additional invasive surgical procedures. This research is aimed at investigating the effects of the growth factors vascular endothelial growth factor, platelet-derived growth factor, brain-derived neurotrophic factor, and vascular endothelial growth factor/platelet-derived growth factor on hippocampal-derived neural stem cells. Cell growth and differentiation were assessed using immunohistochemistry and glutaminase enzyme assay. Cells were cultured for 14 days and treated with different growth factors at two different concentrations 20 ng/mL and 100 ng/mL. At 2 weeks, cells were fixed, and immunohistochemistry was conducted to determine cellular differentiation using antibodies against GFAP, nestin, OSP, and NF200. The cell medium supernatant was also collected during treatment to determine glutaminase levels secreted by the cells as an indicator of neural differentiation. VEGF/PDGF at 100 ng/mL had the greatest influence on cellular proliferation of HNSC, which also stained positively for nestin, OSP, and NF200. In comparison, HNSC in other treatments had poorer cell health and adhesion. HNSC in all treatment groups displayed some differentiation markers and morphology, but this is most significant in the 100 ng/ml VEGF/PDGF treatment. VEGF/PDGF combination produced the optimal effect on the HNSCs inducing the differentiation pathway exhibiting oligodendrocytic and neuronal markers. This is a promising finding that should be further investigated in the brain and spinal cord injury.

Peng, D, Zhang, H, Liu, L, Huang, W, Huete, AR, Zhang, X, Wang, F, Yu, L, Xie, Q, Wang, C, Luo, S, Li, C & Zhang, B 2019, 'Estimating the Aboveground Biomass for Planted Forests Based on Stand Age and Environmental Variables', Remote Sensing, vol. 11, no. 19, pp. 2270-2270.
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Measuring forest aboveground biomass (AGB) at local to regional scales is critical to understanding their role in regional and global carbon cycles. The Three-North Shelterbelt Forest Program (TNSFP) is the largest ecological restoration project in the world, and has been ongoing for over 40 years. In this study, we developed models to estimate the planted forest aboveground biomass (PF_AGB) for Yulin, a typical area in the project. Surface reflectances in the study area from 1978 to 2013 were obtained from Landsat series images, and integrated forest z-scores were constructed to measure afforestation and the stand age of planted forest. Normalized difference vegetation index (NDVI) was combined with stand age to develop an initial model to estimate PF_AGB. We then developed additional models that added environment variables to our initial model, including climatic factors (average temperature, total precipitation, and total sunshine duration) and a topography factor (slope). The model which combined the total precipitation and slope greatly improved the accuracy of PF_AGB estimation compared to the initial model, indicating that the environmental variables related to water distribution indirectly affected the growth of the planted forest and the resulting AGB. Afforestation in the study area occurred mainly in the early 1980s and early 21st century, and the PF_AGB in 2003 was 2.3 times than that of 1998, since the fourth term TNSFP started in 2000. The PF_AGB in 2013 was about 3.33 times of that in 2003 because many young trees matured. The leave-one-out cross-validation (LOOCV) approach showed that our estimated PF_AGB had a significant correlation with field-measured data (correlation coefficient (r) = 0.89, p < 0.001, root mean square error (RMSE) = 6.79 t/ha). Our studies provided a method to estimate long time series PF_AGB using satellite repetitive measures, particularly for arid or semi-arid areas.

Pereira, RRC, Scanes, E, Parker, L, Byrne, M, Cole, VJ & Ross, PM 2019, 'Restoring the flat oyster Ostrea angasi in the face of a changing climate', Marine Ecology Progress Series, vol. 625, pp. 27-39.
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Across the globe, restoration efforts are stemming the loss of native oyster reefs and the ecosystem services they provide, but these efforts will need to consider climate change in order to be sustainable. South-eastern Australia is the focus of restoring the once abundant oyster Ostrea angasi. This region is also a climate change ‘hot spot’ where the ocean is warming rapidly, with the potential to be exacerbated by marine heatwaves and coastal acidification. In this study, the impact of near-future (~2050) elevated temperature and pCO2 on O. angasi was determined and considered in context with concerns for the long-term sustainability of oyster reef restoration efforts. Oysters were exposed to ambient and elevated pCO2 concentrations (mean ± SE: 408 ± 19.8 and 1070 ± 53.4 μatm) and ambient and elevated temperatures (22.78 ± 0.17 and 25.73 ± 0.21°C) for 10 wk in outdoor flow-through mesocosms. Shell growth, condition index, standard metabolic rate (SMR), extracellular pH and survival were measured. Elevated temperature caused high mortality (36%) and decreased the condition of oysters (33%). Elevated pCO2 increased SMR almost 4-fold and lowered the extracellular pH of O. angasi by a mean 0.29 pH units. In combination, elevated pCO2 and temperature ameliorated effects on SMR and survivorship of oysters. O. angasi appears to be living near the limits of its thermal tolerance. Restoration projects will need to account for the temperature sensitivity of this species and its changing habitat to ‘climate proof’ long-term restoration efforts.

Pérez-Tomás, A, Chikoidze, E, Dumont, Y, Jennings, MR, Russell, SO, Vales-Castro, P, Catalan, G, Lira-Cantú, M, Ton –That, C, Teherani, FH, Sandana, VE, Bove, P & Rogers, DJ 2019, 'Giant bulk photovoltaic effect in solar cell architectures with ultra-wide bandgap Ga2O3 transparent conducting electrodes', Materials Today Energy, vol. 14, pp. 100350-100350.
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© 2019 Elsevier Ltd The use of ultra-wide bandgap transparent conducting beta gallium oxide (β-Ga2O3) thin films as electrodes in ferroelectric solar cells is reported. In a new material structure for energy applications, we report a solar cell structure (a light absorber sandwiched in between two electrodes - one of them - transparent) which is not constrained by the Shockley–Queisser limit for open-circuit voltage (Voc) under typical indoor light. The solar blindness of the electrode enables a record-breaking bulk photovoltaic effect (BPE) with white light illumination (general use indoor light). This work opens up the perspective of ferroelectric photovoltaics which are not subject to the Shockley-Queisser limit by bringing into scene solar-blind conducting oxides.

Pernice, M & Hughes, DJ 2019, 'Forecasting global coral bleaching', Nature Climate Change, vol. 9, no. 11, pp. 803-804.
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Petroll, K, Care, A, Waterstraat, M, Bergquist, PL & Sunna, A 2019, 'Mixed-mode liquid chromatography for the rapid analysis of biocatalytic glucaric acid reaction pathways', Analytica Chimica Acta, vol. 1066, pp. 136-145.
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Petroll, K, Kopp, D, Care, A, Bergquist, PL & Sunna, A 2019, 'Tools and strategies for constructing cell-free enzyme pathways', Biotechnology Advances, vol. 37, no. 1, pp. 91-108.
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Single enzyme systems or engineered microbial hosts have been used for decades but the notion of assembling multiple enzymes into cell-free synthetic pathways is a relatively new development. The extensive possibilities that stem from this synthetic concept makes it a fast growing and potentially high impact field for biomanufacturing fine and platform chemicals, pharmaceuticals and biofuels. However, the translation of individual single enzymatic reactions into cell-free multi-enzyme pathways is not trivial. In reality, the kinetics of an enzyme pathway can be very inadequate and the production of multiple enzymes can impose a great burden on the economics of the process. We examine here strategies for designing synthetic pathways and draw attention to the requirements of substrates, enzymes and cofactor regeneration systems for improving the effectiveness and sustainability of cell-free biocatalysis. In addition, we comment on methods for the immobilisation of members of a multi-enzyme pathway to enhance the viability of the system. Finally, we focus on the recent development of integrative tools such as in silico pathway modelling and high throughput flux analysis with the aim of reinforcing their indispensable role in the future of cell-free biocatalytic pathways for biomanufacturing.

Petrou, K, Baker, KG, Nielsen, DA, Hancock, AM, Schulz, KG & Davidson, AT 2019, 'Acidification diminishes diatom silica production in the Southern Ocean', Nature Climate Change, vol. 9, no. 10, pp. 781-786.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Diatoms, large bloom-forming marine microorganisms, build frustules out of silicate, which ballasts the cells and aids their export to the deep ocean. This unique physiology forges an important link between the marine silicon and carbon cycles. However, the effect of ocean acidification on the silicification of diatoms is unclear. Here we show that diatom silicification strongly diminishes with increased acidity in a natural Antarctic community. Analyses of single cells from within the community reveal that the effect of reduced pH on silicification differs among taxa, with several species having significantly reduced silica incorporation at CO2 levels equivalent to those projected for 2100. These findings suggest that, before the end of this century, ocean acidification may influence the carbon and silicon cycle by both altering the composition of the diatom assemblages and reducing cell ballasting, which will probably alter vertical flux of these elements to the deep ocean.

Pettit, T, Bettes, M, Chapman, AR, Hoch, LM, James, ND, Irga, PJ & Torpy, FR 2019, 'The botanical biofiltration of VOCs with active airflow: is removal efficiency related to chemical properties?', Atmospheric Environment, vol. 214, pp. 116839-116839.
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© 2019 Elsevier Ltd Botanical biofiltration using active green walls is showing increasing promise as a viable method for the filtration of volatile organic compounds (VOCs) from ambient air; however there is a high level of heterogeneity reported amongst VOC removal efficiencies, and the reasons for these observations have yet to be explained. Comparisons of removal efficiencies amongst studies is also difficult due to the use of many different VOCs, and systems that have been tested under different conditions. The current work describes a procedure to determine whether some of these differences may be related to the chemical properties of the VOCs themselves. This work used an active green wall system to test the single pass removal efficiency (SPRE) of nine different VOCs (acetone, benzene, cyclohexane, ethanol, ethyl acetate, hexane, isopentane, isopropanol and toluene) and explored which chemical properties were meaningful predictor variables of their biofiltration efficiencies. Ethanol was removed most efficiently (average SPRE of 96.34% ± 1.61), while benzene was least efficiently removed (average SPRE of 19.76% ± 2.93). Multiple stepwise linear regression was used to determine that the dipole moment and molecular mass were significant predictors of VOC SPRE, in combination accounting for 54.6% of the variability in SPREs amongst VOCs. The octanol water partition coefficient, proton affinity, Henry's law constant and vapour pressure were not significant predictors of SPRE. The most influential predictor variable was the dipole moment, alone accounting for 49.8% of the SPRE variability. The model thus allows for an estimation of VOC removal efficiency based on a VOC's chemical properties, and supports the idea that system optimisation could be achieved through methods that promote both VOC partitioning into the biofilter's aqueous phase, and substrate development to enhance adsorption.'

Pettit, T, Irga, PJ & Torpy, FR 2019, 'The in situ pilot-scale phytoremediation of airborne VOCs and particulate matter with an active green wall', Air Quality, Atmosphere & Health, vol. 12, no. 1, pp. 33-44.
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© 2018, Springer Nature B.V. Atmospheric pollutant phytoremediation technologies, such as potted plants and green walls, have been thoroughly tested in lab-scale experiments for their potential to remove air pollutants. The functional value of these technologies, however, is yet to be adequately assessed in situ, in ‘high value’ environments, where pollutant removal will provide the greatest occupant health benefits. Air pollution in countries such as China is a significant public health issue, and efficient air pollution control technologies are needed. This work used pilot-scale trials to test the capacity of potted plants, a passive green wall and an active green wall (AGW) to remove particulate matter (PM) and total volatile organic compounds (TVOCs) from a room in a suburban residential house in Sydney, Australia, followed by an assessment of the AGW’s potential to remove these pollutants from a classroom in Beijing. In the residential room, compared to potted plants and the passive green wall, the AGW maintained TVOCs at significantly lower concentrations throughout the experimental period (average TVOC concentration 72.5% lower than the control), with a similar trend observed for PM. In the classroom, the AGW reduced the average TVOC concentration by ~ 28% over a 20-min testing period compared to levels with no green wall and a filtered HVAC system in operation. The average ambient PM concentration in the classroom with the HVAC system operating was 101.18 μg/m 3 , which was reduced by 42.6% by the AGW. With further empirical validation, AGWs may be implemented to efficiently clean indoor air through functional reductions in PM and TVOC concentrations.

Pettit, T, Irga, PJ, Surawski, NC & Torpy, FR 2019, 'An Assessment of the Suitability of Active Green Walls for NO2 Reduction in Green Buildings Using a Closed-Loop Flow Reactor', Atmosphere, vol. 10, no. 12, pp. 801-801.
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Nitrogen dioxide (NO2) is a common urban air pollutant that is associated with several adverse human health effects from both short and long term exposure. Additionally, NO2 is highly reactive and can influence the mixing ratios of nitrogen oxide (NO) and ozone (O3). Active green walls can filter numerous air pollutants whilst using little energy, and are thus a candidate for inclusion in green buildings, however, the remediation of NO2 by active green walls remains untested. This work assessed the capacity of replicate active green walls to filter NO2 at both ambient and elevated concentrations within a closed-loop flow reactor, while the concentrations of NO and O3 were simultaneously monitored. Comparisons of each pollutant’s decay rate were made for green walls containing two plant species (Spathiphyllum wallisii and Syngonium podophyllum) and two lighting conditions (indoor and ultraviolet). Biofilter treatments for both plant species exhibited exponential decay for the biofiltration of all three pollutants at ambient concentrations. Furthermore, both treatments removed elevated concentrations of NO and NO2, (average NO2 clean air delivery rate of 661.32 and 550.8 m3∙h−1∙m−3 of biofilter substrate for the respective plant species), although plant species and lighting conditions influenced the degree of NOx removal. Elevated concentrations of NOx compromised the removal efficiency of O3. Whilst the current work provided evidence that effective filtration of NOx is possible with green wall technology, long-term experiments under in situ conditions are needed to establish practical removal rates and plant health effects from prolonged exposure to air pollution.

Phillips, C, McNevin, D, Kidd, KK, Lagacé, R, Wootton, S, de la Puente, M, Freire-Aradas, A, Mosquera-Miguel, A, Eduardoff, M, Gross, T, Dagostino, L, Power, D, Olson, S, Hashiyada, M, Oz, C, Parson, W, Schneider, PM, Lareu, MV & Daniel, R 2019, 'MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations', Forensic Science International: Genetics, vol. 42, pp. 213-226.
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Current forensic ancestry-informative panels are limited in their ability to differentiate populations in the Asia-Pacific region. MAPlex (Multiplex for the Asia-Pacific), a massively parallel sequencing (MPS) assay, was developed to improve differentiation of East Asian, South Asian and Near Oceanian populations found in the extensive cross-continental Asian region that shows complex patterns of admixture at its margins. This study reports the development of MAPlex; the selection of SNPs in combination with microhaplotype markers; assay design considerations for reducing the lengths of microhaplotypes while preserving their ancestry-informativeness; adoption of new population-informative multiple-allele SNPs; compilation of South Asian-informative SNPs suitable for forensic AIMs panels; and the compilation of extensive reference and test population genotypes from online whole-genome-sequence data for MAPlex markers. STRUCTURE genetic clustering software was used to gauge the ability of MAPlex to differentiate a broad set of populations from South and East Asia, the West Pacific regions of Near Oceania, as well as the other globally distributed population groups. Preliminary assessment of MAPlex indicates enhanced South Asian differentiation with increased divergence between West Eurasian, South Asian and East Asian populations, compared to previous forensic SNP panels of comparable scale. In addition, MAPlex shows efficient differentiation of Middle Eastern individuals from Europeans. MAPlex is the first forensic AIM assay to combine binary and multiple-allele SNPs with microhaplotypes, adding the potential to detect and analyze mixed source forensic DNA.

Phong Vo, HN, Le, GK, Hong Nguyen, TM, Bui, X-T, Nguyen, KH, Rene, ER, Vo, TDH, Thanh Cao, N-D & Mohan, R 2019, 'Acetaminophen micropollutant: Historical and current occurrences, toxicity, removal strategies and transformation pathways in different environments', Chemosphere, vol. 236, pp. 124391-124391.
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Pike, DA, Roznik, EA, Webb, JK & Shine, R 2019, 'Life history and ecology of the elegant snake-eyed skink (Cryptoblepharus pulcher) in south-eastern Australia', Australian Journal of Zoology, vol. 67, no. 1, pp. 51-51.
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Detailed information on life history and ecology is essential for successful conservation and management. However, we have relatively little detailed data on the life history and ecology of most small lizard species, relative to other vertebrates, especially those that have undergone recent taxonomic changes. We studied the ecology of the elegant snake-eyed skink (Cryptoblepharus pulcher), a lizard that occurs on trees, fences, walls, and rock outcroppings in eastern Australia that spans temperate to tropical environments. In our temperate-zone study population living in natural habitat, individuals are active year-round, and gravid females were found during the months of September through December. Sexual maturity is reached in 12 months, lifespan is at least three years, and clutch size is typically two eggs. In laboratory incubation experiments, larger eggs were more likely to hatch. Low incubation temperatures (averaging 23 ± 7.5°C versus high temperatures averaging 26 ± 7.5°C) increased incubation duration significantly (range 56–72 days versus 40–51 days) and reduced the body size of hatchlings significantly (17.8 mm versus 18.7 mm snout–vent length). Skinks sheltered beneath small rocks that were not shared simultaneously with predatory snakes, and that reached average temperatures that were up to 3°C warmer during the day than unused rocks. Preferred microhabitats include substrates of rock or soil, and the largest rocks were occasionally shared by up to four individuals of all body size/sex combinations (5.8% of observations were shared, 30.2% of individual rocks were shared). Our study expands upon knowledge of the widespread genus Cryptoblepharus by providing detailed life history and ecological information on C. pulcher that can serve as a baseline for future studies.

Pires da Silva, I, Wang, KYX, Wilmott, JS, Holst, J, Carlino, MS, Park, JJ, Quek, C, Wongchenko, M, Yan, Y, Mann, G, Johnson, DB, McQuade, JL, Rai, R, Kefford, RF, Rizos, H, Scolyer, RA, Yang, JYH, Long, GV & Menzies, AM 2019, 'Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF-Mutant Melanoma', Clinical Cancer Research, vol. 25, no. 4, pp. 1272-1279.
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Abstract Purpose: BRAF V600E and V600K melanomas have distinct clinicopathologic features, and V600K appear to be less responsive to BRAFi±MEKi. We investigated mechanisms for this and explored whether genotype affects response to immunotherapy. Experimental Design: Pretreatment formalin-fixed paraffin-embedded tumors from patients treated with BRAFi±MEKi underwent gene expression profiling and DNA sequencing. Molecular results were validated using The Cancer Genome Atlas (TCGA) data. An independent cohort of V600E/K patients treated with anti–PD-1 immunotherapy was examined. Results: Baseline tissue and clinical outcome with BRAFi±MEKi were studied in 93 patients (78 V600E, 15 V600K). V600K patients had numerically less tumor regression (median, −31% vs. −52%, P = 0.154) and shorter progression-free survival (PFS; median, 5.7 vs. 7.1 months, P = 0.15) compared with V600E. V600K melanomas had lower expression of the ERK pathway feedback regulator dual-specificity phosphatase 6, confirmed with TCGA data (116 V600E, 17 V600K). Pathway analysis showed V600K had lower expression of ERK and higher expression of PI3K-AKT genes than V600E. Higher mutational load was observed in V600K, with a higher proportion of mutations in PIK3R1 and tumor-suppressor genes. In patients treated with anti–PD-1, V600K (n = 19) had superior outcomes than V600E (n = 84), including response rate (53% vs. 29%, P = 0.059), PFS (median, 19 vs. 2.7 months, P = 0.049), and overall survival (20.4 vs. 11.7 months, P = 0.081).

Polikarpov, D, Liang, L, Care, A, Sunna, A, Campbell, D, Walsh, B, Balalaeva, I, Zvyagin, A, Gillatt, D & Guryev, E 2019, 'Functionalized Upconversion Nanoparticles for Targeted Labelling of Bladder Cancer Cells', Biomolecules, vol. 9, no. 12, pp. 820-820.
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Bladder cancer is the ninth most common cancer worldwide. Due to a high risk of recurrence and progression of bladder cancer, every patient needs long-term surveillance, which includes regular cystoscopy, sometimes followed by a biopsy of suspicious lesions or resections of recurring tumours. This study addresses the development of novel biohybrid nanocomplexes representing upconversion nanoparticles (UCNP) coupled to antibodies for photoluminescent (PL) detection of bladder cancer cells. Carrying specific antibodies, these nanoconjugates selectively bind to urothelial carcinoma cells and make them visible by emitting visible PL upon excitation with deeply penetrating near-infrared light. UCNP were coated with a silica layer and linked to anti-Glypican-1 antibody MIL38 via silica-specific solid-binding peptide. Conjugates have been shown to specifically attach to urothelial carcinoma cells with high expression of Glypican-1. This result highlights the potential of produced conjugates and conjugation technology for further studies of their application in the tumour detection and fluorescence-guided resection.

Popovic, A, Morelato, M, Roux, C & Beavis, A 2019, 'Review of the most common chemometric techniques in illicit drug profiling', Forensic Science International, vol. 302, pp. 109911-109911.
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© 2019 Elsevier B.V. The information generated through drug profiling can be used to infer a common source between one or several seizures as well as drug trafficking routes to provide insights into drug markets. Although well established, it is time-consuming and ineffective to compare all drug profiles manually. In recent years, there has been a push to automate processes to enable a more efficient comparison of illicit drug specimens. Various chemometric methods have been employed to compare and interpret forensic case data promptly. The intelligence that is produced can be used by decision-makers to disrupt or reduce the impact of illicit drug markets. This review highlights the most common chemometric techniques used in drug profiling and more specifically, the most efficient comparison metrics and pattern recognition techniques outlined in the literature.

Popplewell, M, Reizes, J & Zaslawski, C 2019, 'A Novel Approach to Describing Traditional Chinese Medical Patterns: The “Traditional Chinese Medical Diagnostic Descriptor”', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1121-1129.
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OBJECTIVES:In the first of a series of three articles by the present authors, diagnostic agreement between Traditional Chinese Medicine (TCM) practitioners was found to be low. This was the first time that TCM diagnoses had been evaluated with an open population of patients and this result is a cause of concern. In the second article, incorrect statistics were shown to have often been used to calculate chance-removed inter-rater agreement, and appropriate statistics such as Gwet's Agreement Coefficient 2 (AC2) was recommended for future studies. In this, the third article, a novel approach to recording TCM diagnostic patterns, the Traditional Chinese Medical Diagnostic Descriptor (TCMDD), is presented that allows chance-removed agreement calculation. An example of mapping TCM diagnostic patterns to the TCMDD format is given and diagnostic agreement is evaluated. Design, Settings, Subjects: The same 35 subjects used to report agreement in our first article were also diagnosed by additional practitioners using the TCMDD format during the same experimental sessions at the University of Technology, Sydney Clinic. TCM diagnoses from the first article were also mapped to the TCMDD format. OUTCOME MEASURES:Linearly weighted simple agreement and the AC2 statistic were utilized and all results compared. RESULTS:Linearly weighted simple agreement using the TCMDD and TCM mapped to TCMDD format averaged 0.80 ± 0.02 compared with 0.19 for TCM. TCMDD and TCM mapped to TCMDD chance-removed agreement, as calculated with AC2, ranged between 0.67 and 0.73 ± 0.03. CONCLUSIONS:The TCMDD allows the essence of diagnoses expressed by TCM practitioners to be appropriately compared. This was confirmed by the TCM mapped to TCMDD results. In both cases, simple agreement was significantly greater than that obtained with the TCM format. Chance-removed statistics and error estimates can be reliably calculated with the AC2 and the TCMDD in open populations.

Popplewell, M, Reizes, J & Zaslawski, C 2019, 'Appropriate Statistics for Determining Chance-Removed Interpractitioner Agreement', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1115-1120.
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Fleiss' Kappa (FK) has been commonly, but incorrectly, employed as the "standard" for evaluating chance-removed inter-rater agreement with ordinal data. This practice may lead to misleading conclusions in inter-rater agreement research. An example is presented that demonstrates the conditions where FK produces inappropriate results, compared with Gwet's AC2, which is proposed as a more appropriate statistic. A novel format for recording a Chinese Medical (CM) diagnoses, called the Diagnostic System of Oriental Medicine (DSOM), was used to record and compare patient diagnostic data, which, unlike the contemporary CM diagnostic format, allows agreement by chance to be considered when evaluating patient data obtained with unrestricted diagnostic options available to diagnosticians.Five CM practitioners diagnosed 42 subjects drawn from an open population. Subjects' diagnoses were recorded using the DSOM format. All the available data were initially used to evaluate agreement. Then, the subjects were sorted into three groups to demonstrate the effects of differing data marginality on the calculated chance-removed agreement.Agreement between the practitioners for each subject was evaluated with linearly weighted simple agreement, FK and Gwet's AC2.In all cases, overall agreement was much lower with FK than Gwet's AC2. Larger differences occurred when the data were more free marginal. Inter-rater agreement determined with FK statistics is unlikely to be correct unless it can be shown that the data from which agreement is determined are, in fact, fixed marginal. It follows that results obtained on agreement between practitioners with FK are probably incorrect. It is shown that inter-rater agreement evaluated with AC2 statistic is an appropriate measure when fixed marginal data are neither expected nor guaranteed. The AC2 statistic should be used as the standard statistical approach for determining agreement between practitioners.

Popplewell, M, Reizes, J & Zaslawski, C 2019, 'Consensus in Traditional Chinese Medical Diagnosis in Open Populations', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1109-1114.
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An acceptable level of diagnostic agreement is a prerequisite for consistent administration of treatment. It is critical for investigating effectiveness of different treatment approaches using multiple practitioners. To the best of our knowledge, no previous investigation of diagnostic consensus using open populations in Chinese medicine (CM) has been reported. Investigations restricted to individual medical conditions, such as have been usually studied, do not reveal any information as to what occurs in real world clinical settings. This knowledge gap led to the current study being conducted. Design/Location/Subjects/Interventions: Investigating diagnostic agreement specifically in Traditional Chinese Medicine (TCM) in an open population, two or three practitioners diagnosed 35 subjects at the University of Technology, Sydney (UTS), TCM clinic. The practitioners were restricted to a list of the 56 most frequently used TCM diagnoses at the UTS clinic. Up to three diagnostic patterns per subject could be selected, with nominated patterns scored between 1 and 5.Agreement was determined with two criteria, both expressed as simple percentages: pattern and linearly weighted agreements.The results showed that 23% of practitioners obtained pattern agreement, while 19% demonstrated weighted agreement.There appears to be very low diagnostic agreement between practitioners. This is an important finding. If unchallenged by further investigation, the recognition of such poor diagnostic consensus may lead to rejection of TCM theory before it has been adequately assessed. Diagnostic agreement must be improved so that future investigations into treatment effectiveness or mechanisms of action are made on a valid basis. Additionally, the current TCM diagnostic format must be altered to allow the application of chance-removed statistics or the calculation of a standard error with open populations. This article is the first of a series of three that report problems in TCM diagnosti...

Pouwels, SD, Klont, F, Kwiatkowski, M, Wiersma, VR, Faiz, A, van den Berge, M, Horvatovich, P, Bischoff, R & ten Hacken, NHT 2019, 'Reply to Biswas: Acute and Chronic Effects of Cigarette Smoking on sRAGE', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 6, pp. 806-807.
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Praikaew, P, Maniam, S, Charoenpanich, A, Sirirak, J, Promarak, V, Langford, SJ & Wanichacheva, N 2019, 'Water-soluble Cu2+-fluorescent sensor based on core-substituted naphthalene diimide and its application in drinking water analysis and live cell imaging', Journal of Photochemistry and Photobiology A: Chemistry, vol. 382, pp. 111852-111852.
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Water-soluble naphthalene diimide based fluorescent chemosensor, N1, was designed for Cu2+ recognition. The sensor exhibited significant fluorescence modulation and chromogenic change with high Cu2+ sensitivity and selectivity over interfering metal ions. The sensor was able to efficiently monitor Cu2+ in 100% aqueous buffer solution with a low detection limit of 0.7 ppb which is much lower than the recommended value in drinking water by the United States Environmental Protection Agency (U.S. EPA) and the World Health Organization (WHO). The complex formation of N1 with Cu2+ was found to be 1:1 N1-Cu2+ by Job's plot analysis. Furthermore, the sensor was highly tolerant to interference from a matrix of real samples such as drinking water and human liver carcinoma cell line.

Previdi, R, Levchenko, I, Arnold, M, Gali, M, Bazaka, K, Xu, S, Ostrikov, KK, Bray, K, Jin, D & Fang, J 2019, 'Plasmonic platform based on nanoporous alumina membranes: order control via self-assembly', Journal of Materials Chemistry A, vol. 7, no. 16, pp. 9565-9577.
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A novel approach to significantly enhance and comprehensively assess the level of nanochannel ordering in self-assembled nanoporous membranes is proposed and tested.

Prosser, C, Meyer, W, Ellis, J & Lee, R 2019, 'Traveller sentinels for global surveillance of malaria drug resistance and diagnostic test evasion', International Journal of Infectious Diseases, vol. 79, pp. 22-23.
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Pu, N, Gao, S, Yin, H, Li, J-A, Wu, W, Fang, Y, Zhang, L, Rong, Y, Xu, X, Wang, D, Kuang, T, Jin, D, Yu, J & Lou, W 2019, 'Cell-intrinsic PD-1 promotes proliferation in pancreatic cancer by targeting CYR61/CTGF via the hippo pathway', Cancer Letters, vol. 460, pp. 42-53.
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Pu, N, Yin, H, Zhao, G, Nuerxiati, A, Wang, D, Xu, X, Kuang, T, Jin, D, Lou, W & Wu, W 2019, 'Independent effect of postoperative neutrophil-to-lymphocyte ratio on the survival of pancreatic ductal adenocarcinoma with open distal pancreatosplenectomy and its nomogram-based prediction', Journal of Cancer, vol. 10, no. 24, pp. 5935-5943.
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Raina, J-B, Fernandez, V, Lambert, B, Stocker, R & Seymour, JR 2019, 'The role of microbial motility and chemotaxis in symbiosis', Nature Reviews Microbiology, vol. 17, no. 5, pp. 284-294.
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© 2019, Springer Nature Limited. Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis. The pivotal role of these behaviours in the onset and maintenance of symbiotic interactions is well established in a small number of model systems but remains largely overlooked for the many symbioses that involve the recruitment of microbial partners from the environment. In this Review, we highlight when, where and how chemotaxis and motility can enable symbiont recruitment and propose that these symbiont behaviours are important across a wide range of hosts and environments.

Rajeshkumar, S, Menon, S, Venkat Kumar, S, Tambuwala, MM, Bakshi, HA, Mehta, M, Satija, S, Gupta, G, Chellappan, DK, Thangavelu, L & Dua, K 2019, 'Antibacterial and antioxidant potential of biosynthesized copper nanoparticles mediated through Cissus arnotiana plant extract', Journal of Photochemistry and Photobiology B: Biology, vol. 197, pp. 111531-111531.
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© 2019 Elsevier B.V. Environment friendly methods for the synthesis of copper nanoparticles have become a valuable trend in the current scenario. The utilization of phytochemicals from plant extracts has become a unique technology for the synthesis of nanoparticles, as they possess dual nature of reducing and capping agents to the nanoparticles. In the present investigation we have synthesized copper nanoparticles (CuNPs) using a rare medicinal plant Cissus arnotiana and evaluated their antibacterial activity against gram negative and gram positive bacteria. The morphology and characterization of the synthesized CuNPs were studied and done using UV-Visible spectroscopy at a wavelength range of 350–380 nm. XRD studies were performed for analyzing the crystalline nature; SEM and TEM for evaluating the spherical shape within the size range of 60–90 nm and AFM was performed to check the surface roughness. The biosynthesized CuNPs showed better antibacterial activity against the gram-negative bacteria, E. coli with an inhibition zone of 22.20 ± 0.16 mm at 75 μg/ml. The antioxidant property observed was comparatively equal with the standard antioxidant agent ascorbic acid at a maximum concentration of 40 μg/ ml. This is the first study reported on C. arnotiana mediated biosynthesis of copper nanoparticles, where we believe that the findings can pave way for a new direction in the field of nanotechnology and nanomedicine where there is a significant potential for antibacterial and antioxidant activities. We predict that, these could lead to an exponential increase in the field of biomedical applications, with the utilization of green synthesized CuNPs, due to its remarkable properties. The highest antibacterial property was observed with gram-negative strains mainly, E. coli, due to its thin peptidoglycan layer and electrostatic interactions between the bacterial cell wall and CuNPs surfaces. Hence, CuNPs can be potent therapeutic agents in several biomedical ...

Ramarajan, M, Fabris, M, Abbriano, RM, Pernice, M & Ralph, PJ 2019, 'Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526', Algal Research, vol. 44, pp. 101708-101708.
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© 2019 Elsevier B.V. Nannochloropsis is a marine microalga from the Eustigmatophyceae stramenopile lineage that has been studied extensively due to a broad range of industrial applications, mostly related to their oil and pigment production. However, tools to genetically engineer members of this group, and therefore further understand and maximise their industrial potential are still limited. In order to expand the potential industrial uses of this organism, several molecular tools, including gene promoters of different strength, are needed. A comprehensive and diverse set of well-characterized promoters is key to a number of genetic engineering and synthetic biology applications, such as the assembly of complex biological functions or entire metabolic pathways. In this study, we measured the promoter activity of three endogenous constitutive promoters from N. gaditana genes EPPSII (Nga02101); HSP90 (Nga00934); ATPase (Nga06354.1) in driving the expression of a Sh ble- mVenus fluorescent reporter fusion protein. Through a combined approach that includes flow cytometry, RT-qPCR and immunoblotting, we profiled the activity of these promoters at both the transcript and protein level. Two promoters HSP90 (Nga00934) and EPPSII (Nga02101) outperformed the widely used β-tubulin promoter, exhibiting 4.5 and 3.1-fold higher mVenus fluorescence, respectively. A third promoter ATPase (Nga06354.1) was also able to drive the expression of transgenes, albeit at lower levels. We show that the new promoters identified in this study are valuable tools, which can be used for genetic engineering and functional genetics studies in N. gaditana.

Ramsahai, JM, Hansbro, PM & Wark, PAB 2019, 'Mechanisms and Management of Asthma Exacerbations', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 4, pp. 423-432.
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Copyright © 2019 by the American Thoracic Society. Acute asthma remains an important medical emergency, the most frequent cause of acute admissions in children and a major source of morbidity for adults with asthma. In all ages with asthma, the presence of exacerbations is an important defining characteristic of asthma severity. In this review, we assess the epidemiology of acute asthma, the triggers of acute exacerbations, and the mechanisms that underlie these exacerbations. We also assess current treatments that prevent exacerbations, with an emphasis on the role of type 2 airway inflammation in the context of acute exacerbations and the novel treatments that effectively target this. Finally we review current mana ement strate ies of the exacerbations themselves

Rani, A, Viljoen, A, Johansen, MD, Kremer, L & Kumar, V 2019, 'Synthesis, anti-mycobacterial and cytotoxic evaluation of substituted isoindoline-1,3-dione-4-aminoquinolines coupled via alkyl/amide linkers', RSC Advances, vol. 9, no. 15, pp. 8515-8528.
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A series of secondary amine-substituted isoindoline-1,3-dione-4-aminoquinolines were prepared via microwave heating and assayed for their anti-mycobacterial activities.

Rathnayake, SNH, Van den Berge, M & Faiz, A 2019, 'Genetic profiling for disease stratification in chronic obstructive pulmonary disease and asthma', Current Opinion in Pulmonary Medicine, vol. 25, no. 3, pp. 317-322.
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PURPOSE OF REVIEW:In asthma and chronic obstructive pulmonary disease (COPD), the movement towards genetic profiling with a push towards 'personalized medicine' has been hindered by complex environment--gene interactions and lack of tools to identify clear causal genetic traits. In this review, we will discuss the need for genetic profiling in asthma and COPD, what methods are currently used in the clinics and the recent finding using new sequencing methods. RECENT FINDINGS:Over the past 10-15 years, genome-wide association studies analysis of common variants has provide little in the way of new genetic profiling markers for asthma and COPD. Whole exome/genome sequencing has provided a new method to identify lowly abundant alleles, which might have a much higher impact. Although, low population numbers due to high costs has hindered early studies, recent studies have reached genome wide significance. SUMMARY:The use of genetic profiling of COPD in the clinic is current limited to the identification of Alpha-1 antitrypsin deficiency, while being absent in asthma. Advances in sequencing technology provide new avenues to identify disease causes or therapy response altering variants that in the short-term will allow for the development of screening procedures for disease to identify patients at risk of developing asthma or COPD.

Rätsep, M, Linnanto, JM, Muru, R, Biczysko, M, Reimers, JR & Freiberg, A 2019, 'Absorption-emission symmetry breaking and the different origins of vibrational structures of the 1Qy and 1Qx electronic transitions of pheophytin a', The Journal of Chemical Physics, vol. 151, no. 16, pp. 165102-165102.
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The vibrational structure of the optical absorption and fluorescence spectra of the two lowest-energy singlet electronic states (Qy and Qx) of pheophytin a were carefully studied by combining low-resolution and high-resolution spectroscopy with quantum chemical analysis and spectral modeling. Large asymmetry was revealed between the vibrational structures of the Qy absorption and fluorescence spectra, integrally characterized by the total Huang-Rhys factor and reorganization energy in absorption of SvibA = 0.43 ± 0.06, λA = 395 cm−1 and in emission of SvibE = 0.35 ± 0.06, λE = 317 cm−1. Time-dependent density-functional theory using the CAM-B3LYP, ωB97XD, and MN15 functionals could predict and interpret this asymmetry, with the exception of one vibrational mode per model, which was badly misrepresented in predicted absorption spectra; for CAM-B3LYP and ωB97XD, this mode was a Kekulé-type mode depicting aromaticity. Other computational methods were also considered but performed very poorly. The Qx absorption spectrum is broad and could not be interpreted in terms of a single set of Huang-Rhys factors depicting Franck-Condon allowed absorption, with Herzberg-Teller contributions to the intensity being critical. For it, CAM-B3LYP calculations predict that SvibA (for modes &gt;100 cm−1) = 0.87 and λA = 780 cm−1, with effective x and y polarized Herzberg-Teller reorganization energies of 460 cm−1 and 210 cm−1, respectively, delivering 15% y-polarized intensity. However, no method was found to quantitatively determine the observed y-polarized contribution, with contributions of up to 50% being feasible.

Razavi Bazaz, S, Kashaninejad, N, Azadi, S, Patel, K, Asadnia, M, Jin, D & Ebrahimi Warkiani, M 2019, 'Microfluidics: Rapid Softlithography Using 3D‐Printed Molds (Adv. Mater. Technol. 10/2019)', Advanced Materials Technologies, vol. 4, no. 10, pp. 1970056-1970056.
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Razavi Bazaz, S, Kashaninejad, N, Azadi, S, Patel, K, Asadnia, M, Jin, D & Ebrahimi Warkiani, M 2019, 'Rapid Softlithography Using 3D‐Printed Molds', Advanced Materials Technologies, vol. 4, no. 10, pp. 1900425-1900425.
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AbstractPolydimethylsiloxane (PDMS) is a long‐standing material of significant interest in microfluidics due to its unique features. As such, rapid prototyping of PDMS‐based microchannels is of great interest. The most prevalent and conventional method for fabrication of PDMS‐based microchips relies on softlithography, the main drawback of which is the preparation of a master mold, which is costly and time‐consuming. To prevent the attachment of PDMS to the master mold, silanization is necessary, which can be detrimental for cellular studies. Additionally, using coating the mold with a cell‐compatible surfactant adds extra preprocessing time. Recent advances in 3D printing have shown great promise in expediting microfabrication. Nevertheless, current 3D printing techniques are sub‐optimal for PDMS softlithography. The feasibility of producing master molds suitable for rapid softlithography is demonstrated using a newly developed 3D‐printing resin. Moreover, the utility of this technique is showcased for a number of widely used applications, such as concentration gradient generation, particle separation, cell culture (to show biocompatibility of the process), and fluid mixing. This can open new opportunities for biologists and scientists with minimum knowledge of microfabrication to build functional microfluidic devices for their basic and applied research.

Rehn, S & Boakes, RA 2019, 'Bingeing in rats: Persistence of high intakes of palatable solutions induced by 1-day-in-4 intermittent access', Physiology & Behavior, vol. 207, pp. 15-27.
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When animals are given access to a palatable food or drink on some days but not on others, the amount they consume can far exceed the daily amounts consumed by controls given daily access. A previous study demonstrated such bingeing when rats were given 4% sucrose solution. Importantly, it also found that, following 1-day-in-4 access for many weeks, intakes remained persistently higher than that of controls even when the conditions were changed to 1-day-in-2 access for both groups. One aim of the three experiments reported here was to test whether such persistent bingeing could be found for other solutions. This was confirmed in rats for a saccharin solution and a highly palatable saccharin-plus-glucose solution. When a maltodextrin solution was used, the 1-day-in-4 schedule initially produced higher intakes than controls given daily access. However, the difference between these groups was not maintained when both were switched to a 1-day-in-2 schedule. These results suggest that the hedonic value of a solution is more important than its caloric content in determining whether it will support persistent bingeing. A second aim was to test for evidence that the 1-day-in-4 procedure induced an addiction to the target solution. No such evidence was found using multiple measures including instrumental responding and anxiety-like behavior on the elevated plus-maze for craving and withdrawal respectively.

Reichelt, AC, Gibson, GD, Abbott, KN & Hare, DJ 2019, 'A high-fat high-sugar diet in adolescent rats impairs social memory and alters chemical markers characteristic of atypical neuroplasticity and parvalbumin interneuron depletion in the medial prefrontal cortex', Food & Function, vol. 10, no. 4, pp. 1985-1998.
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A hypercaloric diet given to adolescent rats induces social memory deficits and reduced neurochemical markers of normal social development.

Reichelt, AC, Hare, DJ, Bussey, TJ & Saksida, LM 2019, 'Perineuronal Nets: Plasticity, Protection, and Therapeutic Potential', Trends in Neurosciences, vol. 42, no. 7, pp. 458-470.
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The relationship between neurons and perineuronal nets (PNNs) is attracting attention as a central mechanism controlling brain plasticity. In the cortex, PNNs primarily surround inhibitory parvalbumin interneurons, playing roles as both a regulator of synaptic plasticity and a protective barrier. PNNs have a delayed developmental trajectory and are key components in the closure of critical periods of heightened neuroplasticity. In animal models, manipulating PNNs outside this critical window can enhance cognition, suggesting a potentially therapeutic approach for attenuating cognitive decline. However, the crucial role of PNNs in plasticity and protection means that such therapeutic modulation must strike a careful balance: manipulation of PNNs to promote plasticity may have unintended negative consequences resulting from excessive plasticity or from exposure of neurons to neurotoxins.

Reid, CJ, Blau, K, Jechalke, S, Smalla, K & Djordjevic, SP 2019, 'Whole Genome Sequencing of Escherichia coli From Store-Bought Produce', Frontiers in Microbiology, vol. 10, p. 3050.
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The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.

Reid, CJ, DeMaere, MZ & Djordjevic, SP 2019, 'Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny', Microbial Genomics, vol. 5, no. 3, pp. ---.
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We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-i...

Reid, CJ, McKinnon, J & Djordjevic, SP 2019, 'Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids', Microbial Genomics, vol. 5, no. 9.
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The interplay between food production animals, humans and the environment with respect to the transmission of drug-resistant pathogens is widely debated and poorly understood. Pandemic uropathogenic Escherichia coli ST131-H30Rx, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identified in animals. However, the phylogenetic precursor lineage ST131-H22 in animals and associated meat products is being reported with increasing frequency. Here we characterized two highly related ST131-H22 strains, one from a healthy pig and the other from a human infection (in 2007 and 2009, respectively). We used both long and short genome sequencing and compared them to ST131-H22 genome sequences available in public repositories. Even within the context of H22 strains, the two strains in question were highly related, separated by only 20 core SNPs. Furthermore, they were closely related to a faecal strain isolated in 2010 from a geographically distinct, healthy human in New South Wales, Australia. The porcine and hospital strains carried highly similar HI2-ST3 multidrug resistant plasmids with differences in the hospital strain arising due to IS-mediated insertions and rearrangements. Near identical ColV plasmids were also present in both strains, further supporting their shared evolutionary history. This work highlights the importance of adopting a One Health approach to genomic surveillance to gain insights into pathogen evolution and spread.

Reimers, JR 2019, 'Noel S. Hush', The Journal of Physical Chemistry B, vol. 123, no. 18, pp. 3885-3886.
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Reimers, JR 2019, 'Noel S. Hush', The Journal of Physical Chemistry A, vol. 123, no. 18, pp. 3935-3936.
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Reimers, JR, Wang, Y & Kosov, DS 2019, 'Decomposition of Ferrocene on Pt(111) and Its Effect on Molecular Electronic Junctions', The Journal of Physical Chemistry C, vol. 123, no. 25, pp. 15569-15574.
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© 2019 American Chemical Society. From dilute vapor, ferrocene encountering Pt(111) decomposes, producing bound cyclopentadienyl rings, in contrast to its legendary stability in solution electrochemistry. We propose that decomposition occurs through initial chemisorption, making a Pt-C bond to a ferrocenium hydride, followed by step-edge catalyzed decomposition leading to migration of the Fe atom inside the Pt bulk. These conclusions are based on results from density functional theory (DFT) calculations. When Pt(111) approaches ferrocene tethered to a self-assembled monolayer, only the first, spontaneous but mechanically reversible chemisorption is predicted. Nonequilibrium Green's function calculations utilizing DFT predict that chemisorption increases molecular junction conductivities by a factor of 2-5. This could contribute to the extremely high conductivities observed in junctions supporting rectification up to unprecedented high-frequency cutoffs of ∼520 GHz, though squashed junctions at half monolayer coverage are predicted to conduct 104 times better.

Ren, D & Leslie, LM 2019, 'Impacts of Climate Warming on Aviation Fuel Consumption', Journal of Applied Meteorology and Climatology, vol. 58, no. 7, pp. 1593-1602.
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AbstractFactors affecting aviation fuel efficiency are thermal and propulsive efficiencies, and overall drag on aircraft. An along-the-route integration is made for all direct flights in a baseline year, 2010, under current and future atmospheric conditions obtained from 26 climate models under the representative concentration pathway (RCP) 8.5 scenario. Thermal efficiency and propulsive efficiency are affected differently, with the former decreasing by 0.38% and the latter increasing by 0.35%. Consequently, the overall engine efficiency decrease is merely <0.02%. Over the same period, the skin frictional drag increases ~3.5% from the increased air viscosity. This component is only 5.7% of the total drag, and the ~3.5% increase in air viscosity accounts for a 0.2% inefficiency in fuel consumption. A t test is performed for the multiple-model ensemble mean time series of fuel efficiency decrease for two 20-yr periods centered on years 2010 and 2090, respectively. The trend is found to be statistically significant (p value = 0.0017). The total decrease in aircraft fuel efficiency is equivalent to ~0.68 billion gallons of additional fuel annually, a qualitatively robust conclusion, but quantitatively there is a large interclimate model spread.

Ren, D, Dickinson, RE, Fu, R, Bornman, JF, Guo, W, Yang, S & Leslie, LM 2019, 'Impacts of climate warming on maximum aviation payloads', Climate Dynamics, vol. 52, no. 3-4, pp. 1711-1721.
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© 2018, The Author(s). The increasing importance of aviation activities in modern life coincides with a steady warming climate. However, the effect of climate warming on maximum aircraft carrying capacity or payload has been unclear. Here we clarify this issue using primary atmospheric parameters from 27 fully coupled climate models from the Coupled Model Inter-comparison Project 5 (CMIP5) archive, utilizing the direct proportionality of near-surface air density (NSAD) to maximum take-off total weight (MTOW). Historical (twentieth century) runs of these climate models showed high credibility in reproducing the reanalysis period (1950–2015) of NSAD. In particular, the model simulated trends in NSAD are highly aligned with the reanalysis values. This reduction in NSAD is a first order global signal, just as is the warming itself, that continues into the future. To examine the statistical significance of the density reduction, a t-test was performed for two 20-year periods 75 years apart (2080–2100 vs. 2005–2025), using the Representative Concentration Pathways (RCP) 8.5 emission scenario of the Intergovernmental Panel on Climate Change (IPCC). Most continental areas easily passed the test at a P-value of 0.05. These future changes of NSAD will likely have significant economic impacts on the aviation industry. For these two 20-year periods that we examined, the most extreme changes are in the Northern hemisphere in high latitudes, i.e., a 5% decrease in MTOW, or ~ 8.5–19% (aircraft-dependent) reduction in payload. The global average change is about 1%. For the busy North Atlantic Corridor (NAC), the reduction in MTOW is generally greater than 1% and that of payload several times larger.

Ren, M, McGowan, E, Li, Y, Zhu, X, Lu, X, Zhu, Z, Lin, Y & He, S 2019, 'Saikosaponin-d Suppresses COX2 Through p-STAT3/C/EBPβ Signaling Pathway in Liver Cancer: A Novel Mechanism of Action', Frontiers in Pharmacology, vol. 10.
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Saikosaponin d (SSd) is an active extract from Radix Bupleuri, the dried root from the plant Bupleurum falcatum used in China for thousands of years to treat liver diseases. The SSd extract possesses valuable pharmacological activities including anti-cancer and anti-inflammatory effects, however, the mechanism underlying the anti-cancer activity of SSd is largely unknown. Here we explored the mechanism of action of SSd as an anti-cancer agent for liver cancer in two human hepatocellular carcinoma cell lines. Using MTT and annexin-V-FITC/PI assays, Western blots, immunohistochemistry, qRT-PCR, luciferase reporter assay, and a JAK2 specific-inhibitor (AG490), we demonstrated that the anti-tumorigenic effects of SSd acts through the intermediatory p-STAT3/C/EBPβ signaling pathway to suppress cyclooxygenase (COX)-2. SSd effectively inhibited cell proliferation in a dose-dependent manner. Apoptosis was significantly increased in cells treated with SSd (2.5 µg/ml-15 µg/ml) with concurrent increase and decrease in pro-and anti-apoptosis proteins, respectively. COX-2, C/EBPβ, and p-STAT3 were significantly decreased, at both the translational and transcriptional levels, by SSd treatment. AG490 produced similar inhibitory effects on STAT3, p-STAT3, C/EBPβ and COX-2. In conclusion, our data suggests that SSd controls liver cancer proliferation through suppression of the p-STAT3/C/EBPβ signaling pathway inhibiting COX2 expression. These findings further our understanding of the pharmacological action of SSd providing new information on SSd mechanism of action and shows potential for SSd as a novel therapy for liver cancer.

Reyes, L, Bishop, DP, Hawkins, CL & Rayner, BS 2019, 'Assessing the Efficacy of Dietary Selenomethionine Supplementation in the Setting of Cardiac Ischemia/Reperfusion Injury', Antioxidants, vol. 8, no. 11, pp. 546-546.
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Oxidative stress is a major hallmark of cardiac ischemia/reperfusion (I/R) injury. This partly arises from the presence of activated phagocytes releasing myeloperoxidase (MPO) and its production of hypochlorous acid (HOCl). The dietary supplement selenomethionine (SeMet) has been shown to bolster endogenous antioxidant processes as well as readily react with MPO-derived oxidants. The aim of this study was to assess whether supplementation with SeMet could modulate the extent of cellular damage observed in an in vitro cardiac myocyte model exposed to (patho)-physiological levels of HOCl and an in vivo rat model of cardiac I/R injury. Exposure of the H9c2 cardiac myoblast cell line to HOCl resulted in a dose-dependent increase in necrotic cell death, which could be prevented by SeMet supplementation and was attributed to SeMet preventing the HOCl-induced loss of mitochondrial inner trans-membrane potential, and the associated cytosolic calcium accumulation. This protection was credited primarily to the direct oxidant scavenging ability of SeMet, with a minor contribution arising from the ability of SeMet to bolster cardiac myoblast glutathione peroxidase (GPx) activity. In vivo, a significant increase in selenium levels in the plasma and heart tissue were seen in male Wistar rats fed a diet supplemented with 2 mg kg−1 SeMet compared to controls. However, SeMet-supplementation demonstrated only limited improvement in heart function and did not result in better heart remodelling following I/R injury. These data indicate that SeMet supplementation is of potential benefit within pathological settings where excessive HOCl is known to be generated but has limited efficacy as a therapeutic agent for the treatment of heart attack.

Reyna, J, Hanham, J, Vlachopoulos, P & Meier, P 2019, 'Using factor analysis to validate a questionnaire to explore self-regulation in learner-generated digital media (LGDM) assignments in science education', Australasian Journal of Educational Technology, vol. 35, no. 5, pp. 128-152.
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This research is a validation study of a survey instrument to assess student self-regulation which aims to fill a methodological gap by capturing self-regulation processes while completing learner-generated digital media (LGDM) assignments. For this purpose, the study developed and validated a self-regulation learning questionnaire. Data were gathered from seven science subjects (Years 1 to 3, n = 341) which used LGDM assignments during Semester 1, 2017. Students were asked to complete a 40-item online questionnaire. The questionnaire was administered at three times during the semester (Weeks 2, 6, and 10). Exploratory factor analysis was used to identify factor structures, followed by confirmatory factor analysis to test the validity of the constructs defined by exploratory factor analysis. Analysis of the data revealed a ten-factor structure – six concerning self-regulation, two concerning student attitudes towards LGDM assignments, one concerning assignment ownership, and one concerning assignment motivation. The variables empirically verified in this study have important practical implications, as they could provide educators with the direction in which to target interventions to improve learners’ experiences with LDGM. The study findings also contribute to the field by providing scholars with a validated research instrument that can be used in future studies.

Rhumorbarbe, D, Morelato, M, Staehli, L, Roux, C, Jaquet-Chiffelle, D-O, Rossy, Q & Esseiva, P 2019, 'Monitoring new psychoactive substances: Exploring the contribution of an online discussion forum', International Journal of Drug Policy, vol. 73, pp. 273-280.
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© 2019 Elsevier B.V. Background: The rapid emergence of new psychoactive substances (NPS) is a challenge for public health authorities and law enforcement. The phenomenon is strengthened since the increase of the Internet usage. Not only used to trade NPS, the Web is an important source of information for both potential drug consumers and experienced users. Discussion forums are among these sources of information. They are meeting points for different groups of users and include a wide range of trip reports, questions and consumption tips. Since the discussions are archived over a long period, they can be used to monitor the interest of consumers for particular substances over time. This research aims at understanding the contribution of data extracted from a major online discussion forum within a systematic monitoring process. Method: Data were collected from a discussion forum (i.e. Drugs-forum). Within the sections of the forum, the titles, content of discussion, number of replies, and the date of the first discussion were crawled and stored in a dedicated database. The intensity of the discussions related to 42 substances considered as NPS was measured through an indicator allowing to assess the popularity of substances. Furthermore, the appearance of 15 substances on the forum was compared to the date of formal notification to the EU early warning system. Results: An evolution of the different classes of substances, as well as an evolution of specific substances within a class were highlighted. Some substances were discussed for a long period of time (e.g. Kratom, 25i-NBOMe, MDPV) while others were discussed very briefly (e.g. 5-MeO-DPT, NM-2AI). Out of the fifteen substances subjected to a risk assessment from the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA), nine of them appeared on the forum before or at the same time as their first date of notification to the EU early warning system. Conclusion: In line with previous researc...

Rinke, C, Rubino, F, Messer, LF, Youssef, N, Parks, DH, Chuvochina, M, Brown, M, Jeffries, T, Tyson, GW, Seymour, JR & Hugenholtz, P 2019, 'A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)', The ISME Journal, vol. 13, no. 3, pp. 663-675.
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Abstract Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to ...

Robinson, N, Bovey, M, Lee, JA, Zaslawski, C, Tian, P, Kim, T-H, Alraek, T, Bian, Z-X, Lee, MS & Birch, S 2019, 'How do acupuncture practitioners use pattern identification – An international web-based survey?', European Journal of Integrative Medicine, vol. 32, pp. 100997-100997.
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© 2019 Elsevier GmbH Introduction: Training and practice of Traditional East Asian Medicine (TEAM) varies globally although similar diagnostic methods are used based on patients presenting signs and symptoms. These methods assist in determining disease patterns and treatment principles. The use of diagnostic principles and pattern identification (PI) was explored in this survey of TEAM practice across different countries. Methods: A web-based survey was disseminated to acupuncture professional membership organisations in UK, Australia, Italy, Korea and China using a Survey Monkey link between December 2015 and September 2017. Results: The 618 fully completed responses were available for comparison (UK 66, Australia 106, China 87, Italy 226, Korea 133). Demographic characteristics varied; UK practitioners were more likely to be female (71%) compared to the other countries (51-59%), Koreans tended to be under 40yrs (80%), compared to elsewhere (14-27%). Korean, UK and Australian respondents had fewer practitioners with biomedical training, 95% of the Italians had a biomedical qualification. TEAM diagnostic methods were more likely practised in the UK and Australian samples ( > 90%) but were lowest for the Italian sample (78%). TCM differential diagnosis was the predominant type of PI. PI was rated essential by 85% of Chinese practitioners, versus 32% Koreans, 45% Italians, 67% UK and 68% Australian respondents. Conclusion: This first international survey about acupuncturists use of PI demonstrated wide variation. The sample was limited to certain countries and relied on dissemination by specific professional bodies and participants completing an electronic questionnaire which may have affected responses but provides a platform for future studies.

Rose, ML, Copland, D, Nickels, L, Togher, L, Meinzer, M, Rai, T, Cadilhac, DA, Kim, J, Foster, A, Carragher, M, Hurley, M & Godecke, E 2019, 'Constraint-induced or multi-modal personalized aphasia rehabilitation (COMPARE): A randomized controlled trial for stroke-related chronic aphasia', International Journal of Stroke, vol. 14, no. 9, pp. 972-976.
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Rationale The comparative efficacy and cost-effectiveness of constraint-induced and multi-modality aphasia therapy in chronic stroke are unknown. Aims and hypotheses In the COMPARE trial, we aim to determine whether Multi-Modal Aphasia Treatment (M-MAT) and Constraint-Induced Aphasia Therapy Plus (CIAT-Plus) are superior to usual care (UC) for chronic post-stroke aphasia. Primary hypothesis: CIAT-Plus and M-MAT will reduce aphasia severity (Western Aphasia Battery-Revised Aphasia Quotient (WAB-R-AQ)) compared with UC: CIAT-Plus superior for moderate aphasia; M-MAT superior for mild and severe aphasia. Sample size estimates A total of 216 participants (72 per arm) will provide 90% power to detect a 5-point difference on the WAB-R-AQ between CIAT-Plus or M-MAT and UC at α = 0.05. Methods and design Prospective, randomized, parallel group, open-label, assessor blinded trial. Participants: Stroke >6 months; aphasia severity categorized using WAB-R-AQ. Computer-generated blocked and stratified randomization by aphasia severity (mild, moderate, and severe), to 3 arms: CIAT-Plus, M-MAT (both 30 h therapy over two weeks); UC (self-reported usual community care). Study outcomes WAB-R-AQ immediately post-intervention. Secondary outcomes: WAB-R-AQ at 12-week follow-up; naming scores, discourse measures, Communicative Effectiveness Index, Scenario Test, and Stroke and Aphasia Quality of Life Scale-39 g immediately and at 12 weeks post-intervention; incremental cost-effectiveness ratios compared with UC at 12 weeks. Discussion This trial will determine whether CIAT-Plus and M-MAT are superior and more cost-effec...

Ross, C, Warhurst, BC, Brown, A, Huff, C & Ochrietor, JD 2019, 'Mesohaline conditions represent the threshold for oxidative stress, cell death and toxin release in the cyanobacterium Microcystis aeruginosa', Aquatic Toxicology, vol. 206, pp. 203-211.
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Roux, C & Linacre, A 2019, 'Major international forensic science conference to reward Australian and New Zealand cutting-edge research', Australian Journal of Forensic Sciences, vol. 51, no. 6, pp. 609-610.
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Roy Chowdhury, P, Fourment, M, DeMaere, MZ, Monahan, L, Merlino, J, Gottlieb, T, Darling, AE & Djordjevic, SP 2019, 'Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids', Plasmid, vol. 102, pp. 56-61.
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© 2019 Elsevier Inc. IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.

Roy Chowdhury, P, McKinnon, J, Liu, M & Djordjevic, SP 2019, 'Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location', Frontiers in Microbiology, vol. 9, no. JAN, pp. 3212-3212.
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© 2019 Roy Chowdhury, McKinnon, Liu and Djordjevic. Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of blaCTX-M, blaNDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo.

Rutting, S, Xenaki, D, Malouf, M, Horvat, JC, Wood, LG, Hansbro, PM & Oliver, BG 2019, 'Short-chain fatty acids increase TNFα-induced inflammation in primary human lung mesenchymal cells through the activation of p38 MAPK', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 316, no. 1, pp. L157-L174.
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Short-chain fatty acids (SCFAs), produced as by-products of dietary fiber metabolism by gut bacteria, have anti-inflammatory properties and could potentially be used for the treatment of inflammatory diseases, including asthma. The direct effects of SCFAs on inflammatory responses in primary human lung mesenchymal cells have not been assessed. We investigated whether SCFAs can protect against tumor necrosis factor (TNF)α-induced inflammation in primary human lung fibroblasts (HLFs) and airway smooth muscle (ASM) cells in vitro. HLFs and ASM cells were exposed to SCFAs, acetate (C2:0), propionate (C3:0), and butyrate (C4:0) (0.01–25 mM) with or without TNFα, and the release of proinflammatory cytokines, IL-6, and CXCL8 was measured using ELISA. We found that none of the SCFAs suppressed TNFα-induced cytokine release. On the contrary, challenge with supraphysiological concentrations (10–25 mM), as might be used therapeutically, of propionate or butyrate in combination with TNFα resulted in substantially greater IL-6 and CXCL8 release from HLFs and ASM cells than challenge with TNFα alone, demonstrating synergistic effects. In ASM cells, challenge with acetate also enhanced TNFα-induced IL-6, but not CXCL8 release. Synergistic upregulation of IL-6 and CXCL8 was mediated through the activation of free fatty acid receptor (FFAR)3, but not FFAR2. The signaling pathways involved were further examined using specific inhibitors and immunoblotting, and responses were found to be mediated through p38 MAPK signaling. This study demonstrates that proinflammatory, rather than anti-inflammatory effects of SCFAs are evident in lung mesenchymal cells.

Rutting, S, Zakarya, R, Bozier, J, Xenaki, D, Horvat, JC, Wood, LG, Hansbro, PM & Oliver, BG 2019, 'Dietary Fatty Acids Amplify Inflammatory Responses to Infection through p38 MAPK Signaling', American Journal of Respiratory Cell and Molecular Biology, vol. 60, no. 5, pp. 554-568.
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Copyright © 2019 by the American Thoracic Society. Obesity is an important risk factor for severe asthma exacerbations, which are mainly caused by respiratory infections. Dietary fatty acids, which are increased systemically in obese patients and are further increased after high-fat meals, affect the innate immune system and may contribute to dysfunctional immune responses to respiratory infection. In this study we investigated the effects of dietary fatty acids on immune responses to respiratory infection in pulmonary fibroblasts and a bronchial epithelial cell line (BEAS-2B). Cells were challenged with BSA-conjugated fatty acids (v-6 polyunsaturated fatty acids [PUFAs], v-3 PUFAs, or saturated fatty acids [SFAs]) 1/2 the viral mimic polyinosinic:polycytidylic acid (poly[I:C]) or bacterial compound lipoteichoic acid (LTA), and release of proinflammatory cytokines was measured. In both cell types, challenge with arachidonic acid (AA) (v-6 PUFA) and poly(I:C) or LTA led to substantially greater IL-6 and CXCL8 release than either challenge alone, demonstrating synergy. In epithelial cells, palmitic acid (SFA) combined with poly(I:C) also led to greater IL-6 release. The underlying signaling pathways of AA and poly(I:C)- or LTA-induced cytokine release were examined using specific signaling inhibitors and IB. Cytokine production in pulmonary fibroblasts was prostaglandin dependent, and synergistic upregulation occurred via p38 mitogen-activated protein kinase signaling, whereas cytokine production in bronchial epithelial cell lines was mainly mediated through JNK and p38 mitogen-activated protein kinase signaling. We confirmed these findings using rhinovirus infection, demonstrating that AA enhances rhinovirus-induced cytokine release. This study suggests that during respiratory infection, increased levels of dietary v-6 PUFAs and SFAs may lead to more severe airway inflammation and may contribute to and/or increase the severity of asthma exacerbations.

Ryan, L 2019, 'Four papers on child growth modelling', Statistics in Medicine, vol. 38, no. 19, pp. 3505-3506.
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Sadaf, T, John, P & Bhatti, A 2019, 'Comprehensive Computational Analysis of Protein Phenotype Changes Due to Plausible Deleterious Variants of Human SPTLC1 Gene.', Int J Mol Cell Med, vol. 8, no. 1, pp. 67-84.
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Genetic variations found in the coding and non-coding regions of a geneare known to influence the structure as well as the function of proteins. Serine palmitoyltransferase long chain subunit 1 a member of α-oxoamine synthase family is encoded by SPTLC1 gene which is a subunit of enzyme serine palmitoyltransferase (SPT). Mutations in SPTLC1 have been associated with hereditary sensory and autonomic neuropathy type I (HSAN-I). The exact mechanism through which these mutations elicit protein phenotype changes in terms of structure, stability and interaction with other molecules is unknown. Thus, we aimed to perform a comprehensive computational analysis of single nucleotide polymorphisms (SNPs) of SPTLC1 to prioritize a list of potential deleterious SNPs and to investigate the protein phenotype change due to functional polymorphisms. In this study, a diverse set of SPTLC1 SNPs were collected and scrutinized to categorize the potential deleterious variants. Our study concordantly identified 21 non- synonymous SNPs as pathogenic and deleterious that might induce alterations in protein structure, flexibility and stability. Moreover, evaluation of frameshift, 3' and 5' UTR variants shows c.*1302T> Gas effective. This comprehensive in silico analysis of systematically characterized list of potential deleterious variants could open avenues as primary filter to substantiate plausible pathogenic structural and functional impact of variants.

Sadaf, T, John, P, Bhatti, A & Malik, JM 2019, 'Lack of association of –863C/A (rs1800630) polymorphism of tumor necrosis factor-α gene with rheumatoid arthritis', Archives of Medical Science, vol. 15, no. 2, pp. 531-536.
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Salehi, B, Staniak, M, Czopek, K, Stępień, A, Dua, K, Wadhwa, R, Kumar Chellappan, D, Sytar, O, Brestic, M, Ganesh Bhat, N, Venkatesh Anil Kumar, N, del Mar Contreras, M, Sharopov, F, C. Cho, W & Sharifi-Rad, J 2019, 'The Therapeutic Potential of the Labdane Diterpenoid Forskolin', Applied Sciences, vol. 9, no. 19, pp. 4089-4089.
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Forskolin is mainly found in the root of a plant called Coleus forskohlii (Willd.) Briq., which has been used in the traditional medicine of Indian Ayurvedic and Southeast Asia since ancient times. Forskolin is responsible for the pharmacological activity of this species. Forskolin is a labdane diterpenoid with a wide biological effect. Several studies suggested a positive role of forskolin on heart complications, respiratory disorders, high blood pressure, obesity, and asthma. There are numerous clinical and pre-clinical studies representing the effect of forskolin on the above-mentioned disorders but more clinical studies need to be performed to support its efficacy.

Samardzic, K & Rodgers, KJ 2019, 'Cell death and mitochondrial dysfunction induced by the dietary non-proteinogenic amino acid l-azetidine-2-carboxylic acid (Aze)', Amino Acids, vol. 51, no. 8, pp. 1221-1232.
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Samardzic, K & Rodgers, KJ 2019, 'Cytotoxicity and mitochondrial dysfunction caused by the dietary supplement l-norvaline', Toxicology in Vitro, vol. 56, pp. 163-171.
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In addition to the 20 protein amino acids that are encoded for protein synthesis, hundreds of other naturally occurring amino acids, known as non-proteinogenic amino acids (NPAAs) exist. It is well known that some NPAAs are toxic through their ability to mimic protein amino acids, either in protein synthesis or in other metabolic pathways, and this property is utilised by some plants to inhibit the growth of other plants or kill herbivores. L-norvaline is an NPAA readily available for purchase as a dietary supplement. In light of previous evidence of l-norvaline's antifungal, antimicrobial and herbicidal activity, we examined the toxicity of l-norvaline to mammalian cells in vitro and showed that l-norvaline decreased cell viability at concentrations as low as 125 μM, caused necrotic cell death and significant changes to mitochondrial morphology and function. Furthermore, toxicity was reduced in the presence of structurally similar 'protein' amino acids, suggesting l-norvaline's cytotoxicity could be attributed to protein amino acid mimicry.

Sandra, F, Khaliq, NU, Sunna, A & Care, A 2019, 'Developing Protein-Based Nanoparticles as Versatile Delivery Systems for Cancer Therapy and Imaging', Nanomaterials, vol. 9, no. 9, pp. 1329-1329.
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In recent years, it has become apparent that cancer nanomedicine’s reliance on synthetic nanoparticles as drug delivery systems has resulted in limited clinical outcomes. This is mostly due to a poor understanding of their “bio–nano” interactions. Protein-based nanoparticles (PNPs) are rapidly emerging as versatile vehicles for the delivery of therapeutic and diagnostic agents, offering a potential alternative to synthetic nanoparticles. PNPs are abundant in nature, genetically and chemically modifiable, monodisperse, biocompatible, and biodegradable. To harness their full clinical potential, it is important for PNPs to be accurately designed and engineered. In this review, we outline the recent advancements and applications of PNPs in cancer nanomedicine. We also discuss the future directions for PNP research and what challenges must be overcome to ensure their translation into the clinic.

Sankaran, J, Tan, NJHJ, But, KP, Cohen, Y, Rice, SA & Wohland, T 2019, 'Single microcolony diffusion analysis in Pseudomonas aeruginosa biofilms', npj Biofilms and Microbiomes, vol. 5, no. 1, p. 35.
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AbstractThe influence of the biofilm matrix on molecular diffusion is commonly hypothesized to be responsible for emergent characteristics of biofilms such as nutrient trapping, signal accumulation and antibiotic tolerance. Hence quantifying the molecular diffusion coefficient is important to determine whether there is an influence of biofilm microenvironment on the mobility of molecules. Here, we use single plane illumination microscopy fluorescence correlation spectroscopy (SPIM-FCS) to obtain 3D diffusion coefficient maps with micrometre spatial and millisecond temporal resolution of entire Pseudomonas aeruginosa microcolonies. We probed how molecular properties such as size and charge as well as biofilm properties such as microcolony size and depth influence diffusion of fluorescently labelled dextrans inside biofilms. The 2 MDa dextran showed uneven penetration and a reduction in diffusion coefficient suggesting that the biofilm acts as a molecular sieve. Its diffusion coefficient was negatively correlated with the size of the microcolony. Positively charged dextran molecules and positively charged antibiotic tobramycin preferentially partitioned into the biofilm and remained mobile inside the microcolony, albeit with a reduced diffusion coefficient. Lastly, we measured changes of diffusion upon induction of dispersal and detected an increase in diffusion coefficient inside the biofilm before any loss of biomass. Thus, the change in diffusion is a proxy to detect early stages of dispersal. Our work shows that 3D diffusion maps are very sensitive to physiological changes in biofilms, viz. dispersal. However, this study also shows that diffusion, as mediated by the biofilm matrix, does not account for the high level of antibiotic tolerance associated with biofilms.

Santini, NS, Adame, MF, Nolan, RH, Miquelajauregui, Y, Piñero, D, Mastretta-Yanes, A, Cuervo-Robayo, ÁP & Eamus, D 2019, 'Storage of organic carbon in the soils of Mexican temperate forests', Forest Ecology and Management, vol. 446, pp. 115-125.
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© 2019 Elsevier B.V. The deforestation and degradation of natural habitats is the second largest contributor to carbon dioxide (CO2) emissions to the atmosphere. Temperate forests cover ∼16.5% of the Mexican landscape, and are a priority ecosystem for global conservation due to their high rate of endemism and species diversity. These forests also provide valuable ecosystem services, including the storage of organic carbon. Mexican temperate forests have lost more than half of their original cover, with ongoing forest degradation, resulting in CO2 emissions to the atmosphere. Most studies and carbon inventories only consider organic carbon stored in the aboveground biomass, and do not consider the organic carbon stored within soils of temperate forests. As a result, the emissions of CO2 due to deforestation are underestimated, and the value of temperate forests is underappreciated. To address this shortcoming, (1) we examine the extent and factors determining soil organic carbon stocks; (2) we estimate soil organic carbon stocks of Mexican temperate forests, the CO2 emissions caused by deforestation and avoided emissions from conservation and (3) we discuss the causes of loss of soil OC and management strategies to mitigate this loss. We propose that including the soil organic carbon stock-component is a priority for national projects targeting reducing emissions from deforestation. Also, urgent studies on the impacts of forest degradation in stocks of soil organic carbon are needed. Management strategies for conservation and rehabilitation of Mexican temperate forests must consider social and economic aspects of the local communities.

Santos, J, Milthorpe, B & Padula, M 2019, 'Proteomic Analysis of Cyclic Ketamine Compounds Ability to Induce Neural Differentiation in Human Adult Mesenchymal Stem Cells', International Journal of Molecular Sciences, vol. 20, no. 3, pp. 523-523.
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Neural regeneration is of great interest due to its potential to treat traumatic brain injuries and diseases that impact quality of life. Growth factor mediated differentiation can take up to several weeks to months to produce the cell of interest whereas chemical stimulation may be as minimal as a few hours. The smaller time scale is of great clinical relevance. Adipose derived stem cells (ADSCs) were treated for up to 24 h with a novel differentiation media containing the cyclic ketamine compounds to direct neurogenic induction. The extent of differentiation was investigated by proteome changes occurring during the process. The treatments indicated the ADSCs responded favorably to the neurogenic induction media by presenting a number of morphological cues of neuronal phenotype previously seen and a higher cell population post induction compared to previous studies. Furthermore, approximately 3500 proteins were analyzed and identified by mass spectrometric iTRAQ analyses. The bioinformatics analyses revealed hundreds of proteins whose expression level changes were statistically significant and biologically relevant to neurogenesis and annotated as being involved in neurogenic development. Complementing this, the Bioplex cytokine assay profiles present evidence of decreased panel of stress response cytokines and a relative increase in those involved in neurogenesis.

Santos, J, Milthorpe, BK & Padula, MP 2019, 'Correction: Santos, J., et al. Proteomic Analysis of Cyclic Ketamine Compounds Ability to Induce Neural Differentiation in Human Adult Mesenchymal Stem Cells. International Journal of Molecular Sciences 2019, 20, 523', International Journal of Molecular Sciences, vol. 20, no. 14, pp. 3542-3542.
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The authors wish to make the following corrections to this paper [...]

Santucci, P, Johansen, MD, Point, V, Poncin, I, Viljoen, A, Cavalier, J-F, Kremer, L & Canaan, S 2019, 'Nitrogen deprivation induces triacylglycerol accumulation, drug tolerance and hypervirulence in mycobacteria', Scientific Reports, vol. 9, no. 1.
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AbstractMycobacteria share with other actinomycetes the ability to produce large quantities of triacylglycerol (TAG), which accumulate as intracytoplasmic lipid inclusions (ILI) also known as lipid droplets (LD). Mycobacterium tuberculosis (M. tb), the etiologic agent of tuberculosis, acquires fatty acids from the human host which are utilized to synthesize TAG, subsequently stored in the form of ILI to meet the carbon and nutrient requirements of the bacterium during long periods of persistence. However, environmental factors governing mycobacterial ILI formation and degradation remain poorly understood. Herein, we demonstrated that in the absence of host cells, carbon excess and nitrogen starvation promote TAG accumulation in the form of ILI in M. smegmatis and M. abscessus, used as surrogate species of M. tb. Based on these findings, we developed a simple and reversible in vitro model to regulate ILI biosynthesis and hydrolysis in mycobacteria. We also showed that TAG formation is tgs1 dependent and that lipolytic enzymes mediate TAG breakdown. Moreover, we confirmed that the nitrogen-deprived and ILI-rich phenotype was associated with an increased tolerance towards several drugs used for treating mycobacterial infections. Importantly, we showed that the presence of ILI substantially enhanced the bacterial burden and granuloma abundance in zebrafish embryos infected with lipid-rich M. abscessus as compared to embryos infected with lipid-poor M. abscessus, suggesting that ILI are actively contributing to mycobacterial virulence and pathogenesis.

Scanes, E, Wood, H & Ross, P 2019, 'Microplastics detected in haemolymph of the Sydney rock oyster Saccostrea glomerata', Marine Pollution Bulletin, vol. 149, pp. 110537-110537.
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Plastic waste is ubiquitous in marine environments. Despite the sheer volume of plastic waste, it remains relatively unknown how marine invertebrates will interact with microplastics (plastic <1 mm). Microplastics (<2 μm) were ingested by the economically and ecologically significant Sydney rock oyster Saccostrea glomerata and translocated to the haemolymph, perhaps via phagocytosis. The presence of microplastics in the haemolymph indicates that filter feeding S. glomerata can ingest and accumulate microplastics which are prevalent in the environment. This research shows microplastics can enter marine molluscs and highlights the need to monitor microplastics in the marine environment and aquaculture to safeguard the seafood industry.

Schmidt, MK, Poulton, CG, Mashanovich, GZ, Reed, GT, Eggleton, BJ & Steel, MJ 2019, 'Suspended mid-infrared waveguides for Stimulated Brillouin Scattering', Optics Express, vol. 27, no. 4, pp. 4976-4976.
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© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement. We theoretically investigate a new class of silicon waveguides for achieving Stimulated Brillouin Scattering (SBS) in the mid-infrared (MIR). The waveguide consists of a rectangular core supporting a low-loss optical mode, suspended in air by a series of transverse ribs. The ribs are patterned to form a finite quasi-one-dimensional phononic crystal, with the complete stopband suppressing the transverse leakage of acoustic waves, confining them to the core of the waveguide. We derive a theoretical formalism that can be used to compute the opto-acoustic interaction in such periodic structures, and find forward intramodal-SBS gains up to 1750 m -1 W -1 , which compares favorably with the proposed MIR SBS designs based on buried germanium waveguides. This large gain is achieved thanks to the nearly complete suppression of acoustic radiative losses.

Schumann, U, Lee, JM, Smith, NA, Zhong, C, Zhu, J-K, Dennis, ES, Millar, AA & Wang, M-B 2019, 'DEMETER plays a role in DNA demethylation and disease response in somatic tissues of Arabidopsis', Epigenetics, vol. 14, no. 11, pp. 1074-1087.
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DNA demethylases function in conjunction with DNA methyltransferases to modulate genomic DNA methylation levels in plants. The Arabidopsis genome contains four DNA demethylase genes, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1) also known as DEMETER-LIKE 1 (DML1), DML2, and DML3. While ROS1, DML2, and DML3 were shown to function in disease response in somatic tissues, DME has been thought to function only in reproductive tissues to maintain the maternal-specific expression pattern of a subset of imprinted genes. Here we used promoter:β-glucuronidase (GUS) fusion constructs to show that DME is constitutively expressed throughout the plant, and that ROS1, DML2, and DML3 have tissue-specific expression patterns. Loss-of-function mutations in DME cause seed abortion and therefore viable DME mutants are not available for gene function analysis. We knocked down DME expression in a triple ros1 dml2 dml3 (rdd) mutant background using green tissue-specific expression of a hairpin RNA transgene (RNAi), generating a viable 'quadruple' demethylase mutant line. We show that this rdd DME RNAi line has enhanced disease susceptibility to Fusarium oxysporum infection compared to the rdd triple mutant. Furthermore, several defence-related genes, previously shown to be repressed in rdd, were further repressed in the rdd DME RNAi plants. DNA methylation analysis of two of these genes revealed increased differential promoter DNA methylation in rdd DME RNAi plants compared to WT, beyond the difference observed in the parental rdd plants. These results indicate that DME contributes to DNA demethylase activity and disease response in somatic tissues.

Scudder, N, McNevin, D, Kelty, SF, Funk, C, Walsh, SJ & Robertson, J 2019, 'Policy and regulatory implications of the new frontier of forensic genomics: direct-to-consumer genetic data and genealogy records', Current Issues in Criminal Justice, vol. 31, no. 2, pp. 194-216.
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Scudder, N, Robertson, J, Kelty, SF, Walsh, SJ & McNevin, D 2019, 'A law enforcement intelligence framework for use in predictive DNA phenotyping', Australian Journal of Forensic Sciences, vol. 51, no. sup1, pp. S255-S258.
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Scudder, N, Robertson, J, Kelty, SF, Walsh, SJ & McNevin, D 2019, 'An international consideration of a standards-based approach to forensic genetic genealogy', Forensic Science International: Genetics Supplement Series, vol. 7, no. 1, pp. 512-514.
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© 2019 Elsevier B.V. Forensic genetic genealogy has moved into limited operational use in the United States, and received international attention following the arrest of a suspect alleged to be the notorious ‘Golden State Killer’. The interest in this emerging area has seen the development of online courses to train investigators to pursue forensic genetic genealogy leads and the emergence of service providers marketing directly to law enforcement. Forensic genetic genealogy is an intelligence capability and can draw on existing intelligence doctrine. The power of genetic genealogy requires consideration of relevant standards, national or international. The development of these standards requires close consideration of public trust and privacy issues, including the application of the General Data Protection Regulation in Europe and constitutional issues in countries such as the United States. It also requires a consideration of potential regulatory mechanisms and options.

Seckiner, D, Mallett, X, Maynard, P, Meuwly, D & Roux, C 2019, 'Forensic gait analysis — Morphometric assessment from surveillance footage', Forensic Science International, vol. 296, pp. 57-66.
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Following the technological rise of surveillance cameras and their subsequent proliferation in public places, the use of information gathered by such means for investigative and evaluative purposes sparked a large interest in the forensic community and within policing scenarios. In particular, it is suggested that analysis of the body, especially the assessment of gait characteristics, can provide useful information to aid the investigation. This paper discusses the influences upon gait to mitigate some of the limitations of surveillance footage, including those due to the varying anatomical differences between individuals. Furthermore, the differences between various techniques applied to assess gait are discussed, including biometric gait recognition, forensic gait analysis, tracking technology, and marker technology. This review article discusses the limitations of the current methods for assessment of gait; exposing gaps within the literature in regard to various influences impacting upon the gait cycle. Furthermore, it suggests a 'morphometric' technique to enhance the available procedures to potentially facilitate the development of standardised protocols with supporting statistics and database. This in turn will provide meaningful information to forensic investigation, intelligence-gathering processes, and potentially as an additional method of forensic evaluation of evidence.

See-Too, WS, Ambrose, M, Malley, R, Ee, R, Mulcahy, E, Manche, E, Lazenby, J, McEwan, B, Pagnon, J, Chen, JW, Chan, KG, Turnbull, L, Whitchurch, CB & Roddam, LF 2019, 'Pandoraea fibrosis sp. nov., a novel Pandoraea species isolated from clinical respiratory samples', International Journal of Systematic and Evolutionary Microbiology, vol. 69, no. 3, pp. 645-651.
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Pandoraea species have been isolated from diverse environmental samples and are emerging important respiratory pathogens, particularly in people with cystic fibrosis (CF). In the present study, two bacterial isolates initially recovered from consecutive sputum samples collected from a CF patient and identified as Pandoraea pnomenusa underwent a polyphasic taxonomic analysis. The isolates were found to be Gram-negative, facultative anaerobic motile bacilli and subsequently designated as strains 6399T (=LMG29626T=DSM103228T) and 7641 (=LMG29627=DSM103229), respectively. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that 6399T and 7641 formed a distinct phylogenetic lineage within the genus Pandoraea. Genome sequence comparison analysis indicated that strains 6399T and 7641 are clonal and share 100 % similarity, however, similarity to other type strains (ANIb 73.2-88.8 %, ANIm 83.5-89.9 % and OrthoANI 83.2-89.3 %) indicates that 6399T and 7641 do not belong to any of the reported type species. The major cellular fatty acids of 6399T were C16 : 0 (32.1 %) C17 : 0cyclo (18.7 %) and C18 : 1ω7c (14.5 %), while Q-8 was the only respiratory quinone detected. The major polar lipids identified were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of 6399T was 62.9 (mol%). Strain 6399T can be differentiated from other members of Pandoraea by the absence of C19 : 0ω8c cyclo and by the presence of C17 : 0ω8c cyclo. Together our data show that the bacterial strains 6399T and 7641 represent a novel species of the genus Pandoraea, for which the name Pandoraea fibrosis sp. nov. is proposed (type strain 6399T).

Segečová, A, Pérez-Bueno, ML, Barón, M, Červený, J & Roitsch, TG 2019, 'Noninvasive determination of toxic stress biomarkers by high-throughput screening of photoautotrophic cell suspension cultures with multicolor fluorescence imaging', Plant Methods, vol. 15, no. 1.
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Background:With increasing pollution, herbicide application and interest in plant phenotyping, sensors capturing early responses to toxic stress are demanded for screening susceptible or resistant plant varieties. Standard toxicity tests on plants are laborious, demanding in terms of space and material, and the measurement of growth-inhibition based endpoints takes relatively long time. The aim of this work was to explore the potential of photoautotrophic cell suspension cultures for high-throughput early toxicity screening based on imaging techniques. The investigation of the universal potential of fluorescence imaging methods involved testing of three toxicants with different modes of action (DCMU, glyphosate and chromium). Results:The increased pace of testing was achieved by using non-destructive imaging methods-multicolor fluorescence (MCF) and chlorophyll fluorescence (ChlF). These methods detected the negative effects of the toxicants earlier than it was reflected in plant growth inhibition (decrease in leaf area and final dry weight). Moreover, more subtle and transient effects not resulting in growth inhibition could be detected by fluorescence. The pace and sensitivity of stress detection was further enhanced by using photoautotrophic cell suspension cultures. These reacted sooner, more pronouncedly and to lower concentrations of the tested toxicants than the plants. Toxicant-specific stress signatures were observed as a combination of MCF and ChlF parameters and timing of the response. Principal component analysis was found to be useful for reduction of the collected multidimensional data sets to a few informative parameters allowing comparison of the toxicant signatures. Conclusions:Photoautotrophic cell suspension cultures have proved to be useful for rapid high-throughput screening of toxic stress and display a potential for employment as an alternative to tests on whole plants. The MCF and ChlF methods are capable of distinguishing early stress sig...

Seguro, I, Marca, AD, Painting, SJ, Shutler, JD, Suggett, DJ & Kaiser, J 2019, 'High-resolution net and gross biological production during a Celtic Sea spring bloom', Progress in Oceanography, vol. 177, pp. 101885-101885.
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© 2017 The Authors Shelf seas represent only 10% of the ocean area, but support up to 30% of all oceanic primary production. There are few measurements of shelf-sea biological production at high spatial and temporal resolution in such heterogeneous and physically dynamic systems. Here, we use dissolved oxygen-to-argon (O2/Ar) ratios and oxygen triple isotopes (16O, 17O, 18O) to estimate net and gross biological production in the Celtic Sea during spring 2015. O2/Ar ratios were measured continuously using a shipboard membrane inlet mass spectrometer (MIMS). Additional discrete water samples from CTD hydrocasts were used to measure O2/Ar depth profiles and the δ(17O) and δ(18O) values of dissolved O2. These high-resolution data were combined with wind-speed based gas exchange parameterisations to calculate biologically driven air-sea oxygen fluxes. After correction for disequilibrium terms and diapycnal diffusion, these fluxes yielded estimates of net community (N(O2/Ar)) and gross O2 production (G(17O)). N(O2/Ar) was spatially heterogeneous and showed predominantly autotrophic conditions, with an average of (33 ± 41) mmol m−2 d−1. G(17O) showed high variability between 0 and 424 mmol m−2 d−1. The ratio of N(O2/Ar) to G(17O), ƒ(O2), was (0.18 ± 0.03) corresponding to 0.34 ± 0.06 in carbon equivalents. We also observed rapid temporal changes in N(O2/Ar), e.g. an increase of 80 mmol m−2 d−1 in <6 h during the spring bloom, highlighting the importance of high-resolution biological production measurements. Such measurements will help reconcile the differences between satellite and in situ productivity observations, and improve our understanding of the biological carbon pump.

Shah Mohammadi, N, Buapet, P, Pernice, M, Signal, B, Kahlke, T, Hardke, L & Ralph, PJ 2019, 'Transcriptome profiling analysis of the seagrass, Zostera muelleri under copper stress', Marine Pollution Bulletin, vol. 149, pp. 110556-110556.
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Copper (Cu) in an essential trace metal but it can also contaminate coastal waters at high concentrations mainly from agricultural run-off and mining activities which are detrimental to marine organisms including seagrasses. The molecular mechanisms driving Cu toxicity in seagrasses are not clearly understood yet. Here, we investigated the molecular responses of the Australian seagrass, Z. muelleri at the whole transcriptomic level after 7 days of exposure to 250 μg Cu L-1 and 500 μg Cu L-1. The leaf-specific whole transcriptome results showed a concentration-dependent disturbance in chloroplast function, regulatory stress responses and defense mechanisms. This study provided new insights into the responses of seagrasses to trace metal stress and reports possible candidate genes which can be considered as biomarkers to improve conservation and management of seagrass meadows.

Shahcheraghi, N, Gentle, A, Supansomboon, S, Keast, V & Cortie, MB 2019, 'Localized surface plasmons in platinum aluminide semi-shells', Nano Futures, vol. 3, no. 1, pp. 015003-015003.
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© 2019 IOP Publishing Ltd. The dielectric function of the intermetallic compound PtAl2 is assessed and found to be comparable to that of titanium nitride, suggesting that nanostructures of PtAl2 may be suitable for plasmonic devices. In order to probe this further, the optical properties of experimentally produced arrays of nanoscale PtAl2 semi-shells of about 300 nm diameter were examined and compared to the results of numerical simulations. The structures showed a broad localized surface plasmon resonance centered on ∼1.3 eV (∼950 nm), which matched the simulations. Calculations showed that a ten-fold enhancement of the electric field of the incident light will be achieved around the rim of suitably oriented PtAl2 semi-shells. The phase of the oscillation induced by 1060 nm light will be retarded by π/2 relative to the incident light. This is indicative of a resonant condition. These observations suggest that it could be worthwhile to investigate possible applications for this and other intermetallic compounds in nanoscale plasmonic devices.

Shahid, A, Ishfaq, M, Ahmad, MS, Malik, S, Farooq, M, Hui, Z, Batawi, AH, Shafi, ME, Aloqbi, AA, Gull, M & Mehmood, MA 2019, 'Bioenergy potential of the residual microalgal biomass produced in city wastewater assessed through pyrolysis, kinetics and thermodynamics study to design algal biorefinery', Bioresource Technology, vol. 289, pp. 121701-121701.
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The suitability of integrating biological and thermal transformation of microalgal biomass to design a biorefinery was studied. The mixed cultivation of Chlorella sp. and Bracteacoccus sp. in city wastewater produced 12 g L-1 of biomass (0.77 g L-1 day-1) and removed nitrates and phosphates by 68% and 75%, respectively. Microalgae outcompeted the contaminating microbes by raising the pH of wastewater to 9.93. The lipid-free residual biomass was pyrolyzed at four heating rates (10, 20, 30, 40 °C min-1) which showed a three-stage pyrolysis. The activation energies (182-256 kJ mol-1) and their corresponding lower enthalpies at the conversional fractions from 0.2 to 0.6 indicated that product formation was being favored. The values of pre-exponential factors (1015-17 s-1), Gibbs free energy (159-190 kJ mol-1) and entropy (43-81 J mol-1) showed efficient pyrolysis. The data may lead to establish a robust microalgal biorefinery to produce biomass and energy along with primary treatment of city wastewater.

Shalini, Johansen, MD, Kremer, L & Kumar, V 2019, 'Design, synthesis, anti‐mycobacterial and cytotoxic evaluation of C‐4 functionalized 1,8‐naphthalimide‐heterocyclic hydrazide conjugates', Chemical Biology & Drug Design, vol. 94, no. 1, pp. 1300-1305.
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AbstractThis manuscript discloses the design and synthesis of a series of C‐4 functionalized 1,8‐naphthalimide‐heterocyclic hydrazide conjugates along with their anti‐mycobacterial and cytotoxic evaluation. The present work assumes significance as it describes the first report on the amalgamation of C‐4 substituted naphthalimides with various heterocyclic hydrazides. However, contrary to the rationale behind the synthesis of the conjugates, none of them inhibited the growth of Mycobacterium tuberculosis at the tested concentrations though these were non‐cytotoxic towards the Vero kidney epithelial cell line.

Shalini, Johansen, MD, Kremer, L & Kumar, V 2019, 'Variedly connected 1,8-naphthalimide-7-chloroquinoline conjugates: Synthesis, anti-mycobacterial and cytotoxic evaluation', Bioorganic Chemistry, vol. 92, pp. 103241-103241.
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Shan, L, Yang, X & Zhu, Q 2019, 'Effects of DEM resolutions on LS and hillslope erosion estimation in a burnt landscape', Soil Research, vol. 57, no. 7, pp. 797-797.
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The combined slope length and slope steepness factor (LS) is crucial in soil erosion models such as the revised universal soil loss equation (RUSLE), and is often calculated from digital elevation models (DEMs). With high-resolution DEMs becoming increasingly available in recent years, we face considerable challenges in selecting the optimal DEM for erosion modelling. In this paper, we present a case study on LS factor computation using various DEMs at resolutions ranging from 1 to 90 m over a burnt national park in New South Wales, Australia, aiming to assess the effects of DEM resolution on LS and hillslope erosion estimation. The LS was calculated based on RUSLE specifications and incorporated a variable cutoff slope angle that improves the detection of the beginning and the end of each slope length. Results show the trend of an increase in the estimated LS value as the DEM resolution became coarser. We consider 5–10-m DEMs to have optimal resolution because the LS values calculated at this range were closer to the LS values measured at the 12 soil plots over the study area. We also assessed different sampling methods for LS value extraction and statistical analysis. The sampling method based on contributing area was more representative compared with point-based and buffer sampling methods. Findings from this study will be useful for choosing the optimal DEM resolution and sampling method in hillslope erosion modelling.

Shandilya, PK, Fröch, JE, Mitchell, M, Lake, DP, Kim, S, Toth, M, Behera, B, Healey, C, Aharonovich, I & Barclay, PE 2019, 'Hexagonal Boron Nitride Cavity Optomechanics', Nano Letters, vol. 19, no. 2, pp. 1343-1350.
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Copyright © 2019 American Chemical Society. Hexagonal boron nitride (hBN) is an emerging layered material that plays a key role in a variety of two-dimensional devices, and has potential applications in nanophotonics and nanomechanics. Here, we demonstrate the first cavity optomechanical system incorporating hBN. Nanomechanical resonators consisting of hBN beams with average dimensions of 12 μm × 1.2 μm × 28 nm and minimum predicted thickness of 8 nm were fabricated using electron beam induced etching and positioned in the optical near-field of silicon microdisk cavities. Of the multiple devices studied here a maximum 0.16 pm/Hz sensitivity to the hBN nanobeam motion is demonstrated, allowing observation of thermally driven mechanical resonances with frequencies between 1 and 23 MHz, and largest mechanical quality factor of 1100 for a 23 MHz mode, at room temperature in high vacuum. In addition, the role of air damping is studied via pressure dependent measurements. Our results constitute an important step toward realizing integrated optomechanical circuits employing hBN.

Sharif, HMA, Mahmood, A, Cheng, H-Y, Djellabi, R, Ali, J, Jiang, W-L, Wang, S-S, Haider, MR, Mahmood, N & Wang, A-J 2019, 'Fe₃O₄ Nanoparticles Coated with EDTA and Ag Nanoparticles for the Catalytic Reduction of Organic Dyes from Wastewater', ACS Applied Nano Materials, vol. 2, no. 8, pp. 5310-5319.
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Sharma, P, Mehta, M, Dhanjal, DS, Kaur, S, Gupta, G, Singh, H, Thangavelu, L, Rajeshkumar, S, Tambuwala, M, Bakshi, HA, Chellappan, DK, Dua, K & Satija, S 2019, 'Emerging trends in the novel drug delivery approaches for the treatment of lung cancer', Chemico-Biological Interactions, vol. 309, pp. 108720-108720.
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© 2019 Elsevier B.V. Cancer is one of the major diseases that cause a high number of deaths globally. Of the major types of cancers, lung cancer is known to be the most chronic form of cancer in the world. The conventional management of lung cancer includes different medical interventions like chemotherapy, surgical removal, and radiation therapy. However, this type of approach lacks specificity and also harms the adjacent normal cells. Lately, nanotechnology has emerged as a promising intervention in the management and treatment of lung cancers. Nanotechnology has revolutionized the existing modalities and focuses primarily on reducing toxicity and improving the bioavailability of anticancer drugs to the target tumor cells. Nanocarrier systems are being currently used extensively to exploit and to overcome the obstructions induced by cancers in the lungs. The nano-carrier-loaded therapeutic drug delivery methods have shown promising potential in treating lung cancer as its target is to control the growth of tumor cells. In this review, various modes of nano drug delivery options like liposomes, dendrimers, quantum dots, carbon nanotubes and metallic nanoparticles have been discussed. Nano-carrier drug delivery systems emerge as a promising approach and thus is expected to provide newer and advanced avenues in cancer therapeutics.

SHARMA, S, MANN, R, KUMAR, S, MISHRA, N, SRIVASTAVA, B, VALECHA, N & R. ANVIKAR, A 2019, 'A Simple and Cost-Effective Freeze-Thaw Based Method for Plasmodium DNA Extraction from Dried Blood Spot', Iranian Journal of Parasitology, vol. 14, no. 1, pp. 29-40.
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Background: Available DNA isolation methods for Plasmodium involve numerous processing steps, adding to the cost and conferring risk of contamination. Here we devise a simple and cost-effective method for direct extraction of Plasmodium DNA from dried filter paper spot (DBS), appropriate for resource-limited setups. Methods: The protocol involves simple freezing and thawing of DBS, neither involves any purification step nor any chemical reagent. The method was assessed in terms of DNA quantity, PCR detection sensitivity, time requirement, cost effectiveness, labor intensiveness and degree of shearing. The reliability of this method was confirmed by comparing it with other in use methods for Plasmodium DNA isolation. Results: Pure DNA was obtained with this method, as exemplified by the absorbance ratio (260nm /280nm) of 1.2. The protocol produced digestible, PCR-grade genomic DNA, also found to be suitable for sequencing. DNA isolated remained stable and retained its integrity after storage for one month at 4 0C. Conclusion: Our process substantiated as efficient, reproducible, simple, fast, and inexpensive. Development of this optimized freeze-thaw based DNA extraction method for malaria parasite may provide a valuable tool for molecular analysis in resource-limited setups. This is the first report of DNA extraction from DBS of Plasmodium utilizing freeze-thaw.

She, L, Xue, Y, Yang, X, Leys, J, Guang, J, Che, Y, Fan, C, Xie, Y & Li, Y 2019, 'Joint Retrieval of Aerosol Optical Depth and Surface Reflectance Over Land Using Geostationary Satellite Data', IEEE Transactions on Geoscience and Remote Sensing, vol. 57, no. 3, pp. 1489-1501.
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© 1980-2012 IEEE. The advanced Himawari imager (AHI) aboard the Himawari-8 geostationary satellite provides high-frequency observations with broad coverage, multiple spectral channels, and high spatial resolution. In this paper, AHI data were used to develop an algorithm for joint retrieval of aerosol optical depth (AOD) over land and land surface bidirectional reflectance. Instead of performing surface reflectance estimation before calculating AOD, the AOD and surface bidirectional reflectance were retrieved simultaneously using an optimal estimation method. The algorithm uses an atmospheric radiative transfer model coupled with a surface bidirectional reflectance factor (BRF) model. Based on the assumption that the surface bidirectional reflective properties are invariant during a short time period (i.e., a day), multiple temporal AHI observations were combined to calculate the AOD and surface BRF. The algorithm was tested over East Asia for year 2016, and the AOD retrieval results were validated against the aerosol robotic network (AERONET) sites observation and compared with the Moderate Resolution Imaging Spectroradiometer Collection 6.0 AOD product. The validation of the retrieved AOD with AERONET measurements using 14 713 colocation points in 2016 over East Asia shows a high correlation coefficient: R = 0.88 , root-mean-square error = 0.17, and approximately 69.9% AOD retrieval results within the expected error of ± 0.2 AOD AERONET ±0.05. A brief comparison between our retrieval and AOD product provided by Japan Meteorological Agency is also presented. The comparison and validation demonstrates that the algorithm has the ability to estimate AOD with considerable accuracy over land.

Shea, DJ, Nishida, N, Takada, S, Itabashi, E, Takahashi, S, Akter, A, Miyaji, N, Osabe, K, Mehraj, H, Shimizu, M, Seki, M, Kakizaki, T, Okazaki, K, Dennis, ES & Fujimoto, R 2019, 'Long noncoding RNAs in Brassica rapa L. following vernalization', Scientific Reports, vol. 9, no. 1.
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AbstractBrassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.

Shrestha, J, Ghadiri, M, Shanmugavel, M, Razavi Bazaz, S, Vasilescu, S, Ding, L & Ebrahimi Warkiani, M 2019, 'A rapidly prototyped lung-on-a-chip model using 3D-printed molds', Organs-on-a-Chip, vol. 1, pp. 100001-100001.
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Shukla, SD, Shastri, MD, Chong, WC, Dua, K, Budden, KF, Mahmood, MQ, Hansbro, NG, Keely, S, Eri, R, Patel, RP, Peterson, GM & Hansbro, PM 2019, 'Microbiome-focused asthma management strategies', Current Opinion in Pharmacology, vol. 46, pp. 143-149.
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© 2019 Elsevier Ltd Asthma is a common, heterogeneous and serious disease with high prevalence globally. Poorly controlled, steroid-resistant asthma is particularly important as there are no effective therapies and it exerts substantial healthcare and societal burden. The role of microbiomes, particularly in chronic diseases has generated considerable interest in recent times. Existing evidence clearly demonstrates an association between asthma initiation and the microbiome, both respiratory and gastro-intestinal, although its’ roles are poorly understood when assessing the asthma progression or heterogeneity (i.e. phenotypes/endotypes) across different geographical locations. Moreover, modulating microbiomes could be preventive and/or therapeutic in patients with asthma warrants urgent attention. Here, we review recent advances in assessing the role of microbiomes in asthma and present the challenges associated with the potential therapeutic utility of modifying microbiomes in management.

Siddique, J, Daniels, MJ, Carroll, RJ, Raghunathan, TE, Stuart, EA & Freedman, LS 2019, 'Measurement Error Correction and Sensitivity Analysis in Longitudinal Dietary Intervention Studies Using an External Validation Study', Biometrics, vol. 75, no. 3, pp. 927-937.
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Abstract In lifestyle intervention trials, where the goal is to change a participant's weight or modify their eating behavior, self-reported diet is a longitudinal outcome variable that is subject to measurement error. We propose a statistical framework for correcting for measurement error in longitudinal self-reported dietary data by combining intervention data with auxiliary data from an external biomarker validation study where both self-reported and recovery biomarkers of dietary intake are available. In this setting, dietary intake measured without error in the intervention trial is missing data and multiple imputation is used to fill in the missing measurements. Since most validation studies are cross-sectional, they do not contain information on whether the nature of the measurement error changes over time or differs between treatment and control groups. We use sensitivity analyses to address the influence of these unverifiable assumptions involving the measurement error process and how they affect inferences regarding the effect of treatment. We apply our methods to self-reported sodium intake from the PREMIER study, a multi-component lifestyle intervention trial.

Sillapachaiyaporn, C, Nilkhet, S, Ung, AT & Chuchawankul, S 2019, 'Anti-HIV-1 protease activity of the crude extracts and isolated compounds from Auricularia polytricha', BMC Complementary and Alternative Medicine, vol. 19, no. 1.
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Abstract Background Acquired immunodeficiency syndrome (AIDS) is caused by the Human immunodeficiency virus type-1 (HIV-1). HIV-1 protease (HIV-1 PR) is an essential enzyme for the HIV replication, and therefore, it is an important target for antiretroviral drugs development, particularly from natural products. Auricularia polytricha (AP) is an edible mushroom with several important therapeutic properties. These properties will be investigated as HIV-1 PR inhibitors. Methods The sequential hexane (APH), ethanol (APE) and water (APW) extracts from AP were screened for inhibitory activity against HIV-1 PR. The extract that consistently showed the strong HIV-1 PR inhibition was further investigated for its phytochemical constituents. The compounds were purified by column chromatography. The isolated compounds were structurally elucidated using 1D and 2D NMR, HRMS, FTIR, and GC/MS techniques. Each compound was screened against HIV-1 PR to determine its inhibitory activity and to provide an explanation for the activity found in the extract. Results Hexane crude extract of AP (APH) exhibited significant inhibition on HIV-1 PR activity. Four major compounds isolated from APH fraction were identified to be two triacylglycerols, linoleic acid and ergosterol. Moreover, all four compounds showed significant inhibition of HIV-1 PR activity. Conclusion The findings from this study suggest that AP is a good source of fatty esters, fatty acids and ergosterol. These natural products exhibit anti-HIV-1 properties by block...

Simoniello, C, Jencks, J, Lauro, FM, Loftis, JD, Weslawski, JM, Deja, K, Forrest, DR, Gossett, S, Jeffries, TC, Jensen, RM, Kobara, S, Nolan, L, Ostrowski, M, Pounds, D, Roseman, G, Basco, O, Gosselin, S, Reed, A, Wills, P & Wyatt, D 2019, 'Citizen-Science for the Future: Advisory Case Studies From Around the Globe', Frontiers in Marine Science, vol. 6, no. May.
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© 2019 Simoniello, Jencks, Lauro, Loftis, Weslawski, Deja, Forrest, Gossett, Jeffries, Jensen, Kobara, Nolan, Ostrowski, Pounds, Roseman, Basco, Gosselin, Reed, Wills and Wyatt. The democratization of ocean observation has the potential to add millions of observations every day. Though not a solution for all ocean monitoring needs, citizen scientists offer compelling examples showcasing their ability to augment and enhance traditional research and monitoring. Information they are providing is increasing the spatial and temporal frequency and duration of sampling, reducing time and labor costs for academic and government monitoring programs, providing hands-on STEM learning related to real-world issues and increasing public awareness and support for the scientific process. Examples provided here demonstrate the wide range of people who are already dramatically reducing gaps in our global observing network while at the same time providing unique opportunities to meaningfully engage in ocean observing and the research and conservation it supports. While there are still challenges to overcome before widespread inclusion in projects requiring scientific rigor, the growing organization of international citizen science associations is helping to reduce barriers. The case studies described support the idea that citizen scientists should be part of an effective global strategy for a sustained, multidisciplinary and integrated observing system.

Singh, H, Mehta, M, Khurana, N, Sharma, N, Vyas, M, Singh, TG, Mahajan, S & Satija, S 2019, 'Recent patent technologies of tinospora cordifolia for anti-diabetic potential: A review', Plant Archives, vol. 19, pp. 994-999.
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Diabetes Mellitus has been considered an epidemic with great threat of other illness and death by the World Health Organization. The treatment of this pathology consists of glycemic control, which can be done by oral hypoglycemic agents, insulin therapy, dietary guidance, regular physical activity, and psychosocial support. In addition, other adjuvant treatments are employed, such as phototherapy, and one of the most used plants is Tinospora cordifolia. In the current review, patents using Tinospora cordifolia for the Diabetes Mellitus treatment have been analyzed and discussed. Although there are some phytotherapy products containing this medicinal plant which has hypoglycemic effect, here is still a need for the development of more products based on natural resources, for the treatment of this pathology, without side effects and with other benefits, to assist in the control of glycemic level in patients with diabetes mellitus, and to improve their quality of life.

Singh, H, Satija, S, Kaur, H, Khurana, N, Sharma, N, Vyas, M, Singh, TG, Mahajan, S & Mehta, M 2019, 'Novel drug delivery approaches for guggul', Plant Archives, vol. 19, pp. 983-993.
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Guggul, an oleo gum resin released from Commiphora weightii, known for its immense applicability as hypolipidemic, anti-inflammatory, antioxidant, thyroid stimulatory agent, Platelet aggregation, fibrinolytic agent and the cytotoxic agent. Guggulsterones i.e. E & Z guggulsterones are the major constituents responsible for its pharmacological use. Traditionally, it's been used as antimalarial, antidysenteric, anticholesterolemic, antihypertensive, anti-rheumatic and indicated for many clinical conditions like dysmenorrhea, dyspepsia, impotence, leprosy, leucoderma, anemia etc. Nowadays, Guggul is available as the marketed formulation for curing numerous clinical conditions and is accessible in combination with various other ingredients. Though conventional dosage form shows the dominance as patient compliance and easy availability, yet it has found to pose the problems like dose fluctuation, peak-valley effect, non-adjustment of the administered drug, invasiveness etc. Guggul lacks its desired effect due to its low bioavailability and less water solubility. This makes it a partial or a deficient therapy for remedy of many signs and symptoms. Novel drug delivery system (NDDS), a new approach in the pharma sector has excluded many of drawbacks exhibited by conventional dosage forms. Some of the novel dosage forms of guggul has been formed like nanoparticles, nanovesicles, gugglusomes and proniosomal gel. But still, the novel formulations for guggul has its less outspread in the market. Guggul can be executed as a profitable drug using NDDS. There is a need to highlight the unidentified and unexplained facts about guggul so as to make it more efficacious and effective in terms of bioavailability and aqueous insolubility.

Singh, M, Saini, B, Singh, TG, Chander, J, Satija, S & Arora, S 2019, 'Design, synthesis and biological evaluation of chalcone based compounds in Alzheimer's disease', Plant Archives, vol. 19, pp. 1317-1322.
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Alzheimer's disease (AD), a complex neurodegenerative brain disorder, a most common cause of dementia among elderly people. To date, the AD is being managed by maintaining the levels of acetylcholine by inhibiting acetylcholinesterase (AChE). Following this approach, a new series of Chalcones were designed, synthesized and biologically evaluated against acetylcholinesterase (AChE) with additional free radical scavenging activity. The in vitro studies showed that the majority of synthesized derivatives inhibited acetylcholinesterase (AChE) with IC50 values in the micro molar range. Some of the derivatives strongly inhibited AChE. Besides AChE inhibitory activity, these compounds also exhibited greater ability to scavenge free radicals. Thus, chalcones might be the promising lead compound as potential anti-Alzheimer's agents.

Smith, MJA, Wolff, C, Poulton, CG & Martijn de Sterke, C 2019, 'Stimulated Brillouin scattering in layered media: nanoscale enhancement of silicon', Optics Letters, vol. 44, no. 6, pp. 1407-1407.
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© 2019 Optical Society of America. We report a theoretical study of stimulated Brillouin scattering (SBS) in general anisotropic media, incorporating the effects of both acoustic strain and local rotation. We apply our general theoretical framework to compute the SBS gain for layered media with periodic length scales smaller than all optical and acoustic wavelengths, where such composites behave like homogeneous anisotropic media. We predict that a layered medium composing nanometer-thin layers of silicon and As 2 S 3 glass has a bulk SBS gain of 1.28 × 10− 9 W −1 m. This is more than 500 times larger than that of silicon and almost double the gain of As 2 S 3 . The enhancement is due to a combination of roto-optic, photoelastic, and artificial photoelastic contributions in the composite structure.

Söderström, B, Chan, H & Daley, DO 2019, 'Super-resolution images of peptidoglycan remodelling enzymes at the division site of Escherichia coli', Current Genetics, vol. 65, no. 1, pp. 99-101.
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© 2018, The Author(s). Bacterial cells need to divide. This process requires more than 30 different proteins, which gather at the division site. It is widely assumed that these proteins assemble into a macromolecular complex (the divisome), but capturing the molecular layout of this complex has proven elusive. Super-resolution microscopy can provide spatial information, down to a few tens of nanometers, about how the division proteins assemble into complexes and how their activities are co-ordinated. Herein we provide insight into recent work from our laboratories, where we used super-resolution gSTED nanoscopy to explore the molecular organization of FtsZ, FtsI and FtsN. The resulting images show that all three proteins form discrete densities organised in patchy pseudo-rings at the division site. Significantly, two-colour imaging highlighted a radial separation between FtsZ and FtsN, indicating that there is more than one type of macromolecular complex operating during division. These data provide a first glimpse into the spatial organisation of PG-synthesising enzymes during division in Gram-negative bacteria.

Solina, D, Schmidt, W, Kaltofen, R, Krien, C, Lai, C-H & Schreyer, A 2019, 'The magnetic structure of L1₀ ordered MnPt at room temperature determined using polarized neutron diffraction', Materials Research Express, vol. 6, no. 7, pp. 076105-076105.
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© 2019 IOP Publishing Ltd. Neutron scattering studies have been carried out on single crystal films of [001] orientated L10 ordered MnPt grown epitaxially on MgO (001) using DC magnetron sputtering. Polarized neutron diffraction studies at room temperature show that the moments in ordered MnPt are aligned perpendicular to the [001] axis with a tilt of 45° to the [100] axis and not parallel to [100] as inferred from previous powder neutron diffraction measurements.

Sommer, B, Fowler, AM, Macreadie, PI, Palandro, DA, Aziz, AC & Booth, DJ 2019, 'Decommissioning of offshore oil and gas structures – Environmental opportunities and challenges', Science of The Total Environment, vol. 658, pp. 973-981.
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© 2018 Elsevier B.V. Thousands of offshore oil and gas structures are approaching the end of their operating life globally, yet our understanding of the environmental effects of different decommissioning strategies is incomplete. Past focus on a narrow set of criteria has limited evaluation of decommissioning effects, restricting decommissioning options in most regions. We broadly review the environmental effects of decommissioning, analyse case studies, and outline analytical approaches that can advance our understanding of ecological dynamics on oil and gas structures. We find that ecosystem functions and services increase with the age of the structure and vary with geographical setting, such that decommissioning decisions need to take an ecosystem approach that considers their broader habitat and biodiversity values. Alignment of decommissioning assessment priorities among regulators and how they are evaluated, will reduce the likelihood of variable and sub-optimal decommissioning decisions. Ultimately, the range of allowable decommissioning options must be expanded to optimise the environmental outcomes of decommissioning across the broad range of ecosystems in which platforms are located.

Song, J, Guo, X, Zhang, J, Chen, Y, Zhang, C, Luo, L, Wang, F & Wang, G 2019, 'Rational design of free-standing 3D porous MXene/rGO hybrid aerogels as polysulfide reservoirs for high-energy lithium–sulfur batteries', Journal of Materials Chemistry A, vol. 7, no. 11, pp. 6507-6513.
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A Ti₃C₂T_x MXene/rGO hybrid aerogel is applied for the first time as a free-standing polysulfide reservoir to inhibit the shuttle effect and improve the overall performance of Li–S batteries.

Song, Y, Liew, JH, Sim, DZH, Mowe, MAD, Mitrovic, SM, Tan, HTW & Yeo, DCJ 2019, 'Effects of macrophytes on lake‐water quality across latitudes: a meta‐analysis', Oikos, vol. 128, no. 4, pp. 468-481.
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Macrophytes are widely recognized for improving water quality and stabilizing the desirable clear‐water state in lakes. The positive effects of macrophytes on water quality have been noted to be weaker in the (sub)tropics compared to those of temperate regions. We conducted a global meta‐analysis using 47 studies that met our set criteria to assess the overall effects of macrophytes on water quality (measured by phytoplankton chlorophyll a concentration, total nitrogen concentration, total phosphorus concentration, Secchi depth and the trophic state index) and to investigate how these effects correlate with latitude using meta‐regressions. We also examined if the effects of macrophytes on lake‐water quality differ with growth form and study design in (sub)tropical and temperate areas by grouping the data and then comparing the effect sizes. We found that macrophytes significantly reduced phytoplankton chlorophyll a concentration, total nitrogen concentration, total phosphorus concentration, as well as the trophic state index, but they did not have a significant overall effect on Secchi depth. The effects of macrophytes on reducing phytoplankton chlorophyll a concentration, total nitrogen concentration and the trophic state index did not differ with latitude. However, the reduction of total phosphorus concentration was greater at lower latitudes. We showed that at lower latitudes, the positive effects of macrophytes on water quality are similar to or greater than those at higher latitudes, thus challenging the prevailing paradigm of macrophytes being less effective at enhancing lake‐water quality in the (sub)tropics. Furthermore, our data showed that the macrophyte effects vary by growth forms, and the growth forms that positively affect water quality differ between the (sub)tropical and temperate areas. We showed a lack of significant macrophyte effects in surveys w...

Song, Y, Mowe, MAD, Mitrovic, SM, Tan, HTW & Yeo, DCJ 2019, 'An ex-situ mesocosm study of emergent macrophyte effects on phytoplankton communities', Fundamental and Applied Limnology, vol. 192, no. 3, pp. 225-235.
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Soon, L, Ng, PQ, Chellian, J, Madheswaran, T, Panneerselvam, J, Gupta, G, Nammi, S, Hansbro, NG, Hsu, A, Dureja, H, Mehta, M, Satija, S, Hansbro, PM, Dua, K, Collet, T & Chellappan, DK 2019, 'Therapeutic potential of Artemisia vulgaris: An insight into underlying immunological mechanisms', Journal of Environmental Pathology, Toxicology and Oncology, vol. 38, no. 3, pp. 205-216.
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© 2019 by Begell House, Inc. Artemisia vulgaris is a traditional Chinese herb believed to have a wide range of healing properties; it is traditionally used to treat numerous health ailments. The plant is commonly called mugwort or riverside wormwood. The plant is edible, and in addition to its medicinal properties, it is also used as a culinary herb in Asian cooking in the form of a vegetable or in soup. The plant has garnered the attention of researchers in the past few decades, and several research studies have investigated its biological effects, including antioxidant, anti-inflammatory, anticancer, hypolipidemic, and antimicrobial properties. In this review, various studies on these biological effects are discussed along with the tests conducted, compounds involved, and proposed mechanisms of action. This review will be of interest to the researchers working in the field of herbal medicine, pharmacology, medical sciences, and immunology.

Sproles, AE, Oakley, CA, Matthews, JL, Peng, L, Owen, JG, Grossman, AR, Weis, VM & Davy, SK 2019, 'Proteomics quantifies protein expression changes in a model cnidarian colonised by a thermally tolerant but suboptimal symbiont', The ISME Journal, vol. 13, no. 9, pp. 2334-2345.
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Abstract The acquisition of thermally tolerant algal symbionts by corals has been proposed as a natural or assisted mechanism of increasing coral reef resilience to anthropogenic climate change, but the cell-level processes determining the performance of new symbiotic associations are poorly understood. We used liquid chromatography–mass spectrometry to investigate the effects of an experimentally induced symbiosis on the host proteome of the model sea anemone Exaiptasia pallida. Aposymbiotic specimens were colonised by either the homologous dinoflagellate symbiont (Breviolum minutum) or a thermally tolerant, ecologically invasive heterologous symbiont (Durusdinium trenchii). Anemones containing D. trenchii exhibited minimal expression of Niemann-Pick C2 proteins, which have predicted biochemical roles in sterol transport and cell recognition, and glutamine synthetases, which are thought to be involved in nitrogen assimilation and recycling between partners. D. trenchii-colonised anemones had higher expression of methionine-synthesising betaine–homocysteine S-methyltransferases and proteins with predicted oxidative stress response functions. Multiple lysosome-associated proteins were less abundant in both symbiotic treatments compared with the aposymbiotic treatment. The differentially abundant proteins are predicted to represent pathways that may be involved in nutrient transport or resource allocation between partners. These results provide targets for specific experiments to elucidate the mechanisms underpinning compensatory physiology in the coral–dinoflagellate symbiosis.

Stangenberg, S, Nguyen, LT, Chan, YL, Zaky, A, Pollock, CA, Chen, H & Saad, S 2019, 'Maternal L‐carnitine supplementation ameliorates renal underdevelopment and epigenetic changes in male mice offspring due to maternal smoking', Clinical and Experimental Pharmacology and Physiology, vol. 46, no. 2, pp. 183-193.
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SummaryObjectivesEpidemiological and animal studies showed that L‐carnitine (LC) supplementation can ameliorate oxidative stress‐induced tissues damage. We have previously shown that maternal cigarette smoke exposure (SE) can increase renal oxidative stress in newborn offspring with postnatal kidney underdevelopment and renal dysfunction in adulthood, which were normalised by LC administration in the SE dams during pregnancy. Exposure to an adverse intrauterine environment may lead to alteration in the epigenome, a mechanism by which adverse prenatal conditions increase the susceptibility to chronic disease later in life. The current study aimed to determine whether maternal SE induces epigenetic changes in the offspring's kidney are associated with renal underdevelopment, and the protective effect of maternal LC supplementation.MethodFemale Balb/c mice (7 weeks) were exposed to cigarette smoke (SE) or air (Sham) for 6 weeks prior to mating, during gestation and lactation. A subgroup of the SE dams received LC via drinking water (SE + LC, 1.5 mmol/L) throughout gestation and lactation. Male offspring were studied at postnatal day (P)1, P20, and 13 weeks.

Starkey, MR, McKenzie, ANJ, Belz, GT & Hansbro, PM 2019, 'Pulmonary group 2 innate lymphoid cells: surprises and challenges', Mucosal Immunology, vol. 12, no. 2, pp. 299-311.
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© 2019, Society for Mucosal Immunology. Group 2 innate lymphoid cells (ILC2s) are a recently described subset of innate lymphocytes with important immune and homeostatic functions at multiple tissue sites, especially the lung. These cells expand locally after birth and during postnatal lung maturation and are present in the lung and other peripheral organs. They are modified by a variety of processes and mediate inflammatory responses to respiratory pathogens, inhaled allergens and noxious particles. Here, we review the emerging roles of ILC2s in pulmonary homeostasis and discuss recent and surprising advances in our understanding of how hormones, age, neurotransmitters, environmental challenges, and infection influence ILC2s. We also review how these responses may underpin the development, progression and severity of pulmonary inflammation and chronic lung diseases and highlight some of the remaining challenges for ILC2 biology.

Starkey, MR, Plank, MW, Casolari, P, Papi, A, Pavlidis, S, Guo, Y, Cameron, GJM, Haw, TJ, Tam, A, Obiedat, M, Donovan, C, Hansbro, NG, Nguyen, DH, Nair, PM, Kim, RY, Horvat, JC, Kaiko, GE, Durum, SK, Wark, PA, Sin, DD, Caramori, G, Adcock, IM, Foster, PS & Hansbro, PM 2019, 'IL-22 and its receptors are increased in human and experimental COPD and contribute to pathogenesis', European Respiratory Journal, vol. 54, no. 1, pp. 1800174-1800174.
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Chronic obstructive pulmonary disease (COPD) is the third leading cause of morbidity and death globally. The lack of effective treatments results from an incomplete understanding of the underlying mechanisms driving COPD pathogenesis.Interleukin (IL)-22 has been implicated in airway inflammation and is increased in COPD patients. However, its roles in the pathogenesis of COPD is poorly understood. Here, we investigated the role of IL-22 in human COPD and in cigarette smoke (CS)-induced experimental COPD.IL-22 and IL-22 receptor mRNA expression and protein levels were increased in COPD patients compared to healthy smoking or non-smoking controls. IL-22 and IL-22 receptor levels were increased in the lungs of mice with experimental COPD compared to controls and the cellular source of IL-22 included CD4+ T-helper cells, γδ T-cells, natural killer T-cells and group 3 innate lymphoid cells. CS-induced pulmonary neutrophils were reduced in IL-22-deficient (Il22−/−) mice. CS-induced airway remodelling and emphysema-like alveolar enlargement did not occur in Il22−/− mice. Il22−/− mice had improved lung function in terms of airway resistance, total lung capacity, inspiratory capacity, forced vital capacity and compliance.These data highlight important roles for IL-22 and its receptors in human COPD and CS-induced experimental COPD.

Steiner, R, Roux, C & Moret, S 2019, 'Controlling fingermark variability for research purposes: A review', WIREs Forensic Science, vol. 1, no. 4, pp. e1338-e1338.
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AbstractFingermark detection is a very active field of research in forensic science, with many different strategies currently investigated to always improve detection rate. However, each new technique has first to be optimized, assessed and validated with many fingermarks from multiple donors across a wide variety of substrates before being included into laboratories operating procedures. This process often requires the collaboration of research groups and operational laboratories from different countries, and it takes several years for a new method to be applied routinely in casework. One particular challenge that makes the process from R&D to operations complicated is the significant intrinsic within‐ and between‐source variability of fingermarks. Many studies partially addressing fingermark variability have been reported but a comprehensive approach to the problem is yet to be found. This review describes the factors of fingermark variability and provides an extensive overview of various strategies implemented to control it. The use of artificial fingermarks or simulants, containing some of the most abundant compounds found in fingermark residue has been investigated by some research teams. However, most of these formulations are too simplistic and can only be used to assess a restrictive number of detection techniques, such as amino acid reagents. Practical applications of artificial fingermarks such as test strips and proficiency testing are reviewed. The advantage and challenges of using artificial fingermarks in the first stages of fingermark detection research are presented.This article is categorized under:Forensic Chemistry and Trace Evidence > Fingermarks and Other Marks

Stewart, C, Kianinia, M, Previdi, R, Tran, TT, Aharonovich, I & Bradac, C 2019, 'Quantum emission from localized defects in zinc sulfide', Optics Letters, vol. 44, no. 19, pp. 4873-4873.
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© 2019 Optical Society of America Single-photon sources in solid-state systems are widely explored as fundamental constituents of numerous quantum-based technologies. We report the observation of single-photon emitters in zinc sulfide and present their photo-physical properties via established spectroscopy techniques. The emitter behaves like a three-level system with an intermediate metastable state. It emits at ∼640 nm, and its emission is linearly polarized, with a lifetime of (2.2 ± 0.8) ns. The existence of single-photon sources in zinc sulfide is appealing due to the well-established manufacturing techniques of the material, its versatile technological uses, as well as the availability of many zinc isotopes with potential for designing ad hoc emitter–host pairs with tailored properties.

Stiller, B, Merklein, M, Vu, K, Ma, P, Madden, SJ, Poulton, CG & Eggleton, BJ 2019, 'Cross talk-free coherent multi-wavelength Brillouin interaction', APL Photonics, vol. 4, no. 4, pp. 040802-040802.
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Stimulated Brillouin scattering drives a coherent interaction between optical signals and acoustic phonons and can be used for storing optical information in acoustic waves. An important consideration arises when multiple optical frequencies are simultaneously employed in the Brillouin process: in this case, the acoustic phonons that are addressed by each optical wavelength can be separated by frequencies far smaller than the acoustic phonon linewidth, potentially leading to cross talk between the optical modes. Here we extend the concept of Brillouin-based light storage to multiple wavelength channels. We experimentally and theoretically show that the accumulated phase mismatch over the length of the spatially extended phonons allows each optical wavelength channel to address a distinct phonon mode, ensuring negligible cross talk and preserving the coherence, even if the phonons overlap in frequency. This phase-mismatch for broad-bandwidth pulses has far-reaching implications allowing dense wavelength multiplexing in Brillouin-based light storage, multifrequency Brillouin sensing and lasing, parallel microwave processing, and quantum photon-phonon interactions.

Strbenac, D, Wang, K, Wang, X, Dong, J, Mann, GJ, Mueller, S & Yang, JYH 2019, 'Melanoma Explorer: a web application to allow easy reanalysis of publicly available and clinically annotated melanoma omics data sets', Melanoma Research, vol. 29, no. 3, pp. 342-344.
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Validating newly discovered biomarkers in large, publicly available data sets is often difficult and requires specialized computer programming skills. Melanoma Explorer is a web application that enables easy interrogation of melanoma omics data sets that are freely available in online data repositories with a point-and-click interface. Two use cases are demonstrated. First, the relationship of lysozyme mRNA expression is shown to be prognostic in two independent gene expression microarray data sets. Second, a figure from a journal article showing the relationship of tumour thickness and miR-382 abundance is reproduced. Melanoma Explorer is demonstrated to be a useful tool for reproducing results of published studies and providing additional evidence for biomarkers in independent data sets.

Stuart, BH, Thomas, PS, Barrett, M & Head, K 2019, 'Modelling clay materials used in artworks: an infrared spectroscopic investigation', Heritage Science, vol. 7, no. 1.
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Abstract Modelling clays are utilised by artists for their malleable properties. One of the challenges in managing collections containing such materials is the variety of commercial compositions available and, therefore, the variation in the requirements for storage and maintenance of such artefacts. The Art Gallery of New South Wales in Australia is responsible for the care of a range of artworks that contain modelling materials, some of which show detrimental property changes and there is concern for the longevity of such works. The aim of the current research is to determine the compositions of the modelling materials utilised in works produced by different artists in the gallery’s collection. Infrared spectroscopy was used to identify the main constituents of samples collected from the works of four different artists and a variety of material types were determined. Oil-based, air-hardening and polymer clays of varying composition were identified in the survey of artworks. Signs of deterioration in particular artworks were able to be characterised using spectroscopy, with the mechanisms identified including loss and oxidation of the oil component. Where a polymer clay was chosen by one artist, the distortion of the artwork was due to flow of the material over time and demonstrates the need for an understanding of the long term properties of the materials being used. The study has highlighted the need for conservators to have a detailed understanding of modelling materials to ensure the longevity of artworks containing this class of materials.

Sturmberg, BCP, Dossou, KB, Smith, MJA, Morrison, B, Poulton, CG & Steel, MJ 2019, 'Finite Element Analysis of Stimulated Brillouin Scattering in Integrated Photonic Waveguides', Journal of Lightwave Technology, vol. 37, no. 15, pp. 3791-3804.
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© 2019 IEEE. We describe a finite element algorithm for modeling stimulated Brillouin scattering in optical waveguides of arbitrary cross-section. The method allows rapid calculation of optical and elastic dispersion relations, field profiles, and gain. Additionally, we provide an open and extensible set of standard problems and reference materials to facilitate the bench-marking of our solver against subsequent tools. Such a resource is needed to help settle discrepancies between existing formulations and implementations, and to facilitate comparison between results in the literature. The resulting standardized testing framework will allow the community to gain confidence in new algorithms and will provide a common tool for the comparison of experimental designs of opto-acoustic waveguides.

Subedi, D, Kohli, GS, Vijay, AK, Willcox, M & Rice, SA 2019, 'Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34', PLOS ONE, vol. 14, no. 4, pp. e0215038-e0215038.
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Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.

Subedi, D, Vijay, AK, Rice, SA & Willcox, M 2019, 'Cytotoxic factor influencing acquired antimicrobial resistance in Pseudomonas aeruginosa', Microbiology Australia, vol. 40, no. 4, pp. 161-164.
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© 2019 CSIRO. All rights reserved. The Gram-negative opportunistic bacterium Pseudomonas aeruginosa is associated with different types of human infections and because of emerging multidrug-resistant strains, these infections are of major global public health concern. Certain strains possess a unique cytotoxic effector protein ExoU, which contributes to the fitness of this organism in different ecological niches and is associated with acquired antibiotic resistance. This article summarises the current knowledge of the exoU gene in P. aeruginosa, including genetics, distribution in strains from different locations and association with antibiotic resistance. Understanding of this effector protein may have important implications for the understanding of pathogenesis and antimicrobial resistance in P. aeruginosa infections.

Suggett, DJ, Camp, EF, Edmondson, J, Boström‐Einarsson, L, Ramler, V, Lohr, K & Patterson, JT 2019, 'Optimizing return‐on‐effort for coral nursery and outplanting practices to aid restoration of the Great Barrier Reef', Restoration Ecology, vol. 27, no. 3, pp. 683-693.
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Coral nursery and outplanting practices have grown in popularity worldwide for targeted restoration of degraded “high value” reef sites, and recovery of threatened taxa. Success of these practices is commonly gauged from coral propagule growth and survival, which fundamentally determines the return‐on‐effort (RRE) critical to the cost‐effectiveness and viability of restoration programs. In many cases, RRE has been optimized from past successes and failures, which therefore presents a major challenge for locations such as the Great Barrier Reef (GBR) where no local history of restoration exists to guide best practice. In establishing the first multi‐taxa coral nursery on the GBR (Opal Reef, February 2018), we constructed a novel scoring criterion from concurrent measurements of growth and survivorship to guide our relative RRE, including nursery propagule numbers (stock density). We initially retrieved RRE scores from a database of global restoration efforts to date (n = 246; 52 studies) to evaluate whether and how success commonly varied among coral taxa. We then retrieved RRE scores for Opal Reef using initial growth and survivorship data for six key coral taxa, to demonstrate that RRE scores were high for all taxa predominantly via high survivorship over winter. Repeated RRE scoring in summer is therefore needed to capture the full dynamic range of success where seasonal factors regulating growth versus survivorship differ. We discuss how RRE scoring can be easily adopted across restoration practices globally to standardize and benchmark success, but also as a tool to aid decision‐making in optimizing future propagation (and outplanting) efforts.

Sukačová, K, Búzová, D, Trávníček, P, Červený, J, Vítězová, M & Vítěz, T 2019, 'Optimization of microalgal growth and cultivation parameters for increasing bioenergy potential: Case study using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2)', Algal Research, vol. 40, pp. 101519-101519.
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© 2019 The aim of the presented research was application of optimized cultivation conditions for lipid production using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2), followed by an assessment of the bioenergy potential of lipid-rich biomass and biomethane production. The optimization of cultivation parameters led to an increase in lipid production. The average and maximum lipid production for C. pyrenoidosa was 101 ± 22 mg.L −1 .D −1 and 126 mg.L −1 .D −1 , respectively. The average calorific value of the lipid rich-biomass was 27.56 ± 0.93 MJ.kg −1 . However, the recorded biomethane yield of 0.16 ± 0.006 m 3 .kg −1 VS, caused probably by low digestibility of C. pyrenoidosa and by short hydraulic retention time during anaerobic digestion, was interpreted as low. However, the high lipid content along with high calorific value indicated an increased bioenergy potential of microalgal biomass cultivated under the optimized cultivation parameters.

Sullivan, E, Ward, S, Zeki, R, Wayland, S, Sherwood, J, Wang, A, Worner, F, Kendall, S, Brown, J & Chang, S 2019, 'Recidivism, health and social functioning following release to the community of NSW prisoners with problematic drug use: study protocol of the population-based retrospective cohort study on the evaluation of the Connections Program', BMJ Open, vol. 9, no. 7, pp. e030546-e030546.
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IntroductionThe rising rate of incarceration in Australia, driven by high reoffending, is a major public health problem. Problematic drug use is associated with increasing rates of reoffending and return to custody of individuals. Throughcare provides support to individuals during imprisonment through to post-release, improving both the transition to community and health outcomes post-incarceration. The aim of this study is to evaluate the Connections Programme (CP) that utilises a throughcare approach for release planning of people in prison with a history of problematic drug use. The study protocol is described.Methods and analysisPopulation-based retrospective cohort study. The study will use record linkage of the Connections dataset with 10 other New South Wales (NSW) population datasets on offending, health service utilisation, opioid substitution therapy, pregnancy, birth and mortality. The study includes all patients who were eligible to participate in the CP between January 2008 and December 2015 stratified by patients who were offered CP and eligible patients who were not offered the programme (non-CP (NCP)). Propensity-score matching will be used to appropriately adjust for the observable differences between CP and NCP. The differences between two groups will be examined using appropriate univariate and multivariate analyses. A generalised estimating equation approach, which can deal with repeat outcomes for individuals will be used to examine recidivism, mortality and other health outcomes, including perinatal and infant outcomes. Survival analysis techniques will be used to examine the effect of the CP by sex and Indigenous status on the ‘time-to’ health-related outcomes after adjusting for potential confounders.Ethics and disseminationEthical approval was received from the N...

Summerell, AE, Frankham, GJ, Gunn, P & Johnson, RN 2019, 'DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade', Forensic Science International, vol. 295, pp. 46-53.
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© 2018 The Authors The illegal trade in wild animals being sold as ‘captive bred’ is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. As this species is distributed throughout Australia and in New Guinea (currently comprising of five recognised sub-species), this project aimed to develop a DNA based method to definitively determine the source country of an echidna and explore the use of non-invasive sampling techniques. Here we use non-invasively sampled echidna quills and demonstrate the extraction of mitochondrial DNA and amplification of a region of the mitochondrial genome. Phylogenetically informative markers for analysis of a 322 bp segment of the D-loop region were developed, and subsequently validated, using animals with known source locations allowing us to reliably distinguish between echidnas from New Guinea, and Australia. This research presents the first validated forensic protocols for short beaked echidnas and will be an integral tool in understanding the movement of animals in this emerging trade.

Summers, S, Freckelton, ML, Nedved, BT, Rice, SA & Hadfield, MG 2019, 'Complete Genome Sequence of Thalassotalea euphylliae Strain H2', Microbiology Resource Announcements, vol. 8, no. 4.
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A bacterial isolate of Thalassotalea euphylliae H2 was collected from the coral Montipora capitata . MinION long reads were employed for scaffolding and complemented with short-read MiSeq sequences to permit complete genome assembly.

Suvakov, S, Jerotic, D, Damjanovic, T, Milic, N, Pekmezovic, T, Djukic, T, Jelic-Ivanovic, Z, Savic Radojevic, A, Pljesa-Ercegovac, M, Matic, M, McClements, L, Dimkovic, N, Garovic, VD, Albright, RC & Simic, T 2019, 'Markers of Oxidative Stress and Endothelial Dysfunction Predict Haemodialysis Patients Survival', American Journal of Nephrology, vol. 50, no. 2, pp. 115-125.
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<b><i>Introduction:</i></b> Overall survival of patients with end-stage renal disease (ESRD) remains poor. Oxidative stress is one of the major risk factors associated with mortality in this patient group. As glutathione S-transferases (GST) are well-established antioxidants, we hypothesized that a model including GST gene polymorphisms, oxidative damage byproducts and cell adhesion markers has a prognostic role in ESRD patient survival. <b><i>Methods:</i></b> A prospective study of 199 patients with ESRD on haemodialysis was conducted. GST genotype, oxidative stress byproducts and cell adhesion molecules were measured in plasma. Multivariate Cox regression and Kaplan-Meier survival analyses were performed to test the predictive ability of these parameters in the 8-year follow-up period. <b><i>Results:</i></b> GSTM1-null genotype was associated with significantly shorter overall (HR 1.6, <i>p</i> = 0.018) and cardiovascular-specific (HR 2.1, <i>p</i> = 0.010) survival. Oxidative stress byproducts (advanced oxidation protein products [AOPP], prooxidant-antioxidant balance [PAB], malondialdehyde [MDA]) and cell adhesion molecules (soluble vascular cell adhesion molecule-1 [sVCAM-1] and soluble intercellular adhesion molecule-1 [sICAM-1]) demonstrated a significant predictive role in terms of overall and cardiovascular survival. When 6 biomarkers (GSTM1 genotype, high AOPP/PAB/MDA/­sVCAM-1/sICAM-1) were combined into a scoring model, a significantly shorter overall and cardiovascular survival was observed for patients with the highest score (<i>p</i> &#x3c; 0.001). <b><i>Conclusion:</i></b> We identified a novel panel of biomarkers that can be utilized in predicting survival in ESRD patients. This biomarker signature could enable better monitoring of patients and stratification into appropriate treatment groups.

Swinfield, T, Lindsell, JA, Williams, JV, Harrison, RD, Agustiono, Habibi, Gemita, E, Schönlieb, CB & Coomes, DA 2019, 'Accurate Measurement of Tropical Forest Canopy Heights and Aboveground Carbon Using Structure From Motion', Remote Sensing, vol. 11, no. 8, pp. 928-928.
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Unmanned aerial vehicles are increasingly used to monitor forests. Three-dimensional models of tropical rainforest canopies can be constructed from overlapping photos using Structure from Motion (SfM), but it is often impossible to map the ground elevation directly from such data because canopy gaps are rare in rainforests. Without knowledge of the terrain elevation, it is, thus, difficult to accurately measure the canopy height or forest properties, including the recovery stage and aboveground carbon density. Working in an Indonesian ecosystem restoration landscape, we assessed how well SfM derived the estimates of the canopy height and aboveground carbon density compared with those from an airborne laser scanning (also known as LiDAR) benchmark. SfM systematically underestimated the canopy height with a mean bias of approximately 5 m. The linear models suggested that the bias increased quadratically with the top-of-canopy height for short, even-aged, stands but linearly for tall, structurally complex canopies (>10 m). The predictions based on the simple linear model were closely correlated to the field-measured heights when the approach was applied to an independent survey in a different location ( R 2 = 67% and RMSE = 1.85 m), but a negative bias of 0.89 m remained, suggesting the need to refine the model parameters with additional training data. Models that included the metrics of canopy complexity were less biased but with a reduced R 2 . The inclusion of ground control points (GCPs) was found to be important in accurately registering SfM measurements in space, which is essential if the survey requirement is to produce small-scale restoration interventions or to track changes through time. However, at the scale of several hectares, the top-of-canopy height and above-ground carbon density estimates from SfM and LiDAR were very similar even without GCPs. The ability to produce accurate top-of-canopy height and carbon stock me...

Szychlinska, MA, Di Rosa, M, Castorina, A, Mobasheri, A & Musumeci, G 2019, 'A correlation between intestinal microbiota dysbiosis and osteoarthritis', Heliyon, vol. 5, no. 1, pp. e01134-e01134.
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Osteoarthritis (OA) is a degenerative disease of the articular cartilage, resulting in pain and total joint disability. Recent studies focused on the role of the metabolic syndrome in inducing or worsening joint damage suggest that chronic low-grade systemic inflammation may represent a possible linking factor. This finding supports the concept of a new phenotype of OA, a metabolic OA. The gut microbiome is fundamental for human physiology and immune system development, among the other important functions. Manipulation of the gut microbiome is considered an important topic for the individual health in different medical fields such as medical biology, nutrition, sports, preventive and rehabilitative medicine. Since intestinal microbiota dysbiosis is strongly associated with the pathogenesis of several metabolic and inflammatory diseases, it is conceivable that also the pathogenesis of OA might be related to it. However, the mechanisms and the contribution of intestinal microbiota metabolites in OA pathogenesis are still not clear. The aim of this narrative review is to review recent literature concerning the possible contribution of dysbiosis to OA onset and to discuss the importance of gut microbiome homeostasis maintenance for optimal general health preservation.

Takada, S, Akter, A, Itabashi, E, Nishida, N, Shea, DJ, Miyaji, N, Mehraj, H, Osabe, K, Shimizu, M, Takasaki-Yasuda, T, Kakizaki, T, Okazaki, K, Dennis, ES & Fujimoto, R 2019, 'The role of FRIGIDA and FLOWERING LOCUS C genes in flowering time of Brassica rapa leafy vegetables', Scientific Reports, vol. 9, no. 1.
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AbstractThere is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.

Tang, V, Fu, S, Rayner, BS & Hawkins, CL 2019, '8-Chloroadenosine induces apoptosis in human coronary artery endothelial cells through the activation of the unfolded protein response', Redox Biology, vol. 26, pp. 101274-101274.
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Infiltration of leukocytes within the vessel at sites of inflammation and the subsequent generation of myeloperoxidase-derived oxidants, including hypochlorous acid, are key characteristics of atherosclerosis. Hypochlorous acid is a potent oxidant that reacts readily with most biological molecules, including DNA and RNA. This results in nucleic acid modification and the formation of different chlorinated products. These products have been used as biomarkers of inflammation, owing to their presence in elevated amounts in different inflammatory fluids and diseased tissue, including atherosclerotic lesions. However, it is not clear whether these materials are simply biomarkers, or could also play a role in the development of chronic inflammatory pathologies. In this study, we examined the reactivity of different chlorinated nucleosides with human coronary artery endothelial cells (HCAEC). Evidence was obtained for the incorporation of each chlorinated nucleoside into the cellular RNA or DNA. However, only 8-chloro-adenosine (8ClA) had a significant effect on the cell viability and metabolic activity. Exposure of HCAEC to 8ClA decreased glycolysis, and resulted in a reduction in ATP, with a corresponding increase in the chlorinated analogue, 8Cl-ATP in the nucleotide pool. 8ClA also induced sustained endoplasmic reticulum stress within the HCAEC, which resulted in activation of the unfolded protein response, the altered expression of antioxidant genes and culminated in the release of calcium into the cytosol and cell death by apoptosis. Taken together, these data provide new insight into pathways by which myeloperoxidase activity and resultant hypochlorous acid generation could promote endothelial cell damage during chronic inflammation, which could be relevant to the progression of atherosclerosis.

Tang, X, Zhou, D, Li, P, Guo, X, Wang, C, Kang, F, Li, B & Wang, G 2019, 'High-Performance Quasi-Solid-State MXene-Based Li–I Batteries', ACS Central Science, vol. 5, no. 2, pp. 365-373.
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© 2019 American Chemical Society. Lithium-iodine (Li-I) batteries have attracted tremendous attention due to their high energy and power densities as well as the low cost of iodine. However, the severe shuttle effect of iodine species and the uncontrollable lithium dendrite growth have strongly hindered their practical applications. Here we successfully develop a quasi-solid-state Li-I battery enabled by a MXene-based iodine cathode and a composite polymer electrolyte (CPE) containing NaNO 3 particles dispersing in a pentaerythritol-tetraacrylate-based (PETEA-based) gel polymer electrolyte. As verified by experimental characterizations and first-principle calculations, the abundant functional groups on the surface of MXene sheets provide strong chemical binding to iodine species, and therefore immobilize their shuttling. The PETEA-based polymer matrix simultaneously suppresses the diffusion of iodine species and stabilizes the Li anode/CPE interface against dendrite growth. The NaNO 3 particles act as an effective catalyst to facilitate the transformation kinetics of LiI 3 on the cathode. Owing to such synergistic optimization, the as-developed Li-I batteries deliver high energy/power density with long cycling stability and good flexibility. This work opens up a new avenue to improve the performance of Li-I batteries.

Taranto, V, Ueland, M, Forbes, SL & Blanes, L 2019, 'The analysis of nitrate explosive vapour samples using Lab-on-a-chip instrumentation', Journal of Chromatography A, vol. 1602, pp. 467-473.
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The detection and analysis of explosives and explosive-related compounds is a heightened priority in recent years for homeland security and counter-terrorism applications. This study aimed to evaluate the use of a commercial Lab-On-a-Chip (LOC) instrument for the analysis of explosive vapours, with the long-term goal of developing a portable instrument for passively detecting explosives in air samples. A simple method to collect explosive vapour residues was developed using a glass vial containing varying amounts of the target explosives (1 mg/mL). Standards were diluted to the desired concentration in 150 μL of acetone to facilitate the evaporation. The top of the vial was covered with a circular 0.5 cm diameter filter paper and exposed to a range of temperatures from 22 °C to 80 °C for 15 min. Following evaporation, the filter paper chads were folded and inserted into the LOC wells containing the separation buffer for the analysis, avoiding any further extraction step. After successfully separating and detecting eight explosives via liquid analysis, three explosives were chosen as targets for the vapour analysis experiments. 1,3,5-Trinitrobenzene (TNB), 2,4,6-Trinitrotoluene (TNT), and 2,4,6-Trinitrophenylmethylnitramine (Tetryl) were successfully separated, detected and identified following the vapour extraction of explosive standards onto filter paper chads. Limits of detection for the liquid analysis were demonstrated to be 2.32 ng for TNB, 2.35 ng for Tetryl, and 3.25 ng for TNT. The minimum detectable mass found for the vapour analysis was 6.03 for TNB, 9.99 ng for TNT, and 14.22 ng for Tetryl. The average recovery from the paper chads was 29% for Tetryl, 47% for TNB, and 75% for TNT (n = 4), comparable with findings from previous studies. Results show that a minimum temperature of 40 °C is necessary to vaporize the compounds using acetone, while the best results were achieved when heating the vial to 80 °C. The use of a filter paper to collect the explosi...

Tawfik, SA, Isayev, O, Stampfl, C, Shapter, J, Winkler, DA & Ford, MJ 2019, 'Efficient Prediction of Structural and Electronic Properties of Hybrid 2D Materials Using Complementary DFT and Machine Learning Approaches', Advanced Theory and Simulations, vol. 2, no. 1, pp. 1800128-1800128.
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AbstractThere are now, in principle, a limitless number of hybrid van der Waals (vdW) heterostructures that can be built from the rapidly growing number of 2D layers. The key question is how to explore this vast parameter space in a practical way. Computational methods can guide experimental work. However, even the most efficient electronic structure methods such as density functional theory, are too time consuming to explore more than a tiny fraction of all possible hybrid 2D materials. A combination of density functional theory (DFT) and machine learning techniques provide a practical method for exploring this parameter space much more efficiently than by DFT or experiments. As a proof of concept, this methodology is applied to predict the interlayer distance and band gap of bilayer heterostructures. The methods quickly and accurately predict these important properties for a large number of hybrid 2D materials. This work paves the way for rapid computational screening of the vast parameter space of vdW heterostructures to identify new hybrid materials with useful and interesting properties.

Tekwe, CD, Zoh, RS, Yang, M, Carroll, RJ, Honvoh, G, Allison, DB, Benden, M & Xue, L 2019, 'Instrumental variable approach to estimating the scalar‐on‐function regression model with measurement error with application to energy expenditure assessment in childhood obesity', Statistics in Medicine, vol. 38, no. 20, pp. 3764-3781.
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Wearable device technology allows continuous monitoring of biological markers and thereby enables study of time‐dependent relationships. For example, in this paper, we are interested in the impact of daily energy expenditure over a period of time on subsequent progression toward obesity among children. Data from these devices appear as either sparsely or densely observed functional data and methods of functional regression are often used for their statistical analyses. We study the scalar‐on‐function regression model with imprecisely measured values of the predictor function. In this setting, we have a scalar‐valued response and a function‐valued covariate that are both collected at a single time period. We propose a generalized method of moments‐based approach for estimation, while an instrumental variable belonging in the same time space as the imprecisely measured covariate is used for model identification. Additionally, no distributional assumptions regarding the measurement errors are assumed, while complex covariance structures are allowed for the measurement errors in the implementation of our proposed methods. We demonstrate that our proposed estimator is L2 consistent and enjoys the optimal rate of convergence for univariate nonparametric functions. In a simulation study, we illustrate that ignoring measurement error leads to biased estimations of the functional coefficient. The simulation studies also confirm our ability to consistently estimate the function‐valued coefficient when compared to approaches that ignore potential measurement errors. Our proposed methods are applied to our motivating example to assess the impact of baseline levels of energy expenditure on body mass index among elementary school–aged children.

Thomson, ACG, Trevathan‐Tackett, SM, Maher, DT, Ralph, PJ & Macreadie, PI 2019, 'Bioturbator‐stimulated loss of seagrass sediment carbon stocks', Limnology and Oceanography, vol. 64, no. 1, pp. 342-356.
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AbstractSeagrass ecosystems are highly productive, and are sites of significant carbon sequestration. Sediment‐held carbon stocks can be many thousands of years old, and persist largely due to sediment anoxia and because microbial activity is decreasing with depth. However, the carbon sequestered in seagrass ecosystems may be susceptible to remineralization via the activity of bioturbating fauna. Microbial priming is a process whereby remineralization of sediment carbon (recalcitrant organic matter) is stimulated by disturbance, i.e., burial of a labile source of organic matter (seagrass). We investigated the hypothesis that bioturbation could mediate remineralization of sediment carbon stocks through burial of seagrass leaf detritus. We carried out a 2‐month laboratory study to compare the remineralization (measured as CO2 release) of buried seagrass leaves (Zostera muelleri) to the total rate of sediment organic matter remineralization in sediment with and without the common Australian bioturbating shrimp Trypaea australiensis (Decapoda: Axiidea). In control sediment containing seagrass but no bioturbators, we observed a negative microbial priming effect, whereby seagrass remineralization was favored over sediment remineralization (and thus preserving sediment stocks). Bioturbation treatments led to a two‐ to five‐fold increase in total CO2 release compared to controls. The estimated bioturbator‐stimulated microbial priming effect was equivalent to 15% of the total daily sediment‐derived CO2 releases. We propose that these results indicate that bioturbation is a potential mechanism that converts these sediments from carbon sinks to sources through stimulation of priming‐enhanced sediment carbon remineralization. We further hypothesized that significant changes to seagrass faunal communities may influence...

Tian, H, Liang, J & Liu, J 2019, 'Nanoengineering Carbon Spheres as Nanoreactors for Sustainable Energy Applications', Advanced Materials, vol. 31, no. 50, pp. 1903886-1903886.
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AbstractColloidal carbon sphere nanoreactors have been explored extensively as a class of versatile materials for various applications in energy storage, electrochemical conversion, and catalysis, due to their unique properties such as excellent electrical conductivity, high specific surface area, controlled porosity and permeability, and surface functionality. Here, the latest updated research on colloidal carbon sphere nanoreactor, in terms of both their synthesis and applications, is summarized. Various synthetic strategies are first discussed, including the hard template method, the soft template method, hydrothermal carbonization, the microemulsion polymerization method, and extension of the Stöber method. Then, the functionalization of colloidal carbon sphere nanoreactors, including the nanoengineering of compositions and the surface features, is discussed. Afterward, recent progress in the major applications of colloidal carbon sphere nanoreactors, in the areas of energy storage, electrochemical conversion, and catalysis, is presented. Finally, the perspectives and challenges for future developments are discussed in terms of controlled synthesis and functionalization of the colloidal carbon sphere nanoreactors with tunable structure, and the composition and properties that are desirable for practical applications.

Tian, H, Liu, X, Dong, L, Ren, X, Liu, H, Price, CAH, Li, Y, Wang, G, Yang, Q & Liu, J 2019, 'Enhanced Hydrogenation Performance over Hollow Structured Co‐CoOx@N‐C Capsules', Advanced Science, vol. 6, no. 22, pp. 1900807-1900807.
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AbstractIt is desirable to design nonprecious metal nanocatalysts with high stability and catalytic performance for fine chemicals production. Here, a method is reported for the preparation of cobalt metal and cobalt oxide cores confined within nanoporous nitrogen‐doped hollow carbon capsules. Core–shell structured Zn/Co‐ZIF@polymer materials are fabricated through a facile coating polymer strategy on the surface of zeolitic imidazolate frameworks (ZIF). A series of hollow carbon capsules with cobalt metal and cobalt oxide are derived from a facile confined pyrolysis of Zn/Co‐ZIF@polymer. The hollow Co‐CoOx@N‐C capsules can prevent sintering and agglomeration of the cobalt nanoparticles and the nanoporous shell allows for efficient mass transport. The specific surface area and Co particle size are optimized through finely tuning the original Zn content in ZIF particles, thus enhancing overall catalytic activity. The yolk–shell structured Zn4Co1Ox@carbon hollow capsules are shown to be a highly active and selective catalyst (selectivity >99%) for hydrogenation of nitrobenzene to aniline. Furthermore, Zn4Co1Ox@carbon hollow particles show superior catalytic stability, and no deactivation after 8 cycles of reaction. The hollow Co‐CoOx@N‐C capsules may shed light on a green and sustainable catalytic process for fine chemicals production.

Tian, H, Liu, X, Dong, L, Ren, X, Liu, H, Price, CAH, Li, Y, Wang, G, Yang, Q & Liu, J 2019, 'Submicroreactors: Enhanced Hydrogenation Performance over Hollow Structured Co‐CoOx@N‐C Capsules (Adv. Sci. 22/2019)', Advanced Science, vol. 6, no. 22, pp. 1970135-1970135.
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Tian, H, Shao, H, Chen, Y, Fang, X, Xiong, P, Sun, B, Notten, PHL & Wang, G 2019, 'Ultra-stable sodium metal-iodine batteries enabled by an in-situ solid electrolyte interphase', Nano Energy, vol. 57, pp. 692-702.
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© 2018 Elsevier Ltd High capacity sodium (Na) metal anodes open up new opportunities for developing next-generation rechargeable batteries with both high power and high energy densities. However, many challenges still plagued their practical application, including low plating/stripping Coulombic efficiency (CE) and dendrite growth after repeated cycle inducing safety issue. Especially, the sodium metal is less stable in organic (i.e. carbonate-based) electrolytes than lithium metal, due to the more unstable organic solid–electrolyte interface (SEI). Herein, we report a facile technology to stabilize sodium metal anode and inhibit the growth of sodium dendrites. The in-situ ultrathin NaI SEI layer successfully endows best-performance Na/I 2 metal batteries (>2200 cycles) with high capacity (210 mA h g −1 at 0.5 C) based on the conversion reaction chemistry with higher discharge voltage plateau (> 2.7 V) and lower overpotential (134 mV) due to the fast charge transfer dynamics and interfacial stability compared with pristine Na anode. The detailed theoretical calculations and experimental results elucidate that NaI layer has a much lower diffusion barrier compared to that of NaF (NaF as one the most commonly found inorganic components in Na-based SEI layer), and actually facilitates more uniform sodium deposition. This work provides a new avenue for designing low-cost, high-performance and high-safety sodium metal-iodine batteries and other metal-iodine batteries.

Toh, S-L, Lee, BB, Ryan, S, Simpson, JM, Clezy, K, Bossa, L, Rice, SA, Marial, O, Weber, GH, Kaur, J, Boswell-Ruys, CL, Goodall, S, Middleton, JW, Tuderhope, M & Kotsiou, G 2019, 'Probiotics [LGG-BB12 or RC14-GR1] versus placebo as prophylaxis for urinary tract infection in persons with spinal cord injury [ProSCIUTTU]: a randomised controlled trial', Spinal Cord, vol. 57, no. 7, pp. 550-561.
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© 2019, The Author(s). Study design: Randomised double-blind factorial-design placebo-controlled trial. Objective: Urinary tract infections (UTIs) are common in people with spinal cord injury (SCI). UTIs are increasingly difficult to treat due to emergence of multi-resistant organisms. Probiotics are efficacious in preventing UTIs in post-menopausal women. We aimed to determine whether probiotic therapy with Lactobacillus reuteri RC-14+Lactobacillus GR-1 (RC14-GR1) and/or Lactobacillus rhamnosus GG+Bifidobacterium BB-12 (LGG-BB12) are effective in preventing UTI in people with SCI. Setting: Spinal units in New South Wales, Australia with their rural affiliations. Methods: We recruited 207 eligible participants with SCI and stable neurogenic bladder management. They were randomised to one of four arms: RC14-GR1+LGG-BB12, RC14-GR1+placebo, LGG-BB12+ placebo or double placebos for 6 months. Randomisation was stratified by bladder management type and inpatient or outpatient status. The primary outcome was time to occurrence of symptomatic UTI. Results: Analysis was based on intention to treat. Participants randomised to RC14-GR1 had a similar risk of UTI as those not on RC14-GR1 (HR 0.67; 95% CI: 0.39–1.18; P = 0.17) after allowing for pre-specified covariates. Participants randomised to LGG-BB12 also had a similar risk of UTI as those not on LGG-BB12 (HR 1.29; 95% CI: 0.74–2.25; P = 0.37). Multivariable post hoc survival analysis for RC14-GR1 only vs. the other three groups showed a potential protective effect (HR 0.46; 95% CI: 0.21–0.99; P = 0.03), but this result would need to be confirmed before clinical application. Conclusion: In this RCT, there was no effect of RC14-GR1 or LGG-BB12 in preventing UTI in people with SCI.

Torabian, P, Dehestani, M, Morshedi Rad, D, Peiravi, S, Aghaie-Hakkak, M & Ashraf, H 2019, 'Genomic and Personalized Medicine Perspective in Genetic Generalized Epilepsy.', Arch Iran Med, vol. 22, no. 9, pp. 516-526.
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The genetic generalized epilepsies (GGEs) are a set of disorders presenting with generalized seizures, in addition to general spike-wave activity. The present study aims to investigate the clinical manifestations and genetic origin of generalized tonicclonic seizures and the subgroups of GGEs, including childhood absence epilepsy (CAE), juvenile absence epilepsy, and juvenile myoclonic epilepsy (JME). Information compiled from genome-wide association studies (GWASs) in the EPICure project revealed associations with many genes. Besides, copy number variant (CNV) discoveries have been the most inspiring turning point of epilepsy genetic research. This phenomenon could give us an idea about microdeletions/microduplications as genetic variants throughout the whole genome. Nowadays, next-generation sequencing (NGS) approaches support neurogeneticists to unravel the predisposed putative variants in GGE to establish a better diagnosis. Consequently, previous experiments supply data for antiepileptic drugs (AEDs) to test susceptible variants, which influence the response to drugs. As a final point, all these data should provide the current GGE patients with better genetic counseling and follow-up services.

Toth, M & Aharonovich, I 2019, 'Single Photon Sources in Atomically Thin Materials', Annual Review of Physical Chemistry, vol. 70, no. 1, pp. 123-142.
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Layered materials are very attractive for studies of light–matter interactions at the nanoscale. In particular, isolated quantum systems such as color centers and quantum dots embedded in these materials are gaining interest due to their potential use in a variety of quantum technologies and nanophotonics. Here, we review the field of nonclassical light emission from van der Waals crystals and atomically thin two-dimensional materials. We focus on transition metal dichalcogenides and hexagonal boron nitride and discuss the fabrication and properties of quantum emitters in these systems and proof-of-concept experiments that provide a foundation for their integration in on-chip nanophotonic circuits. These experiments include tuning of the emission wavelength, electrical excitation, and coupling of the emitters to waveguides, dielectric cavities, and plasmonic resonators. Finally, we discuss current challenges in the field and provide an outlook to further stimulate scientific discussion.

Tran, TT, Bradac, C, Solntsev, AS, Toth, M & Aharonovich, I 2019, 'Suppression of spectral diffusion by anti-Stokes excitation of quantum emitters in hexagonal boron nitride', Applied Physics Letters, vol. 115, no. 7, pp. 071102-071102.
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Solid-state quantum emitters are garnering a lot of attention due to their role in scalable quantum photonics. A notable majority of these emitters, however, exhibit spectral diffusion due to local, fluctuating electromagnetic fields. In this work, we demonstrate efficient anti-Stokes (AS) excitation of quantum emitters in hexagonal boron nitride (hBN) and show that the process results in the suppression of a specific mechanism responsible for spectral diffusion of the emitters. We also demonstrate an all-optical gating scheme that exploits Stokes and anti-Stokes excitation to manipulate spectral diffusion so as to switch and lock the emission energy of the photon source. In this scheme, reversible spectral jumps are deliberately enabled by pumping the emitter with high energy (Stokes) excitation; AS excitation is then used to lock the system into a fixed state characterized by a fixed emission energy. Our results provide important insights into the photophysical properties of quantum emitters in hBN and introduce a strategy for controlling the emission wavelength of quantum emitters.

Tran, TT, Regan, B, Ekimov, EA, Mu, Z, Zhou, Y, Gao, W-B, Narang, P, Solntsev, AS, Toth, M, Aharonovich, I & Bradac, C 2019, 'Anti-Stokes excitation of solid-state quantum emitters for nanoscale thermometry', Science Advances, vol. 5, no. 5.
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We demonstrate anti-Stokes excitation of single color centers in diamond for high-sensitivity, nanoscale temperature measurements.

Trevathan-Tackett, SM, Sherman, CDH, Huggett, MJ, Campbell, AH, Laverock, B, Hurtado-McCormick, V, Seymour, JR, Firl, A, Messer, LF, Ainsworth, TD, Negandhi, KL, Daffonchio, D, Egan, S, Engelen, AH, Fusi, M, Thomas, T, Vann, L, Hernandez-Agreda, A, Gan, HM, Marzinelli, EM, Steinberg, PD, Hardtke, L & Macreadie, PI 2019, 'A horizon scan of priorities for coastal marine microbiome research', Nature Ecology & Evolution, vol. 3, no. 11, pp. 1509-1520.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth’s climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and the environment or their hosts — termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.

Trist, BG, Hare, DJ & Double, KL 2019, 'Oxidative stress in the aging substantia nigra and the etiology of Parkinson's disease', Aging Cell, vol. 18, no. 6.
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AbstractParkinson's disease prevalence is rapidly increasing in an aging global population. With this increase comes exponentially rising social and economic costs, emphasizing the immediate need for effective disease‐modifying treatments. Motor dysfunction results from the loss of dopaminergic neurons in the substantia nigra pars compacta and depletion of dopamine in the nigrostriatal pathway. While a specific biochemical mechanism remains elusive, oxidative stress plays an undeniable role in a complex and progressive neurodegenerative cascade. This review will explore the molecular factors that contribute to the high steady‐state of oxidative stress in the healthy substantia nigra during aging, and how this chemical environment renders neurons susceptible to oxidative damage in Parkinson's disease. Contributing factors to oxidative stress during aging and as a pathogenic mechanism for Parkinson's disease will be discussed within the context of how and why therapeutic approaches targeting cellular redox activity in this disorder have, to date, yielded little therapeutic benefit. We present a contemporary perspective on the central biochemical contribution of redox imbalance to Parkinson's disease etiology and argue that improving our ability to accurately measure oxidative stress, dopaminergic neurotransmission and cell death pathways in vivo is crucial for both the development of new therapies and the identification of novel disease biomarkers.

Trivedi, T, Jain, D, Mulla, NSS, Mamatha, SS, Damare, SR, Sreepada, RA, Kumar, S & Gupta, V 2019, 'Improvement in biomass, lipid production and biodiesel properties of a euryhaline Chlorella vulgaris NIOCCV on mixotrophic cultivation in wastewater from a fish processing plant', Renewable Energy, vol. 139, pp. 326-335.
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Trycz, A, Regan, B, Kianinia, M, Bray, K, Toth, M & Aharonovich, I 2019, 'Bottom up engineering of single crystal diamond membranes with germanium vacancy color centers', Optical Materials Express, vol. 9, no. 12, pp. 4708-4708.
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© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement. Color centers in diamond have garnered significant attention for applications in integrated quantum photonics. The availability of thin (~ hundred of nanometers) diamond membranes is paramount to achieve this goal. In this paper, we describe in detail a robust, reproducible and cost effective fabrication method that enables engineering high quality thin diamond membranes with uniform distribution of germanium vacancies employing microwave plasma chemical vapor deposition. We use a combination of different germanium precursors for homogeneous doping of the membranes to increase the probability of germanium incorporation into the diamond lattice. Our fabrication methodology can be further extended to implementation of other color centers in thin diamond membranes and be used for engineering quantum photonic devices.

Tulau, MJ, McInnes‐Clarke, SK, Yang, X, McAlpine, RA, Karunaratne, SB, Zhu, Q & Morand, DT 2019, 'The Warrumbungle Post‐Fire Recovery Project—raising the profile of soils', Soil Use and Management, vol. 35, no. 1, pp. 63-74.
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AbstractThe impacts of a wildfire and subsequent rainfall event in 2013 in the Warrumbungle National Park in New South Wales, Australia were examined in a project designed to provide information on post‐fire recovery expectations and options to land managers. A coherent suite of sub‐projects was implemented, including soil mapping, and studies on soil organic carbon (SOC) and nitrogen (N), erosion rates, groundcover recovery and stream responses. It was found that the loss of SOC and N increased with fire severity, with the greatest losses from severely burnt sandstone ridges. Approximately 2.4 million t of SOC and ~74,000 t of N were lost from soil to a depth of 10 cm across the 56,290 ha affected. Soil loss from slopes during the subsequent rainfall event was modelled up to 25 t ha−1, compared to a long‐term mean annual soil loss of 1.06 t ha−1 year−1. Groundcover averages generally increased after the fire until spring 2015, by which time rates of soil loss returned to near pre‐fire levels. Streams were filled with sand to bank full levels after the fire and rainfall. Rainfall events in 2015–2016 shifted creek systems into a major erosive phase, with incision through the post‐fire sandy bedload deposits, an erosive phase likely related to loss of topsoils over much of the catchment. The effectiveness of the research was secured by a close engagement with park managers in issue identification and a communications programme. Management outcomes flowing from the research included installation of erosion control works, redesign of access and monitoring of key mass movement hazard areas.

Ueland, M, Forbes, SL & Stuart, BH 2019, 'Understanding clothed buried remains: the analysis of decomposition fluids and their influence on clothing in model burial environments', Forensic Science, Medicine and Pathology, vol. 15, no. 1, pp. 3-12.
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Previous studies of fabric degradation have shown promising results for post-mortem interval estimations based on differences in the degradation states of clothing in the presence of decomposing remains. It is crucial to determine if a body was present when using the degradation state as an indicator of time since death. For this study, fabric samples from buried pig remains were collected and analyzed using attenuated total reflectance Fourier transform infrared spectroscopy and chromatography- mass spectrometry. Three different fabrics were investigated; 100% cotton, 100% polyester and a polyester-cotton blend. Distinct visual changes were observed between the experimental and control graves, with the fabrics in the control grave degrading more rapidly. There was also a difference between the fabric types, whereby the natural fabrics degraded much faster than the synthetic ones. Principal component analysis was used to determine that the cotton control samples could be statistically separated based on their degradation state. The presence of lipids and proteins were useful for separating "wetter" graves from those drier in nature as well as the control graves. Clothing evidence was demonstrated to provide quantitative time since death information, as well as indicating the decomposition site in the event of intentional or unintentional movement.

Usman, B, Sharma, N, Satija, S, Mehta, M, Vyas, M, Khatik, GL, Khurana, N, Hansbro, PM, Williams, K & Dua, K 2019, 'Recent Developments in Alpha-Glucosidase Inhibitors for Management of Type-2 Diabetes: An Update', Current Pharmaceutical Design, vol. 25, no. 23, pp. 2510-2525.
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The incidence of diabetes has increased globally in recent years and figures of diabetic patients were estimated to rise up to 642 million by 2040. The disorder is accompanied with various complications if not managed at the early stages, and interlinked high mortality rate and morbidity with time. Different classes of drugs are available for the management of type 2 diabetes but were having certain limitations of their safety. Alphaglucosidase is a family of enzyme originated from the pancreas which plays a role in the anabolism of 80-90% of carbohydrate consumed into glucose. This glucose is absorbed into the blood and results in frank postprandial hyperglycemia and worsens the conditions of diabetic patients which precipitate complications. Inhibition of these enzymes helps to prevent postprandial hyperglycemia and the formation of glycated end products. Alphaglucosidase inhibitors are reported to be more important in adequate control of type 2, but marketed drugs have various side effects, such as poor patient compliance and also expensive. This proves the needs for other class of drugs with better efficacy, safety, patient compliance and economic. In this review, we have emphasized the recent advances in the field of new alpha-glucosidase inhibitors with improved safety and pharmacological profile.

van den Berge, M, Brandsma, C-A, Faiz, A, de Vries, M, Rathnayake, SNH, Paré, PD, Sin, DD, Bossé, Y, Laviolette, M, Nickle, DC, Hao, K, Obeidat, M, Dragani, TA, Colombo, F, Timens, W & Postma, DS 2019, 'Differential lung tissue gene expression in males and females: implications for the susceptibility to develop COPD', European Respiratory Journal, vol. 54, no. 1, pp. 1702567-1702567.
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van der Plaat, DA, Vonk, JM, Lahousse, L, de Jong, K, Faiz, A, Nedeljkovic, I, Amin, N, van Diemen, CC, Brusselle, GG, Bossé, Y, Brandsma, C-A, Hao, K, Paré, PD, van Duijn, CM, Postma, DS & Boezen, HM 2019, 'Limited overlap in significant hits between genome-wide association studies on two airflow obstruction definitions in the same population', BMC Pulmonary Medicine, vol. 19, no. 1.
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BACKGROUND:Airflow obstruction is a hallmark of chronic obstructive pulmonary disease (COPD), and is defined as either the ratio between forced expiratory volume in one second and forced vital capacity (FEV1/FVC) < 70% or < lower limit of normal (LLN). This study aimed to assess the overlap between genome-wide association studies (GWAS) on airflow obstruction using these two definitions in the same population stratified by smoking. METHODS:GWASes were performed in the LifeLines Cohort Study for both airflow obstruction definitions in never-smokers (NS = 5071) and ever-smokers (ES = 4855). The FEV1/FVC < 70% models were adjusted for sex, age, and height; FEV1/FVC < LLN models were not adjusted. Ever-smokers models were additionally adjusted for pack-years and current-smoking. The overlap in significantly associated SNPs between the two definitions and never/ever-smokers was assessed using several p-value thresholds. To quantify the agreement, the Pearson correlation coefficient was calculated between the p-values and ORs. Replication was performed in the Vlagtwedde-Vlaardingen study (NS = 432, ES = 823). The overlapping SNPs with p < 10- 4 were validated in the Vlagtwedde-Vlaardingen and Rotterdam Study cohorts (NS = 1966, ES = 3134) and analysed for expression quantitative trait loci (eQTL) in lung tissue (n = 1087). RESULTS:In the LifeLines cohort, 96% and 93% of the never- and ever-smokers were classified concordantly based on the two definitions. 26 and 29% of the investigated SNPs were overlapping at p < 0.05 in never- and ever-smokers, respectively. At p < 10- 4 the overlap was 4% and 6% respectively, which could be change findings as shown by simulation studies. The effect estimates of the SNPs of the two definitions correlated strongly, but the p-values showed more variation and correlated only moderately. Similar observations were made in the Vlagtwedde-Vlaardingen study. Two overlapping SNPs in never-smokers (NFYC and FABP7) had the same direction of eff...

van Oorschot, RAH, Szkuta, B, Meakin, GE, Kokshoorn, B & Goray, M 2019, 'DNA transfer in forensic science: A review', Forensic Science International: Genetics, vol. 38, pp. 140-166.
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© 2018 Elsevier B.V. Understanding the variables impacting DNA transfer, persistence, prevalence and recovery (DNA-TPPR) has become increasingly relevant in investigations of criminal activities to provide opinion on how the DNA of a person of interest became present within the sample collected. This review considers our current knowledge regarding DNA-TPPR to assist casework investigations of criminal activities. There is a growing amount of information available on DNA-TPPR to inform the relative probabilities of the evidence given alternative scenarios relating to the presence or absence of DNA from a specific person in a collected sample of interest. This information should be used where relevant. However, far more research is still required to better understand the variables impacting DNA-TPPR and to generate more accurate probability estimates of generating particular types of profiles in more casework relevant situations. This review explores means of achieving this. It also notes the need for all those interacting with an item of interest to have an awareness of DNA transfer possibilities post criminal activity, to limit the risk of contamination or loss of DNA. Appropriately trained forensic practitioners are best placed to provide opinion and guidance on the interpretation of profiles at the activity level. However, those requested to provide expert opinion on DNA-related activity level issues are often insufficiently trained to do so. We advocate recognition of DNA activity associated expertise to be distinct from expertise associated with the identification of individuals. This is to be supported by dedicated training, competency testing, authorisation, and regular fit for purpose proficiency testing. The possibilities for experts to report on activity-related issues will increase as our knowledge increases through further research, access to relevant data is enhanced, and tools to assist interpretations are better exploited. Improvement opp...

Vaughan, A, Frazer, ZA, Hansbro, PM & Yang, IA 2019, 'COPD and the gut-lung axis: the therapeutic potential of fibre', Journal of Thoracic Disease, vol. 11, no. S17, pp. S2173-S2180.
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Current management strategies for chronic obstructive pulmonary disease (COPD) incorporate a step-wise, multidisciplinary approach to effectively manage patient symptoms and prevent disease progression. However, there has been limited advancement in therapies to address the underlying cause of COPD pathogenesis. Recent research has established the link between the lungs and the gut-the gut-lung axis -and the gut microbiome is a major component. The gut microbiome is likely perturbed in COPD, contributing to chronic inflammation. Diet is a readily modifiable factor and the diet of COPD patients is often deficient in nutrients such as fibre. The metabolism of dietary fibre by gut microbiomes produces anti-inflammatory short chain fatty acid (SCFAs), which could protect against inflammation in the lungs. By addressing the 'fibre gap' in the diet of COPD patients, this targeted dietary intervention may reduce inflammation, both systemically and in the airways, and value-add to the paradigm shift in respiratory medicine, from reactive to personalised and participatory medicine.

Venturini, C, Zingali, T, Wyrsch, ER, Bowring, B, Iredell, J, Partridge, SR & Djordjevic, SP 2019, 'Diversity of P1 phage-like elements in multidrug resistant Escherichia coli', Scientific Reports, vol. 9, no. 1.
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AbstractThe spread of multidrug resistance via mobile genetic elements is a major clinical and veterinary concern. Pathogenic Escherichia coli harbour antibiotic resistance and virulence genes mainly on plasmids, but also bacteriophages and hybrid phage-like plasmids. In this study, the genomes of three E. coli phage-like plasmids, pJIE250-3 from a human E. coli clinical isolate, pSvP1 from a porcine ETEC O157 isolate, and pTZ20_1P from a porcine commensal E. coli, were sequenced (PacBio RSII), annotated and compared. All three elements are coliphage P1 variants, each with unique adaptations. pJIE250-3 is a P1-derivative that has lost lytic functions and contains no accessory genes. In pTZ20_1P and pSvP1, a core P1-like genome is associated with insertion sequence-mediated acquisition of plasmid modules encoding multidrug resistance and virulence, respectively. The transfer ability of pTZ20_1P, carrying antibiotic resistance markers, was also tested and, although this element was not able to transfer by conjugation, it was able to lysogenize a commensal E. coli strain with consequent transfer of resistance. The incidence of P1-like plasmids (~7%) in our E. coli collections correlated well with that in public databases. This study highlights the need to investigate the contribution of phage-like plasmids to the successful spread of antibiotic resistant pathotypes.

Verma, A, Barua, A, Ruvindy, R, Savela, H, Ajani, PA & Murray, SA 2019, 'The Genetic Basis of Toxin Biosynthesis in Dinoflagellates', Microorganisms, vol. 7, no. 8, pp. 222-222.
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In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.

Verma, A, Kazandjian, A, Sarowar, C, Harwood, DT, Murray, JS, Pargmann, I, Hoppenrath, M & Murray, SA 2019, 'Morphology and Phylogenetics of Benthic Prorocentrum Species (Dinophyceae) from Tropical Northwestern Australia', Toxins, vol. 11, no. 10, pp. 571-571.
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Approximately 70 species of Prorocentrum are known, of which around 30 species are associated with benthic habitats. Some produce okadaic acid (OA), dinophysistoxin (DTX) and their derivatives, which are involved in diarrhetic shellfish poisoning. In this study, we isolated and characterized Prorocentrum concavum and P. malayense from Broome in north Western Australia using light and scanning electron microscopy as well as molecular sequences of large subunit regions of ribosomal DNA, marking the first record of these species from Australian waters. The morphology of the motile cells of P. malayense was similar to P. concavum in the light microscopy, but differed by the smooth thecal surface, the pore pattern and the production of mucous stalk-like structures and a hyaline sheath around the non-motile cells. P. malayense could also be differentiated from other closely related species, P. leve and P. foraminosum, despite the similarity in thecal surface and pore pattern, by its platelet formula and morphologies. We tested the production of OA and DTXs from both species, but found that they did not produce detectable levels of these toxins in the given culturing conditions. This study aids in establishing more effective monitoring of potential harmful algal taxa in Australian waters for aquaculture and recreational purposes.

Verma, A, Kohli, GS, Harwood, DT, Ralph, PJ & Murray, SA 2019, 'Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species', Environmental Microbiology, vol. 21, no. 11, pp. 4196-4211.
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SummaryIn marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth. Their ecological success may be related to their production of complex toxic polyketide compounds. Ostreopsis species produce potent palytoxin‐like compounds (PLTX), which are associated with human skin and eye irritations, and illnesses through the consumption of contaminated seafood. To investigate the genetic basis of PLTX‐like compounds, we sequenced and annotated transcriptomes from two PLTX‐producing Ostreopsis species; O. cf. ovata, O. cf. siamensis, one non‐PLTX producing species, O. rhodesae and compared them to a close phylogenetic relative and non‐PLTX producer, Coolia malayensis. We found no clear differences in the presence or diversity of ketosynthase and ketoreductase transcripts between PLTX producing and non‐producing Ostreopsis and Coolia species, as both groups contained >90 and > 10 phylogenetically diverse ketosynthase and ketoreductase transcripts, respectively. We report for the first‐time type I single‐, multi‐domain polyketide synthases (PKSs) and hybrid non‐ribosomal peptide synthase/PKS transcripts from all species. The long multi‐modular PKSs were insufficient by themselves to synthesize the large complex polyether backbone of PLTX‐like compounds. This implies that numerous PKS domains, including both single and multi‐, work together on the biosynthesis of PLTX‐like and other related polyketide compounds.

Verzosa, DMB, De Las Peñas, MLAN, Aberin, MAQ & Garces, LPDM 2019, 'App-based scaffolds for writing two-column proofs', International Journal of Mathematical Education in Science and Technology, vol. 50, no. 5, pp. 766-778.
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Viljoen, A, Raynaud, C, Johansen, MD, Roquet-Banères, F, Herrmann, J-L, Daher, W & Kremer, L 2019, 'Verapamil Improves the Activity of Bedaquiline against Mycobacterium abscessusIn Vitro and in Macrophages', Antimicrobial Agents and Chemotherapy, vol. 63, no. 9.
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Due to intrinsic multidrug resistance, pulmonary infections with Mycobacterium abscessus are extremely difficult to treat. Previously, we demonstrated that bedaquiline is highly effective against Mycobacterium abscessus both in vitro and in vivo . Here, we report that verapamil improves the efficacy of bedaquiline activity against M. abscessus clinical isolates and low-level resistant strains, both in vitro and in macrophages.

Violi, JP, Facey, JA, Mitrovic, SM, Colville, A & Rodgers, KJ 2019, 'Production of β-methylamino-L-alanine (BMAA) and Its Isomers by Freshwater Diatoms', Toxins, vol. 11, no. 9, pp. 512-512.
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β-methylamino-L-alanine (BMAA) is a non-protein amino acid that has been implicated as a risk factor for motor neurone disease (MND). BMAA is produced by a wide range of cyanobacteria globally and by a small number of marine diatoms. BMAA is commonly found with two of its constitutional isomers: 2,4-diaminobutyric acid (2,4-DAB), and N-(2-aminoethyl)glycine (AEG). The isomer 2,4-DAB, like BMAA, has neurotoxic properties. While many studies have shown BMAA production by cyanobacteria, few studies have looked at other algal groups. Several studies have shown BMAA production by marine diatoms; however, there are no studies examining freshwater diatoms. This study aimed to determine if some freshwater diatoms produced BMAA, and which diatom taxa are capable of BMAA, 2,4-DAB and AEG production. Five axenic diatom cultures were established from river and lake sites across eastern Australia. Cultures were harvested during the stationary growth phase and intracellular amino acids were extracted. Using liquid chromatography triple quadrupole mass spectrometry (LC-MS/MS), diatom extracts were analysed for the presence of both free and protein-associated BMAA, 2,4-DAB and AEG. Of the five diatom cultures analysed, four were found to have detectable BMAA and AEG, while 2,4-DAB was found in all cultures. These results show that BMAA production by diatoms is not confined to marine genera and that the prevalence of these non-protein amino acids in Australian freshwater environments cannot be solely attributed to cyanobacteria.

Violi, JP, Mitrovic, SM, Colville, A, Main, BJ & Rodgers, KJ 2019, 'Prevalence of β-methylamino-L-alanine (BMAA) and its isomers in freshwater cyanobacteria isolated from eastern Australia', Ecotoxicology and Environmental Safety, vol. 172, pp. 72-81.
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© 2019 Elsevier Inc. Environmental exposure to the amino acid β-methylamino-L-alanine (BMAA) was linked to the high incidence of neurodegenerative disease first reported on the island of Guam in the 1940s and has more recently been implicated in an increased incidence of amyotrophic lateral sclerosis (ALS) in parts of the USA. BMAA has been shown to be produced by a range of cyanobacteria and some marine diatoms and dinoflagellates in different parts of the world. BMAA is commonly found with two of its constitutional isomers: 2,4- diaminobutyric acid (2,4-DAB) and N-(2-aminoethyl) glycine (AEG). These isomers are thought to be co-produced by the same organisms that produce BMAA and MS/MS analysis following LC separation can add an additional level of specificity over LC-FL. Although the presence of BMAA and 2,4-DAB in surface scum samples from several sites in Australia has been reported, which Australian cyanobacterial species are capable of BMAA, 2,4-DAB and AEG production remains unknown. The aims of the present studies were to identify some of the cyanobacterial genera or species that can produce BMAA, 2,4-DAB and AEG in freshwater cyanobacteria blooms in eastern Australia. Eleven freshwater sites were sampled and from these, 19 single-species cyanobacterial cultures were established. Amino acids were extracted from cyanobacterial cultures and analysed using liquid chromatography-tandem mass spectrometry. BMAA was detected in 17 of the 19 isolates, 2,4-DAB was detected in all isolates, and AEG was detected in 18 of the 19 isolates, showing the prevalence of these amino acids in Australian freshwater cyanobacteria. Concentrations of all three isomers in Australian cyanobacteria were generally higher than the concentrations reported elsewhere. This study confirmed the presence of BMAA and its isomers in cyanobacteria isolated from eastern Australian freshwater systems, and determined which Australian cyanobacterial genera or species were capable of pr...

Vo, HNP, Koottatep, T, Chapagain, SK, Panuvatvanich, A, Polprasert, C, Nguyen, TMH, Chaiwong, C & Nguyen, NL 2019, 'Removal and monitoring acetaminophen-contaminated hospital wastewater by vertical flow constructed wetland and peroxidase enzymes', Journal of Environmental Management, vol. 250, pp. 109526-109526.
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© 2019 Elsevier Ltd Hospital wastewater contains acetaminophen (ACT) and nutrient, which need adequate removal and monitoring to prevent impact to environment and community. This study developed a pilot scale vertical flow constructed wetland (CW) to (1) remove high-dose ACT and pollutants in hospital wastewater and (2) identify the correlation of peroxidase enzyme extruded by Scirpus validus and pollutants removal efficiency. By that correlation, a low-cost method to monitor pollutants removal was drawn. Plants, such as Scirpus validus, generated peroxidase enzymes to alleviate pollutants’ stress. Results showed that the CW removed 3.5 to 6 logs of initial concentration 10 mg ACT/L to a recommended level for drinking water. The CW eliminated COD, TKN and TP efficiently, meeting the wastewater discharged standards of Thailand and Vietnam. By various multivariable regression models, concentrations of ACT in CW effluent and enzymes in S. validus exhibited a significant correlation (p < 0.01, R2 = 68.3%). These findings suggested that (i) vertical flow CW could remove high-dose ACT and nutrient and (ii) peroxidase enzymes generated in S. validus, such as soluble and covalent ones, could track ACT removal efficiency. This would help to reduce facilities and analytical cost of micro-pollutants.

Vo, HNP, Ngo, HH, Guo, W, Liu, Y, Chang, SW, Nguyen, DD, Nguyen, PD, Bui, XT & Ren, J 2019, 'Identification of the pollutants’ removal and mechanism by microalgae in saline wastewater', Bioresource Technology, vol. 275, pp. 44-52.
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© 2018 Elsevier Ltd This study investigated the growth dynamics of a freshwater and marine microalgae with supported biochemical performance in saline wastewater, the pollutants assimilation by a developed method, and the mechanism of salinity's effect to pollutants assimilation. Maximal biomass yield was 400–500 mg/L at 0.1–1% salinity while the TOC, NO3−-N, PO43−-P were eliminated 39.5–92.1%, 23–97.4% and 7–30.6%, respectively. The biomass yield and pollutants removal efficiencies reduced significantly when salinity rose from 0.1 to 5%. The freshwater Chlorella vulgaris performed its best with a focus on TOC removal at 0.1% salinity. The marine Chlorella sp. was prominent for removing NO3−-N at 0.1–1% salinity. Through the developed method, the freshwater C. vulgaris competed to the marine microalgae referring to pollutants assimilation up to 5% salinity. This study unveiled the mechanism of salinity's effect with evidence of salt layer formation and salt accumulation in microalgae.

Vo, HNP, Ngo, HH, Guo, W, Nguyen, TMH, Liu, Y, Liu, Y, Nguyen, DD & Chang, SW 2019, 'A critical review on designs and applications of microalgae-based photobioreactors for pollutants treatment', Science of The Total Environment, vol. 651, no. Pt 1, pp. 1549-1568.
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© 2018 Elsevier B.V. The development of the photobioreactors (PBs) is recently noticeable as cutting-edge technology while the correlation of PBs' engineered elements such as modellings, configurations, biomass yields, operating conditions and pollutants removal efficiency still remains complex and unclear. A systematic understanding of PBs is therefore essential. This critical review study is to: (1) describe the modelling approaches and differentiate the outcomes; (2) review and update the novel technical issues of PBs' types; (3) study microalgae growth and control determined by PBs types with comparison made; (4) progress and compare the efficiencies of contaminants removal given by PBs' types and (5) identify the future perspectives of PBs. It is found that Monod model's shortcoming in internal substrate utilization is well fixed by modified Droop model. The corroborated data also remarks an array of PBs' types consisting of flat plate, column, tubular, soft-frame and hybrid configuration in which soft-frame and hybrid are the latest versions with higher flexibility, performance and smaller foot-print. Flat plate PBs is observed with biomass yield being 5 to 20 times higher than other PBs types while soft-frame and membrane PBs can also remove pharmaceutical and personal care products (PPCPs) up to 100%. Looking at an opportunity for PBs in sustainable development, the flat plate PBs are applicable in PB-based architectures and infrastructures indicating an encouraging revenue-raising potential.

Voerman, SE, Glasby, TM, Gladstone, W & Gribben, PE 2019, 'Morphological variation of a rapidly spreading native macroalga across a range of spatial scales and its tolerance to sedimentation', Marine Environmental Research, vol. 147, pp. 149-158.
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Understanding how species' traits can shape winners and losers of environmental change can help resolve drivers of current community composition patterns and predict future drivers. Sedimentation is one of the main environmental stressors shaping coastal marine communities and tolerance of high sedimentation rates (e.g. via morphological variation) may allow for competitive dominance. In New South Wales, Australia, the abundance and range of the native green macroalga Caulerpa filiformis have increased over recent decades, apparently associated with sediment disturbance. We used field measurements to test hypotheses about morphological variability in C. filiformis in relation to local- and large-scale environmental variation in water depth, sediment cover and latitude. Using a lab experiment, we tested hypotheses about survival and morphological change under different sedimentation regimes. In the field, C. filiformis fronds were more elongated and less branched when a sediment veneer is present and when water depth increased (i.e. reduced light). At larger spatial scales, frond length and width decreased with increased latitude, but latitude was less important in explaining the variation C. filiformis' length than were depth or sedimentation. Our lab experiment showed a high tolerance to sedimentation, aided by increased investment in vertical growth. This study shows that rapid morphological plasticity is a likely key attribute of the spreading native macroalga C. filiformis. We argue that having a broad environmental tolerance is key to define a species success under environmental change.

Vuckovic, S, Bryant, C, Marsh-Wakefield, F, Kruzins, A, McGuire, H, Yang, S, Fazekas de St. Groth, B, Nassif, N, Byrne, SN, Gibson, J, Brown, C, Larsen, S, McCulloch, D, Boyle, R, Clark, G, Joshua, D & Ho, PJ 2019, 'Activated and Bone-marrow Resident Treg Alterations Underlie Malignant Transformation from MGUS to Multiple Myeloma', Clinical Lymphoma Myeloma and Leukemia, vol. 19, no. 10, pp. e100-e100.
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Wadhwa, R, Aggarwal, T, Malyla, V, Kumar, N, Gupta, G, Chellappan, DK, Dureja, H, Mehta, M, Satija, S, Gulati, M, Maurya, PK, Collet, T, Hansbro, PM & Dua, K 2019, 'Identification of biomarkers and genetic approaches toward chronic obstructive pulmonary disease', Journal of Cellular Physiology, vol. 234, no. 10, pp. 16703-16723.
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AbstractChronic obstructive pulmonary disease accounts as the leading cause of mortality worldwide prominently affected by genetic and environmental factors. The disease is characterized by persistent coughing, breathlessness airways inflammation followed by a decrease in forced expiratory volume1 and exacerbations, which affect the quality of life. Determination of genetic, epigenetic, and oxidant biomarkers to evaluate the progression of disease has proved complicated and challenging. Approaches including exome sequencing, genome‐wide association studies, linkage studies, and inheritance and segregation studies played a crucial role in the identification of genes, their pathways and variation in genes. This review highlights multiple approaches for biomarker and gene identification, which can be used for differential diagnosis along with the genome editing tools to study genes associated with the development of disease and models their function. Further, we have discussed the approaches to rectify the abnormal gene functioning of respiratory tissues and various novel gene editing techniques like Zinc finger nucleases (ZFN), transcription activator‐like effector nucleases (TALEN), and clustered regulatory interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9).

Wadhwa, R, Aggarwal, T, Thapliyal, N, Kumar, A, Priya, Yadav, P, Kumari, V, Reddy, BSC, Chandra, P & Maurya, PK 2019, 'Red blood cells as an efficient in vitro model for evaluating the efficacy of metallic nanoparticles', 3 Biotech, vol. 9, no. 7.
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© 2019, King Abdulaziz City for Science and Technology. Blood and the linings of blood vessels may be regarded as a fifth tissue type. The human body contains 5 × 109 red blood cells (RBCs) per ml, a total of 2.5 × 1013 cells in the 5 l of blood present in the body. With an average lifetime of 125 days, human RBCs are destroyed by leukocytes in the spleen and liver. Nowadays red blood cells are extensively used to study various metabolic functions. Nanoparticles (NP) are being widely accepted for drug delivery system. This review summarizes the red blood cells, NPs and their characteristics on the basis of the RBC components along with drug delivery systems through RBCs. Further, we also discussed that how erythrocytes can be used as an efficient in vitro model for evaluating the efficacy of various nanocomposite materials.

Wadhwa, R, Dua, K, Adcock, IM, Horvat, JC, Kim, RY & Hansbro, PM 2019, '“Cellular mechanisms underlying steroid-resistant asthma.” Ridhima Wadhwa, Kamal Dua, Ian M. Adcock, Jay C. Horvat, Richard Y. Kim and Philip M. Hansbro. Eur Respir Rev 2019; 28: 190021.', European Respiratory Review, vol. 28, no. 154, pp. 195096-195096.
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Wadhwa, R, Dua, K, Adcock, IM, Horvat, JC, Kim, RY & Hansbro, PM 2019, 'Cellular mechanisms underlying steroid-resistant asthma', European Respiratory Review, vol. 28, no. 153, pp. 190096-190096.
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Severe steroid-resistant asthma is clinically important, as patients with this form of the disease do not respond to mainstay corticosteroid therapies. The heterogeneity of this form of asthma and poor understanding of the pathological mechanisms involved hinder the identification of therapeutic targets and the development of more effective therapies. A major limiting factor in the understanding of severe steroid-resistant asthma is the existence of multiple endotypes represented by different immunological and inflammatory phenotypes, particularly in adults. Several clinical and experimental studies have revealed associations between specific respiratory infections and steroid-resistant asthma in adults. Here, we discuss recent findings from other authors as well as our own studies that have developed novel experimental models for interrogating the association between respiratory infections and severe steroid-resistant asthma. These models have enabled the identification of new therapies using macrolides, as well as several novel disease mechanisms, including the microRNA-21/phosphoinositide 3-kinase/histone deacetylase 2 axis and NLRP3 inflammasomes, and highlight the potential of these mechanisms as therapeutic targets.

Wadhwa, R, Gupta, R & Maurya, PK 2019, 'Oxidative Stress and Accelerated Aging in Neurodegenerative and Neuropsychiatric Disorder', Current Pharmaceutical Design, vol. 24, no. 40, pp. 4711-4725.
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Background: Neurodegenerative diseases are becoming more and more common in today’s world. Aspeople are continuously being exposed to exogenous factors like UV radiations, gamma rays, X-Rays,environmental pollutants and heavy metals, the cases of increased oxidative damage are increasing. Even thoughsome amount of oxidative damage occurs in all metabolic reactions but their increase from the normal level inorganisms causes neurodegenerative diseases. These neurodegenerative disorders like Alzeimers, Parkinsonsdisease and neuropsychiatric disorders such as schizophrenia, bipolar, depression are caused due to the decline inphysiological and psychological functions caused by ROS and RNS. These ROS and RNS are formed as theresult of excess oxidative damage in the system.Methods: The following article goes into detail explaining all the effects caused by excess oxidative damage likeROS/RNS formation and telomere shortening. Further, it explains the pathways of neurodegenerative diseasesand neuropsychiatric diseases. This article also sheds light on the effective treatments of such disorders by changinglifestyle and activating antioxidant pathways.Conclusion: It is clear that neurodegenerative diseases are caused due to excess oxidative stress and alter thefunctioning of the central nervous system. The central nervous system undergoes neurodegenerative orneuropsychiatric changes.

Wadhwa, R, Pandey, P, Gupta, G, Aggarwal, T, Kumar, N, Mehta, M, Satija, S, Gulati, M, Madan, JR, Dureja, H, Balusamy, SR, Perumalsamy, H, Maurya, PK, Collet, T, Tambuwala, MM, Hansbro, PM, Chellappan, DK & Dua, K 2019, 'Emerging Complexity and the Need for Advanced Drug Delivery in Targeting Candida Species', Current Topics in Medicinal Chemistry, vol. 19, no. 28, pp. 2593-2609.
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Background:Candida species are the important etiologic agents for candidiasis, the most prevalent cause of opportunistic fungal infections. Candida invasion results in mucosal to systemic infections through immune dysfunction and helps in further invasion and proliferation at several sites in the host. The host defence system utilizes a wide array of the cells, proteins and chemical signals that are distributed in blood and tissues which further constitute the innate and adaptive immune system. The lack of antifungal agents and their limited therapeutic effects have led to high mortality and morbidity related to such infections.Methods:The necessary information collated on this review has been gathered from various literature published from 1995 to 2019.Results:This article sheds light on novel drug delivery approaches to target the immunological axis for several Candida species (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, C. rugose, C. hemulonii, etc.).Conclusion:It is clear that the novel drug delivery approaches include vaccines, adoptive transfer of primed immune cells, recombinant cytokines, therapeutic antibodies, and nanoparticles, which have immunomodulatory effects. Such advancements in targeting various underpinning mechanisms using the concept of novel drug delivery will provide a new dimension to the fungal infection clinic particularly due to Candida species with improved patient compliance and lesser side effects. This advancement in knowledge can also be extended to target various other similar microbial species and infections.

Waltham, NJ, Burrows, D, Wegscheidl, C, Buelow, C, Ronan, M, Connolly, N, Groves, P, Marie-Audas, D, Creighton, C & Sheaves, M 2019, 'Lost Floodplain Wetland Environments and Efforts to Restore Connectivity, Habitat, and Water Quality Settings on the Great Barrier Reef', Frontiers in Marine Science, vol. 6, no. May.
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Wang, C, Zhang, L, Al‐Mamun, M, Dou, Y, Liu, P, Su, D, Wang, G, Zhang, S, Wang, D & Zhao, H 2019, 'A Hollow‐Shell Structured V₂O₅ Electrode‐Based Symmetric Full Li‐Ion Battery with Highest Capacity', Advanced Energy Materials, vol. 9, no. 31, pp. 1900909-1900909.
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AbstractThe symmetric batteries with an electrode material possessing dual cathodic and anodic properties are regarded as an ideal battery configuration because of their distinctive advantages over the asymmetric batteries in terms of fabrication process, cost, and safety concerns. However, the development of high‐performance symmetric batteries is highly challenging due to the limited availability of suitable symmetric electrode materials with such properties of highly reversible capacity. Herein, a triple‐hollow‐shell structured V2O5 (THS‐V2O5) symmetric electrode material with a reversible capacity of >400 mAh g−1 between 1.5 and 4.0 V and >600 mAh g−1 between 0.1 and 3.0 V, respectively, when used as the cathode and anode, is reported. The THS‐V2O5 electrodes assembled symmetric full lithium‐ion battery (LIB) exhibits a reversible capacity of ≈290 mAh g−1 between 2 and 4.0 V, the best performed symmetric energy storage systems reported to date. The unique triple‐shell structured electrode makes the symmetric LIB possessing very high initial coulombic efficiency (94.2%), outstanding cycling stability (with 94% capacity retained after 1000 cycles), and excellent rate performance (over 140 mAh g−1 at 1000 mA g−1). The demonstrated approach in this work leaps forward the symmetric LIB performance and paves a way to develop high‐performance symmetric battery electrode materials.

Wang, C, Zhang, L, Al‐Mamun, M, Dou, Y, Liu, P, Su, D, Wang, G, Zhang, S, Wang, D & Zhao, H 2019, 'Lithium Ion Batteries: A Hollow‐Shell Structured V₂O₅ Electrode‐Based Symmetric Full Li‐Ion Battery with Highest Capacity (Adv. Energy Mater. 31/2019)', Advanced Energy Materials, vol. 9, no. 31, pp. 1970120-1970120.
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Wang, G, Fu, L, Walker, A, Chen, X, Lovejoy, DB, Hao, M, Lee, A, Chung, R, Rizos, H, Irvine, M, Zheng, M, Liu, X, Lu, Y & Shi, B 2019, 'Label-Free Fluorescent Poly(amidoamine) Dendrimer for Traceable and Controlled Drug Delivery', Biomacromolecules, vol. 20, no. 5, pp. 2148-2158.
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Wang, J, Su, P, Zhang, J, Wang, F, Chen, Y, Liu, H & Liu, J 2019, 'The formation of yolk–shell structured NiO nanospheres with enhanced lithium storage capacity', Materials Chemistry Frontiers, vol. 3, no. 8, pp. 1619-1625.
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Yolk–shell structured NiO nanospheres were successfully fabricated and showed excellent performance as an anode for lithium-ion batteries.

Wang, JJ & Weatherburn, D 2019, 'Are police cautions a soft option? Reoffending among juveniles cautioned or referred to court', Australian & New Zealand Journal of Criminology, vol. 52, no. 3, pp. 334-347.
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During the 1990s, many jurisdictions introduced police cautions as an alternative to referral to court for juveniles committing comparatively minor offences. The policy was motivated by a concern that contact with the court system for such offenders might be criminogenic. In recent years, however, elected officials have criticised police cautions as a ‘soft option’ and this (in some jurisdictions at least) has led to a decline in their use. Past research has often failed to ensure that the comparison group for a police caution consists of children referred to court who could have received a police caution. The current study overcomes this problem and employs a rigorous set of procedures for minimising the risk of selection bias. Our results indicate that cautioning young offenders who have committed comparatively minor offences and who have not previously been referred to court results in a lower risk of reoffending than referral to court. We conclude that restrictions on the use of cautions in these circumstances could increase the risk of juvenile reoffending.

Wang, JJ, Weatherburn, D & Wan, W 2019, 'The long-term effect of routine police activity on property and violent crime in NSW, Australia'.

Wang, KYX, Menzies, AM, Silva, IP, Wilmott, JS, Yan, Y, Wongchenko, M, Kefford, RF, Scolyer, RA, Long, GV, Tarr, G, Mueller, S & Yang, JYH 2019, 'bcGST—an interactive bias-correction method to identify over-represented gene-sets in boutique arrays', Bioinformatics, vol. 35, no. 8, pp. 1350-1357.
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Abstract Motivation Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes are important tools in Gene-Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene-set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene-set selection bias induced during the construction of these platforms. Results We propose bcGST, a bias-corrected GST by introducing bias-correction terms in the contingency table needed for calculating the Fisher’s Exact Test. The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and the Cancer Genome Atlas cancer studies. Availability and implementation The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/.

Wang, KYX, Tarr, G, Yang, JYH & Mueller, S 2019, 'Fast and approximate exhaustive variable selection for generalised linear models with APES', Australian & New Zealand Journal of Statistics, vol. 61, no. 4, pp. 445-465.
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SummaryWe present APproximated Exhaustive Search (APES), which enables fast and approximated exhaustive variable selection in Generalised Linear Models (GLMs). While exhaustive variable selection remains as the gold standard in many model selection contexts, traditional exhaustive variable selection suffers from computational feasibility issues. More precisely, there is often a high cost associated with computing maximum likelihood estimates (MLE) for all subsets of GLMs. Efficient algorithms for exhaustive searches exist for linear models, most notably the leaps‐and‐bound algorithm and, more recently, the mixed integer optimisation (MIO) algorithm. The APES method learns from observational weights in a generalised linear regression super‐model and reformulates the GLM problem as a linear regression problem. In this way, APES can approximate a true exhaustive search in the original GLM space. Where exhaustive variable selection is not computationally feasible, we propose a best‐subset search, which also closely approximates a true exhaustive search. APES is made available in both as a standalone R package as well as part of the already existing mplot package.

Wang, L, Cui, D, Ren, L, Zhou, J, Wang, F, Casillas, G, Xu, X, Peleckis, G, Hao, W, Ye, J, Dou, SX, Jin, D & Du, Y 2019, 'Boosting NIR-driven photocatalytic water splitting by constructing 2D/3D epitaxial heterostructures', Journal of Materials Chemistry A, vol. 7, no. 22, pp. 13629-13634.
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YF₃:Yb, Tm@BiOCl possesses epitaxial heterostructure, which can quantitatively activate multiple energy transfer channels including excited-state energy transfer and fluorescence reabsorption, and then promote the NIR-driven photocatalytic properties.

Wang, L, Liu, P-C, Wu, LM, Tan, J, Peacock, WJ & Dennis, ES 2019, 'Cotyledons contribute to plant growth and hybrid vigor in Arabidopsis', Planta, vol. 249, no. 4, pp. 1107-1118.
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MAIN CONCLUSION:In hybrids of Arabidopsis, cotyledons influence the amount and proportion of hybrid vigor in total plant growth. We found Arabidopsis cotyledons are essential for plant growth and in some hybrids for hybrid vigor. In hybrids between C24 and Landsberg erecta (Ler), biomass vigor (heterosis) occurs in the first few days after sowing (DAS), with hybrid cotyledons being larger than those of their parents. C24xLer hybrids are ahead of their parents in activating photosynthesis and auxin pathway genes in cotyledons at 3-4 DAS. "Earliness" is also present in newly emerged C24xLer hybrid leaves. We showed cotyledon removal at 4 DAS caused significant biomass reduction in later growth in hybrids and parental lines. The biomass decrease caused by cotyledon removal can be partially rescued by exogenous sucrose or auxin with different genotypes responding to sucrose and/or auxin differently. Cotyledon removal has different effects on heterosis in different hybrids. After cotyledon removal, in C24xLer hybrids, both growth and heterosis were reduced in similar proportions, but the level of hybrid vigor was reduced as a proportion of growth in C24xColumbia (Col) and ColxLer hybrids. The removal of cotyledons at 4 DAS markedly decreased the level of growth and eliminated the heterotic phenotype of Wassilewskija (Ws)/Ler hybrids. In mutant Ws/Ler hybrids which had a reduced level of photosynthesis in the cotyledons, there was a reduction in plant growth and loss of heterosis. The variation in contribution of cotyledons to heterosis in different hybrids indicates there are multiple pathways to achieve heterotic phenotypes.

Wang, L, Wen, Q, Jia, P, Jia, M, Lu, D, Sun, X, Jiang, L & Guo, W 2019, 'Light‐Driven Active Proton Transport through Photoacid‐ and Photobase‐Doped Janus Graphene Oxide Membranes', Advanced Materials, vol. 31, no. 36, p. e1903029.
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AbstractBiological electrogenic systems use protein‐based ionic pumps to move salt ions uphill across a cell membrane to accumulate an ion concentration gradient from the equilibrium physiological environment. Toward high‐performance and robust artificial electric organs, attaining an antigradient ion transport mode by fully abiotic materials remains a great challenge. Herein, a light‐driven proton pump transport phenomenon through a Janus graphene oxide membrane (JGOM) is reported. The JGOM is fabricated by sequential deposition of graphene oxide (GO) nanosheets modified with photobase (BOH) and photoacid (HA) molecules. Upon ultraviolet light illumination, the generation of a net protonic photocurrent through the JGOM, from the HA‐GO to the BOH‐GO side, is observed. The directional proton flow can thus establish a transmembrane proton concentration gradient of up to 0.8 pH units mm−2 membrane area at a proton transport rate of 3.0 mol h−1 m−2. Against a concentration gradient, antigradient proton transport can be achieved. The working principle is explained in terms of asymmetric surface charge polarization on HA‐GO and BOH‐GO multilayers triggered by photoisomerization reactions, and the consequent intramembrane proton concentration gradient. The implementation of membrane‐scale light‐harvesting 2D nanofluidic system that mimics the charge process of the bioelectric organs makes a straightforward step toward artificial electrogenic and photosynthetic applications.

Wang, L, Wu, LM, Greaves, IK, Dennis, ES & Peacock, WJ 2019, 'In Arabidopsis hybrids and Hybrid Mimics, up‐regulation of cell wall biogenesis is associated with the increased plant size', Plant Direct, vol. 3, no. 11.
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AbstractHybrid breeding is of economic importance in agriculture for increasing yield, yet the basis of heterosis is not well understood. In Arabidopsis, crosses between different accessions produce hybrids with different levels of heterosis relative to parental phenotypes in biomass. In all hybrids, the advantage of the F1 hybrid in both phenotypic uniformity and yield gain is lost in the heterogeneous F2. F5/F6 Hybrid Mimics generated from a cross between C24 and Landsberg erecta (Ler) ecotypes demonstrated that the large plant phenotype of the F1 hybrids can be stabilized. Hybrid Mimic selection was applied to Wassilewskija (Ws)/Ler and Col/Ler hybrids. The two hybrids show different levels of heterosis. The Col/Ler hybrid generated F7 Hybrid Mimics with rosette diameter and fresh weight equivalent to the F1 hybrid at 30 DAS; F7 Ws/Ler Hybrid Mimics outperformed the F1 hybrid in both the rosette size and biomass. Transcriptome analysis revealed up‐regulation of cell wall biosynthesis, and cell wall expansion genes could be a common pathway in increased size in the Arabidopsis hybrids and Hybrid Mimics. Intercross of two independent Hybrid Mimic lines can further increase the biomass gain. Our results encourage the use of Hybrid Mimics for breeding and for investigating the molecular basis of heterosis.

Wang, S, Ju, W, Peñuelas, J, Cescatti, A, Zhou, Y, Fu, Y, Huete, A, Liu, M & Zhang, Y 2019, 'Urban−rural gradients reveal joint control of elevated CO2 and temperature on extended photosynthetic seasons', Nature Ecology & Evolution, vol. 3, no. 7, pp. 1076-1085.
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Photosynthetic phenology has large effects on the land-atmosphere carbon exchange. Due to limited experimental assessments, a comprehensive understanding of the variations of photosynthetic phenology under future climate and its associated controlling factors is still missing, despite its high sensitivities to climate. Here, we develop an approach that uses cities as natural laboratories, since plants in urban areas are often exposed to higher temperatures and carbon dioxide (CO2) concentrations, which reflect expected future environmental conditions. Using more than 880 urban-rural gradients across the Northern Hemisphere (≥30° N), combined with concurrent satellite retrievals of Sun-induced chlorophyll fluorescence (SIF) and atmospheric CO2, we investigated the combined impacts of elevated CO2 and temperature on photosynthetic phenology at the large scale. The results showed that, under urban conditions of elevated CO2 and temperature, vegetation photosynthetic activity began earlier (-5.6 ± 0.7 d), peaked earlier (-4.9  ± 0.9 d) and ended later (4.6 ± 0.8 d) than in neighbouring rural areas, with a striking two- to fourfold higher climate sensitivity than greenness phenology. The earlier start and peak of season were sensitive to both the enhancements of CO2 and temperature, whereas the delayed end of season was mainly attributed to CO2 enrichments. We used these sensitivities to project phenology shifts under four Representative Concentration Pathway climate scenarios, predicting that vegetation will have prolonged photosynthetic seasons in the coming two decades. This observation-driven study indicates that realistic urban environments, together with SIF observations, provide a promising method for studying vegetation physiology under future climate change.

Wang, S, Leslie, L, Rai, T, Speer, M & Kuleshov, Y 2019, 'Analysis of a southerly buster event and associated solitary waves', Journal of Southern Hemisphere Earth Systems Science, vol. 69, no. 1, pp. 205-205.
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This paper is a detailed case study of the southerly buster of 6–7 October 2015, along the New South Wales coast. It takes advantage of recently available Himawari-8 high temporal- and spatial-resolution satellite data, and other observational data. The data analyses support the widespread view that the southerly buster is a density current, coastally trapped by the Great Dividing Range. In addition, it appeared that solitary waves developed in this event because the prefrontal boundary layer was shallow and stable. A simplified density current model produced speeds matching well with observational southerly buster data, at both Nowra and Sydney airports. Extending the density current theory, to include inertia-gravity effects, suggested that the solitary waves travel at a speed of ~20% faster than the density current. This speed difference was consistent with the high-resolution satellite data, which shows the solitary waves moving increasingly ahead of the leading edge of the density current.

Wang, Y, Jia, L, Wang, X, Fu, L, Liu, J & Qian, L 2019, 'Diagnostic Performance of 2-D Shear Wave Elastography for Differentiation of Hepatoblastoma and Hepatic Hemangioma in Children under 3 Years of Age', Ultrasound in Medicine & Biology, vol. 45, no. 6, pp. 1397-1406.
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Wang, Z, Luo, C, Anwand, W, Wagner, A, Butterling, M, Rahman, MA, Phillips, MR, Ton-That, C, Younas, M, Su, S & Ling, FC-C 2019, 'Vacancy cluster in ZnO films grown by pulsed laser deposition', Scientific Reports, vol. 9, no. 1.
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AbstractUndoped and Ga-doped ZnO films were grown on c-sapphire using pulsed laser deposition (PLD) at the substrate temperature of 600 °C. Positron annihilation spectroscopy study (PAS) shows that the dominant VZn-related defect in the as-grown undoped ZnO grown with relative low oxygen pressure P(O2) is a vacancy cluster (most likely a VZn-nVO complex with n = 2, 3) rather than the isolated VZn which has a lower formation energy. Annealing these samples at 900 °C induces out-diffusion of Zn from the ZnO film into the sapphire creating the VZn at the film/sapphire interface, which favors the formation of vacancy cluster containing relatively more VZn. Increasing the P(O2) during growth also lead to the formation of the vacancy cluster with relatively more VZn. For Ga-doped ZnO films, the oxygen pressure during growth has significant influence on the electron concentration and the microstructure of the VZn-related defect. Green luminescence (GL) and yellow luminescence (YL) were identified in the cathodoluminescence study (CL) study, and both emission bands were quenched after hydrogen plasma treatment. The origin of the GL is discussed.

Wangpraseurt, D, Larkum, AWD, Ferrier-Pagès, C, Salih, A, Warner, ME, Dubinsky, Z & Kühl, M 2019, 'Editorial: Optics and Ecophysiology of Coral Reef Organisms', Frontiers in Marine Science, vol. 6.
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Wangpraseurt, D, Lichtenberg, M, Jacques, SL, Larkum, AWD & Kühl, M 2019, 'Optical Properties of Corals Distort Variable Chlorophyll Fluorescence Measurements', Plant Physiology, vol. 179, no. 4, pp. 1608-1619.
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© 2019 American Society of Plant Biologists. All rights reserved. Pulse-amplitude–modulated (PAM) fluorimetry is widely used in photobiological studies of corals, as it rapidly provides numerous photosynthetic parameters to assess coral ecophysiology. Coral optics studies have revealed the presence of light gradients in corals, which are strongly affected by light scattering in coral tissue and skeleton. We investigated whether coral optics affects variable chlorophyll (Chl) fluorescence measurements and derived photosynthetic parameters by developing planar hydrogel slabs with immobilized microalgae and with bulk optical properties similar to those of different types of corals. Our results show that PAM-based measurements of photosynthetic parameters differed substantially between hydrogels with different degrees of light scattering but identical microalgal density, yielding deviations in apparent maximal electron transport rates by a factor of 2. Furthermore, system settings such as the measuring light intensity affected F0, Fm, and Fv/Fm in hydrogels with identical light absorption but different degrees of light scattering. Likewise, differences in microalgal density affected variable Chl fluorescence parameters, where higher algal densities led to greater Fv/Fm values and relative electron transport rates. These results have important implications for the use of variable Chl fluorimetry in ecophysiological studies of coral stress and photosynthesis, as well as other optically dense systems such as plant tissue and biofilms.

Ward, J, Johnson, RN & Wilson-Wilde, L 2019, 'Gender equity: how do the forensic sciences fare?', Australian Journal of Forensic Sciences, vol. 51, no. sup1, pp. S263-S267.
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© 2019, © Crown Copyright in the Commonwealth of Australia 2019. NSW Health Pathology. Females are underrepresented in science, technology, engineering and mathematics (STEM) at all levels of society. Fewer females are completing STEM school subjects, graduating with STEM degrees, being employed as STEM professionals, and holding senior leadership and academic positions in STEM. However, unlike almost every other STEM discipline, the overall ratio of females is higher in many forensic science disciplines. For our sector, rather than having difficulty in attracting females, the bigger issue is how we retain and promote female talent. This complex issue is exacerbated by: gender pay gaps; family role expectations; lack of visible role models or mentors; discrimination and harassment; and bias during recruitment and promotion practices. We discuss barriers relevant for women in the forensic industry and offer potential solutions. These include flexible work arrangements, sponsorship programmes, and fostering and practising an inclusive workplace culture. Gender equity programmes and exemplar STEM organizations focused on a commitment to gender parity will be explored. Harnessing untapped female talent is as much a social justice issue as employing best practices for improving the quality, diversity and output of our forensic science workforce, and research and innovation strategies.

Waters, DW, Blokland, KEC, Pathinayake, PS, Wei, L, Schuliga, M, Jaffar, J, Westall, GP, Hansbro, PM, Prele, CM, Mutsaers, SE, Bartlett, NW, Burgess, JK, Grainge, CL & Knight, DA 2019, 'STAT3 Regulates the Onset of Oxidant-induced Senescence in Lung Fibroblasts', American Journal of Respiratory Cell and Molecular Biology, vol. 61, no. 1, pp. 61-73.
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Copyright © 2019 by the American Thoracic Society. Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown cause with a median survival of only 3 years. Other investigators and we have shown that fibroblasts derived from IPF lungs display characteristics of senescent cells, and that dysregulated activation of the transcription factor signal transducer and activator of transcription 3 (STAT3) correlates with IPF progression. The question of whether STAT3 activation is involved in fibroblast senescence remains unanswered. We hypothesized that inhibiting STAT3 activation after oxidantinduced senescence would attenuate characteristics of the senescent phenotype. We aimed to characterize a model of oxidant-induced senescence in human lung fibroblasts and to determine the effect of inhibiting STAT3 activity on the development of senescence. Exposing human lung fibroblasts to 150 μM hydrogen peroxide (H2O2) resulted in increased senescence-associated β-galactosidase content and expression of p21 and IL-6, all of which are features of senescence. The shift into senescence was accompanied by an increase of STAT3 translocation to the nucleus and mitochondria. Additionally, Seahorse analysis provided evidence of increased mitochondrial respiration characterized by increased basal respiration, proton leak, and an associated increase in superoxide (O2-) production in senescent fibroblasts. Targeting STAT3 activity using the small-molecule inhibitor STA-21 attenuated IL-6 production, reduced p21 levels, decreased senescence-associated b-galactosidase accumulation, and restored normalmitochondrial function. The results of this study illustrate that stress-induced senescence in lung fibroblasts involves the activation of STAT3, which can be pharmacologically modulated.

Waters, L, Padula, MP, Marks, DC & Johnson, L 2019, 'Cryopreservation of UVC pathogen‐inactivated platelets', Transfusion, vol. 59, no. 6, pp. 2093-2102.
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BACKGROUNDExtending the platelet (PLT) shelf life and enhancing product safety may be achieved by combining cryopreservation and pathogen inactivation (PI). Although studied individually, limited investigations into combining these treatments has been performed. The aim of this study was to investigate the effect of PI treating PLTs before cryopreservation on in vitro PLT quality and function.STUDY DESIGN AND METHODSABO‐matched buffy coat–derived PLTs in PLT additive solution (SSP+; Macopharma) were pooled and split to form matched pairs (n = 8). One unit remained untreated and the other was treated with the THERAFLEX UV‐Platelets System (UVC; Macopharma). For cryopreservation, 5% to 6% dimethyl sulfoxide was added to the PLTs, and they were frozen at −80°C. After being thawed, untreated cryopreserved PLTs (CPPs) and UVC‐treated CPPs (UVC‐CPPs) were resuspended in plasma. In vitro quality was assessed immediately after thawing and after 24 hours of room temperature storage.RESULTSUVC‐CPPs had lower in vitro recovery compared to CPPs. By flow cytometry, PLTs demonstrated a similar abundance of GPIX (CD42a), GPIIb (CD41a), and GPIbα (CD42b‐HIP1), while the activation of GPIIb/IIIa (PAC‐1) was increased in UVC‐CPPs compared to CPPs. UVC‐CPPs demonstrated greater phosphatidylserine exposure (annexin V) and microparticle shedding but similar P‐selectin (CD62P) abundance compared to CPPs. UVC‐CPPs displayed similar functionality to CPPs when assessed using aggregometry, thromboelastography, and thrombin generation.CONCLUSIONSThis study demonstrates the feasibility of cryopreserving UVC‐PI–treated PLT products. UVC‐PI treatment may increase the susceptibility of PLTs to damage caused during cryopreservation, but this is more pronoun...

Watherston, J, Bruce, D, Ward, J, Gahan, ME & McNevin, D 2019, 'Automating direct-to-PCR for disaster victim identification', Australian Journal of Forensic Sciences, vol. 51, no. sup1, pp. S39-S43.
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© 2019, © 2019 Australian Academy of Forensic Sciences. Direct-to-PCR methodology adds samples directly to PCR tubes offering gains in efficiency and sensitivity. The approach has been applied to a variety of biological sources including blood, saliva, tissue, hair and nail. We added various preservative solutions to a range of biological samples to leech DNA into solution, whilst preserving at room temperature. Tubes containing ‘free DNA’ then followed automated workflows for amplification and capillary electrophoresis. Routine FASS-automated workflows (including DNA extraction and quantification) were compared with published direct-to-PCR methodology and automated amplification of an aliquot of preservative solution. Applying preservative solutions to ~30-year-old blood stains stored at room temperature resulted in recovery of a larger quantity of DNA and more alleles (using PowerPlex 21) when compared with routine automated typing. Trials were extended to blood, saliva, hair and nail, mimicking ante-mortem samples collected in a disaster victim identification effort. Despite slightly lower allelic recovery, the faster processing times, lower costs and storage potential offers advantages for the processing of ante-mortem samples.

Watson, CJ, Restrepo-Coupe, N & Huete, AR 2019, 'Multi-Scale Phenology of Temperate Grasslands: Improving Monitoring and Management With Near-Surface Phenocams', Frontiers in Environmental Science, vol. 7, no. FEB.
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© 2019 Watson, Restrepo-Coupe and Huete. Grasslands of the Australian Southern Tablelands represent a patchwork of native and exotic systems, occupying a continuum of C 3 -dominated to C 4 -dominated grasslands where composition depends on disturbance factors (e.g., grazing) and climate. Managing these complex landscapes is both challenging and critical for maintaining the security of Australia's pasture industries, and for protecting the biodiversity of native remnants. Differentiating C 3 from C 4 vegetation has been a prominent theme in remote sensing research due to distinct C 3 /C 4 seasonal productivity patterns (phenology) and high uncertainty about how C 3 /C 4 vegetation will respond to a changing climate. Phenology is used in northern hemisphere ecosystems for a range of purposes but has not been widely adopted in Australia, where dynamic climate often results in non-repetitive seasonal vegetation patterns. We employed time-lapse cameras (phenocams) to study the phenology of twelve grassland areas dominated by cool season (C 3 ) and warm season (C 4 ), native or exotic grasses near Canberra, Australia. Our aims were to assess phenological characteristics of the functional types and to determine the drivers of phenological variability. We compared the fine-scale phenocam seasonal profiles with field sampling and MODIS/Landsat satellite products to assess paddock-to-landscape functioning. We found C 3 /C 4 species dominance to be the primary driver of phenological differences among grassland types, with C 3 grasslands demonstrating peak greenness in spring, and senescing rapidly in response to high summer temperatures. In contrast, C 4 grasslands showed peak activity in Austral summer and autumn (January-March). Some sites displayed primary and secondary peaks dependent on rainfall and species composition. We found that the proportion of dead vegetation is an important biophysical driver of grassland phenology, as were grazing pressures and spec...

Webster, J, Lee, M, Gurba, LW, Manefield, M & Thomas, T 2019, 'The effect of oxidative treatment on soluble compounds from Australian coal', Fuel, vol. 257, pp. 116071-116071.
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The production of biogenic methane from coal has been observed through isotope analysis of coal bed methane (CBM). Microbial degradation of coal leads to the production of chemical compounds, which, under anaerobic conditions, can be biologically converted into methane. However, the types of coal compounds accessible to these microbial processes are poorly defined. This study aims to define the nature of chemical compounds released from coal under oxidative conditions. Coal from three different coal seams were extracted and released compounds were analysed with GC–MS and H-NMR. Coals were then exposed to hydrogen peroxide, calcium peroxide and peroxidase, which mimic microbial oxidation. Our analysis showed that the three coals shared around half of their apolar, mobile compounds, including alkanes ranging from C11 to C27 and methylated variations thereof, as well as poly-aromatic hydrocarbons, such as methylated naphthalenes, phenanthrenes and fluorenes. Oxidative treatments of coal caused significant changes in chemical profiles compared to untreated coal. All treatments resulted in the production of propionate, an important substrate for syntrophic methanogenesis. However, there were also qualitative and quantitative differences in the polar compounds produced during enzymatic and peroxide treatments. These results show how different chemical and enzymatic processes that are relevant to microbial oxidation will produce distinct profiles in intermediate metabolites that will likely then determine the subsequent pathways of microbial methane production.

Wei, Y, Xing, G, Liu, K, Li, G, Dang, P, Liang, S, Liu, M, Cheng, Z, Jin, D & Lin, J 2019, 'New strategy for designing orangish-red-emitting phosphor via oxygen-vacancy-induced electronic localization', Light: Science & Applications, vol. 8, no. 1.
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AbstractPhosphor-converted white-light-emitting diodes (pc-WLED) have been extensively employed as solid-state lighting sources, which have a very important role in people’s daily lives. However, due to the scarcity of the red component, it is difficult to realize warm white light efficiently. Hence, red-emitting phosphors are urgently required for improving the illumination quality. In this work, we develop a novel orangish-red La4GeO8:Bi3+ phosphor, the emission peak of which is located at 600 nm under near-ultraviolet (n-UV) light excitation. The full width at half maximum (fwhm) is 103 nm, the internal quantum efficiency (IQE) exceeds 88%, and the external quantum efficiency (EQE) is 69%. According to Rietveld refinement analysis and density functional theory (DFT) calculations, Bi3+ ions randomly occupy all La sites in orthorhombic La4GeO8. Importantly, the oxygen-vacancy-induced electronic localization around the Bi3+ ions is the main reason for the highly efficient orangish-red luminescence. These results provide a new perspective and insight from the local electron structure for designing inorganic phosphor materials that realize the unique luminescence performance of Bi3+ ions.

Welford, A, Maniam, S, Gann, E, Jiao, X, Thomsen, L, Langford, SJ & McNeill, CR 2019, 'Influence of alkyl side-chain type and length on the thin film microstructure and OFET performance of naphthalene diimide-based organic semiconductors', Organic Electronics, vol. 75, pp. 105378-105378.
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Wen, S, Zhou, J, Schuck, PJ, Suh, YD, Schmidt, TW & Jin, D 2019, 'Future and challenges for hybrid upconversion nanosystems', Nature Photonics, vol. 13, no. 12, pp. 828-838.
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© 2019, Springer Nature Limited. To improve the efficiency of photon upconversion, a hybrid approach of combining organic dyes and inorganic nanoparticles is proving successful, especially in the form of dye-sensitized lanthanide-doped upconversion nanoparticles, nanoparticle-sensitized molecular triplet–triplet annihilation systems and metal–organic-framework nanoparticles. In this Review, we survey the latest advances and examine the key factors affecting upconversion performance, such as spectral overlap, core–shell design and the management of triplet excitons and quenchers at the interface between materials. Although issues such as stability, triplet-state quenching, concentration quenching and reabsorption must still be overcome, smart designs of hybrid nanosystems offer exciting opportunities for applications such as solar photovoltaic devices, deep-tissue biomedical imaging, optogenetics and nanomedicine among others.

Wenzel, RG, Major, D, Hesp, KF, Hall, E & Doble, P 2019, 'Cobalt accumulation in horses following repeated administration of cobalt chloride', Australian Veterinary Journal, vol. 97, no. 11, pp. 465-472.
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ObjectiveTo monitor cobalt concentrations in urine, red blood cells and plasma after chronic parenteral administration of cobalt chloride evaluate these results against the current International Federation of Horseracing Authorities thresholds for detecting cobalt misuse.DesignEight mares were randomly assigned to four treatment groups, with two mares in each group: Group 1 – control group, Group 2 – 25 milligrams cobalt intravenously as CoCl2 weekly, Group 3 – 50 milligrams cobalt intravenously as CoCl2 weekly, and Group 4 – 25 milligrams cobalt intravenously mid‐week and at the end of the week. Urine and blood samples were collected before each weekly administration so that trough levels were assessed. In the group receiving two doses per week, urine and blood were collected prior to the dose given at the end of each week. Samples were initially collected at time zero then weekly for 10 weeks. Three further collections of urine and blood were made at days 81, 106 and 127.MethodsUrine creatinine measurements to assess horse hydration status were performed by the Jaffe reaction method. Cobalt determinations in plasma, blood and urine were by inductively coupled plasma—mass spectrometry. Haematocrit concentrations, used to calculate red cell cobalt levels, were performed using a microhematocrit centrifuge. Statistical analyses were conducted in Genstat (v17, VSNi).ResultsMarked cobalt accumulation was evident with increasing cobalt concentrations for all sample matrices in specimens collected immediately prior to cobalt administration. Correlation between the sample matrices improved when urine cobalt concentration was adjusted for creatinine level. Red cell cobalt levels remained elev...

West, M & Kachoyan, B 2019, 'Survival modelling of Australian politicians', Political Science, vol. 71, no. 2, pp. 140-157.
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© 2019, © 2019 The Research Trust of Victoria. Are Australian political leaders an endangered species? A survival analysis of Australian politicians shows that modern leaders are having almost as tough a time as leaders were in the early days of Australian politics. This article examines the tenures of Prime Ministers and Federal Opposition Leaders to show that while the leadership turnover of the last decade has been high, the modern era is not unlike the Australian parliament after 1901, albeit for different reasons. The parliamentary tenures of members of the House of Representatives and the Senate, male and female members of both houses, and Labor and Liberal leaders have been compared using the survival analysis technique, and while simple statistical tests and descriptors may show little overall difference between the various survival curves, there are often intriguing differences in the detail. For instance, there is evidence supporting the notion that women have historically not been preselected in safe seats. The differing electoral cycles are apparent in the Senate and House of Representative data, as is the historical under-representation of women. Labor leaders tend to have had a higher survival rate, at least in the short term, than their Liberal counterparts, while longer time periods are influenced by long-serving Liberal Prime Ministers.

Westerhausen, MT, Bishop, DP, Dowd, A, Wanagat, J, Cole, N & Doble, PA 2019, 'Super-Resolution Reconstruction for Two- and Three-Dimensional LA-ICP-MS Bioimaging', Analytical Chemistry, vol. 91, no. 23, pp. 14879-14886.
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© 2019 American Chemical Society. The resolution of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) elemental bioimaging is usually constrained by the diameter of the laser spot size and is often not adequate to explore in situ subcellular distributions of elements and proteins in biological tissue sections. Super-resolution reconstruction is a method typically used for many imaging modalities and combines multiple lower resolution images to create a higher resolution image. Here, we present a super-resolution reconstruction method for LA-ICP-MS imaging by ablating consecutive layers of a biological specimen with offset orthogonal scans, resulting in a 10× improvement in resolution for quantitative measurement of dystrophin in murine muscle fibers. Layer-by-layer image reconstruction was also extended to the third dimension without the requirement of image registration across multiple thin section specimens. Quantitative super-resolution reconstruction, combined with Gaussian filtering and application of the Richardson-Lucy total variation algorithm, provided superior image clarity and fidelity in two-and three-dimensions.

Westerhausen, MT, Lockwood, TE, Gonzalez de Vega, R, Röhnelt, A, Bishop, DP, Cole, N, Doble, PA & Clases, D 2019, 'Low background mould-prepared gelatine standards for reproducible quantification in elemental bio-imaging', The Analyst, vol. 144, no. 23, pp. 6881-6888.
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Raw intensities obtained from the ablation of mould-prepared gelatine.

Williams, TJ, Allen, MA, Liao, Y, Raftery, MJ & Cavicchioli, R 2019, 'Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics', Applied and Environmental Microbiology, vol. 85, no. 6.
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Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When genomic or metagenomic data are used, metabolic capacity is inferred from genetic potential. Here, we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase occurs only in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).

Wood, LG, Li, Q, Scott, HA, Rutting, S, Berthon, BS, Gibson, PG, Hansbro, PM, Williams, E, Horvat, J, Simpson, JL, Young, P, Oliver, BG & Baines, KJ 2019, 'Saturated fatty acids, obesity, and the nucleotide oligomerization domain–like receptor protein 3 (NLRP3) inflammasome in asthmatic patients', Journal of Allergy and Clinical Immunology, vol. 143, no. 1, pp. 305-315.
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© 2018 American Academy of Allergy, Asthma & Immunology Background: Both obesity and high dietary fat intake activate the nucleotide oligomerization domain–like receptor protein 3 (NLRP3) inflammasome. Objective: We aimed to examine NLRP3 inflammasome activity in the airways of obese asthmatic patients after macronutrient overload and in immune cells challenged by inflammasome triggers. Methods: Study 1 was a cross-sectional observational study of nonobese (n = 51) and obese (n = 76) asthmatic adults. Study 2 was a randomized, crossover, acute feeding study in 23 asthmatic adults (n = 12 nonobese and n = 11 obese subjects). Subjects consumed 3 isocaloric meals on 3 separate occasions (ie, saturated fatty acid, n-6 polyunsaturated fatty acid, and carbohydrate) and were assessed at 0 and 4 hours. For Studies 1 and 2, airway inflammation was measured based on sputum differential cell counts, IL-1β protein levels (ELISA), and sputum cell gene expression (Nanostring nCounter). In Study 3 peripheral blood neutrophils and monocytes were isolated by using Ficoll density gradient and magnetic bead separation and incubated with or without palmitic acid, LPS, or TNF-α for 24 hours, and IL-1β release was measured (ELISA). Results: In Study 1 NLRP3 and nucleotide oligomerization domain 1 (NOD1) gene expression was upregulated, and sputum IL-1β protein levels were greater in obese versus nonobese asthmatic patients. In Study 2 the saturated fatty acid meal led to increases in sputum neutrophil percentages and sputum cell gene expression of Toll-like receptor 4 (TLR4) and NLRP3 at 4 hours in nonobese asthmatic patients. In Study 3 neutrophils and monocytes released IL-1β when challenged with a combination of palmitic acid and LPS or TNF-α. Conclusion: The NLRP3 inflammasome is a potential therapeutic target in asthmatic patients. Behavioral interventions that reduce fatty acid exposure, such as weight loss and dietary saturated fat restriction, warrant further exploration.

Wood, RJ, Mitrovic, SM, Lim, RP, Warne, MSJ, Dunlop, J & Kefford, BJ 2019, 'Benthic diatoms as indicators of herbicide toxicity in rivers – A new SPEcies At Risk (SPEARherbicides) index', Ecological Indicators, vol. 99, pp. 203-213.
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© 2018 Elsevier Ltd Benthic diatom communities are used widely as indicators of river health due to their rapid response to changes in water quality. The ability for diatom-based indices to detect eutrophication has been well documented; however, an index designed specifically to detect herbicide impacts is yet to be established. This is required as herbicide contamination of rivers is common in agricultural regions and poses a potential threat to aquatic ecosystems. This study developed a new biomonitoring index (SPEARherbicides) using benthic diatom communities to detect the toxic impacts of herbicides in rivers, and tested it across 14 rivers in the Great Barrier Reef catchment area, Australia. The new index uses diatom species traits to classify diatoms as either sensitive or tolerant to herbicides and calculates the fraction of sensitive taxa within a sample. The SPEARherbicides index showed a decline in herbicide sensitive diatoms with increasing herbicide toxicity of the sites. The impacts of herbicide toxicity on the diatom community were only apparent after the wet season when aqueous herbicide concentrations typically peak and diatoms were able to recover during the dry season when herbicide concentrations were lower. SPEARherbicides values had a negative relationship with the percentage of grazing and cropping in catchments but had a positive relationship with the percentage of conservation in catchments. SPEARherbicides also had a negative relationship with co-occurring potential stressors such as nutrients and total suspended solids.

Wu, S, Gu, W, Huang, A, Li, Y, Kumar, M, Lim, PE, Huan, L, Gao, S & Wang, G 2019, 'Elevated CO2 improves both lipid accumulation and growth rate in the glucose-6-phosphate dehydrogenase engineered Phaeodactylum tricornutum', Microbial Cell Factories, vol. 18, no. 1.
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Abstract Background Numerous studies have shown that stress induction and genetic engineering can effectively increase lipid accumulation, but lead to a decrease of growth in the majority of microalgae. We previously found that elevated CO2 concentration increased lipid productivity as well as growth in Phaeodactylum tricornutum, along with an enhancement of the oxidative pentose phosphate pathway (OPPP) activity. The purpose of this work directed toward the verification of the critical role of glucose-6-phosphate dehydrogenase (G6PDH), the rate-limiting enzyme in the OPPP, in lipid accumulation in P. tricornutum and its simultaneous rapid growth rate under high-CO2 (0.15%) cultivation. Results In this study, G6PDH was identified as a target for algal strain improvement, wherein G6PDH gene was successfully overexpressed and antisense knockdown in P. tricornutum, and systematic comparisons of the photosynthesis performance, algal growth, lipid content, fatty acid profiles, NADPH production, G6PDH activity and transcriptional abundance were performed. The results showed that, due to the enhanced G6PDH activity, transcriptional abundance and NAPDH production, overexpression of G6PDH accompanied by high-CO2 cultivation resulted in a much higher of both lipid content and growth in P. tricornutum, while knockdown of G6PDH greatly decreased algal growth as well as lipid accumulation. In addition, the total proportions of saturated and unsaturated fatty acid, especially the polyunsaturated fatty acid eicosapentaenoic acid (EPA; C20:5, n-3), were highly incre...

Wu, W, Qi, W, Zhao, Y, Tang, X, Qiu, Y, Su, D, Fan, H & Wang, G 2019, 'Hollow CeO2 spheres conformally coated with graphitic carbon for high-performance supercapacitor electrodes', Applied Surface Science, vol. 463, pp. 244-252.
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© 2018 Elsevier B.V. Electrode material is essential for supercapacitors which are an important energy storage device that can deliver high power. Herein, we report the successful synthesis of hollow CeO 2 nanospheres conformally coated with graphitic carbon (H-CeO 2 @GC) via a facile hydrothermal method as a kind of electrode materials of supercapacitors. The as-prepared H-CeO 2 @GC hollow spheres presented a high specific surface area (153 m 2 ∙g −1 ), a well-defined hollow structure (a monodisperse size of ∼260 nm with inner diameter of ∼200 nm and shell thickness of ∼30 nm), and nanocrystals of CeO 2 (∼10 nm) conformally encapsulated in ultra-thin graphitic carbon layers. When applied in supercapacitors, the H-CeO 2 @GC hollow spheres delivered a high specific capacitance of 501 F∙g −1 at a current density of 1 A∙g −1 , a high energy/power density, excellent rate capability and long cycle life owing to its unique architecture. In particular, an energy density of 17.2 Wh∙kg −1 with a power density of 2600 W∙kg −1 was achieved. The supercapacitors retained 85% of the specific capacitance (refer to 1 A∙g −1 ) even at a high current density of 15 A∙g −1 and exhibited excellent cycling stability with 93% of the capacity retention after 5000 cycles at 10 A∙g −1 . This work offers a new approach to developing high-performance supercapacitors using the strategy of combining hollow nanosphere architecture and conductive graphitic carbon nanocoating.

Wu, W, Zhao, Y, Li, S, He, B, Liu, H, Zeng, X, Zhang, J & Wang, G 2019, 'P doped MoS2 nanoplates embedded in nitrogen doped carbon nanofibers as an efficient catalyst for hydrogen evolution reaction', Journal of Colloid and Interface Science, vol. 547, pp. 291-298.
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© 2019 Elsevier Inc. Two-dimensional (2D) molybdenum sulfide (MoS 2 ) is considered as a promising catalyst for hydrogen evolution reaction (HER), originated from its abundant hydrogen evolution active sites. However, the HER performance of MoS 2 is currently hindered by the limited exposed density of the active sites and low conductivity. Herein, we report a facile and scalable electrospinning technique to fabricate 2D MoS 2 nanoplates doped with phosphorus within one-dimensional nitrogen doped-carbon nanofibers (NCNFs-MoS 2 |P) as a highly efficient HER catalyst. The space-confined growth with the presence of NCNFs avoided the stacking and aggregation of the MoS 2 nanoplates, resulting in more exposed edge sites. The introduction of phosphorus atoms further activated the surface of MoS 2 and enhanced the electron transfer. The overpotential of NCNFs-MoS 2 |P reached 98 mV at 10 mA cm −2 , exhibiting excellent HER catalytic activity. Besides, almost no decay was observed after the stability test (5000 cycles or 20 h). The density functional calculations (DFT) elucidated that the incorporation of phosphorus atoms significantly improved the electrical conductivity and decreased the H adsorption energy barrier on MoS 2 , leading to a high catalytic performance of NCNFs-MoS 2 |P.

Wu, X, Small, JR, Cataldo, A, Withecombe, AM, Turner, P & Gale, PA 2019, 'Cover Picture: Voltage‐Switchable HCl Transport Enabled by Lipid Headgroup–Transporter Interactions (Angew. Chem. Int. Ed. 42/2019)', Angewandte Chemie International Edition, vol. 58, no. 42, pp. 14775-14775.
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Wu, X, Small, JR, Cataldo, A, Withecombe, AM, Turner, P & Gale, PA 2019, 'Titelbild: Voltage‐Switchable HCl Transport Enabled by Lipid Headgroup–Transporter Interactions (Angew. Chem. 42/2019)', Angewandte Chemie, vol. 131, no. 42, pp. 14917-14917.
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Wu, X, Small, JR, Cataldo, A, Withecombe, AM, Turner, P & Gale, PA 2019, 'Voltage‐Switchable HCl Transport Enabled by Lipid Headgroup–Transporter Interactions', Angewandte Chemie, vol. 131, no. 42, pp. 15286-15291.
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AbstractSynthetic anion transporters that facilitate transmembrane H+/Cl− symport (cotransport) have anti‐cancer potential due to their ability to neutralize pH gradients and inhibit autophagy in cells. However, compared to the natural product prodigiosin, synthetic anion transporters have low‐to‐modest H+/Cl− symport activity and their mechanism of action remains less well understood. We report a chloride‐selective tetraurea macrocycle that has a record‐high H+/Cl− symport activity similar to that of prodigiosin and most importantly demonstrates unprecedented voltage‐switchable transport properties that are linked to the lack of uniport activity. By studying the anion binding affinity and transport mechanisms of four other anion transporters, we show that the lack of uniport and voltage‐dependent H+/Cl− symport originate from strong binding to phospholipid headgroups that hampers the diffusion of the free transporters through the membrane, leading to an unusual H+/Cl− symport mechanism that involves only charged species. Our work provides important mechanistic insights into different classes of anion transporters and a new approach to achieve voltage‐switchability in artificial membrane transport systems.

Wu, X, Small, JR, Cataldo, A, Withecombe, AM, Turner, P & Gale, PA 2019, 'Voltage‐Switchable HCl Transport Enabled by Lipid Headgroup–Transporter Interactions', Angewandte Chemie International Edition, vol. 58, no. 42, pp. 15142-15147.
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AbstractSynthetic anion transporters that facilitate transmembrane H+/Cl− symport (cotransport) have anti‐cancer potential due to their ability to neutralize pH gradients and inhibit autophagy in cells. However, compared to the natural product prodigiosin, synthetic anion transporters have low‐to‐modest H+/Cl− symport activity and their mechanism of action remains less well understood. We report a chloride‐selective tetraurea macrocycle that has a record‐high H+/Cl− symport activity similar to that of prodigiosin and most importantly demonstrates unprecedented voltage‐switchable transport properties that are linked to the lack of uniport activity. By studying the anion binding affinity and transport mechanisms of four other anion transporters, we show that the lack of uniport and voltage‐dependent H+/Cl− symport originate from strong binding to phospholipid headgroups that hampers the diffusion of the free transporters through the membrane, leading to an unusual H+/Cl− symport mechanism that involves only charged species. Our work provides important mechanistic insights into different classes of anion transporters and a new approach to achieve voltage‐switchability in artificial membrane transport systems.

Wu, X, Wang, P, Turner, P, Lewis, W, Catal, O, Thomas, DS & Gale, PA 2019, 'Tetraurea Macrocycles: Aggregation-Driven Binding of Chloride in Aqueous Solutions', Chem, vol. 5, no. 5, pp. 1210-1222.
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Wyres, KL, Hawkey, J, Hetland, MAK, Fostervold, A, Wick, RR, Judd, LM, Hamidian, M, Howden, BP, Löhr, IH & Holt, KE 2019, 'Emergence and rapid global dissemination of CTX-M-15-associatedKlebsiella pneumoniaestrain ST307', Journal of Antimicrobial Chemotherapy, vol. 74, no. 3, pp. 577-581.
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Recent reports indicate the emergence of a new carbapenemase-producing Klebsiella pneumoniae clone, ST307. We sought to better understand the global epidemiology and evolution of this clone and evaluate its association with antimicrobial resistance (AMR) genes. We collated information from the literature and public databases and performed a comparative analysis of 95 ST307 genomes (including 37 that were newly sequenced). We show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the blaCTX-M-15 ESBL gene and several other AMR determinants. Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance has occasionally emerged.

Wyrsch, ER, Hawkey, J, Judd, LM, Haites, R, Holt, KE, Djordjevic, SP & Billman-Jacobe, H 2019, 'Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production', Microorganisms, vol. 7, no. 9, pp. 299-299.
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Knowledge of mobile genetic elements that capture and disseminate antimicrobial resistance genes between diverse environments, particularly across human–animal boundaries, is key to understanding the role anthropogenic activities have in the evolution of antimicrobial resistance. Plasmids that circulate within the Enterobacteriaceae and the Proteobacteria more broadly are well placed to acquire resistance genes sourced from separate niche environments and provide a platform for smaller mobile elements such as IS26 to assemble these genes into large, complex genomic structures. Here, we characterised two atypical Z/I1 hybrid plasmids, pSTM32-108 and pSTM37-118, hosting antimicrobial resistance and virulence associated genes within endemic pathogen Salmonella enterica serovar Typhimurium 1,4,[5],12:i:-, sourced from Australian swine production facilities during 2013. We showed that the plasmids found in S. Typhimurium 1,4,[5],12:i:- are close relatives of two plasmids identified from Escherichia coli of human and bovine origin in Australia circa 1998. The older plasmids, pO26-CRL125 and pO111-CRL115, encoded a putative serine protease autotransporter and were host to a complex resistance region composed of a hybrid Tn21-Tn1721 mercury resistance transposon and composite IS26 transposon Tn6026. This gave a broad antimicrobial resistance profile keyed towards first generation antimicrobials used in Australian agriculture but also included a class 1 integron hosting the trimethoprim resistance gene dfrA5. Genes encoding resistance to ampicillin, trimethoprim, sulphonamides, streptomycin, aminoglycosides, tetracyclines and mercury were a feature of these plasmids. Phylogenetic analyses showed very little genetic drift in the sequences of these plasmids over the past 15 years; however, some alterations within the complex resistance regions present on each plasmid have led to the loss of various resistance genes, presumably as a result of the activity o...

Wyrsch, ER, Reid, CJ, DeMaere, MZ, Liu, MY, Chapman, TA, Roy Chowdhury, P & Djordjevic, SP 2019, 'Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia', Frontiers in Sustainable Food Systems, vol. 3.
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© Copyright © 2019 Wyrsch, Reid, DeMaere, Liu, Chapman, Roy Chowdhury and Djordjevic. IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related IncHI2 ST3 plasmids, pSDE-SvHI2, and pSDC-F2_12BHI2, from phylogenetically unrelated multiple-drug resistant Escherichia coli strains SvETEC (CC23:O157:H19) and F2_12B (ST93:O7:H4) from geographically disparate pig production operations in New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina) and long read (PacBio SMRT) nucleotide sequence data. The plasmids encoded three drug-resistance loci, two of which carried class 1 integrons. One integron, hosting drfA12-orfF-aadA2, was within a hybrid Tn1721/Tn21, with the second residing within a copper/silver resistance transposon, comprising part of an atypical sul3-associated structure. The third resistance locus was flanked by IS15DI and encoded neomycin resistance (neoR). An oqx-encoding transposon (quinolone resistance), similar in structure to Tn6010, was identified only in pSDC-F2_12BHI2. Both plasmids showed high sequence identity to plasmid pSTM6-275, recently described in Salmonella enterica serotype 1,4,[5],12:i:- that has risen to prominence and become endemic in Australia. IncHI2 ST3 plasmids circulating in commensal and pathogenic E. coli from Australian swine belong to a lineage of plasmids often in association with sul3 and host multiple complex antibiotic and metal resistance structures, formed in part by IS26.

Xiao, J, Chevallier, F, Gomez, C, Guanter, L, Hicke, JA, Huete, AR, Ichii, K, Ni, W, Pang, Y, Rahman, AF, Sun, G, Yuan, W, Zhang, L & Zhang, X 2019, 'Remote sensing of the terrestrial carbon cycle: A review of advances over 50 years', Remote Sensing of Environment, vol. 233, pp. 111383-111383.
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© 2019 Elsevier Inc. Quantifying ecosystem carbon fluxes and stocks is essential for better understanding the global carbon cycle and improving projections of the carbon-climate feedbacks. Remote sensing has played a vital role in this endeavor during the last five decades by quantifying carbon fluxes and stocks. The availability of satellite observations of the land surface since the 1970s, particularly the early 1980s, has made it feasible to quantify ecosystem carbon fluxes and stocks at regional to global scales. Here we provide a review of the advances in remote sensing of the terrestrial carbon cycle from the early 1970s to present. First, we present an overview of the terrestrial carbon cycle and remote sensing of carbon fluxes and stocks. Remote sensing data acquired in a broad wavelength range (visible, infrared, and microwave) of the electromagnetic spectrum have been used to estimate carbon fluxes and/or stocks. Second, we provide a historical overview of the key milestones in remote sensing of the terrestrial carbon cycle. Third, we review the platforms/sensors, methods, findings, and challenges in remote sensing of carbon fluxes. The remote sensing data and techniques used to quantify carbon fluxes include vegetation indices, light use efficiency models, terrestrial biosphere models, data-driven (or machine learning) approaches, solar-induced chlorophyll fluorescence (SIF), land surface temperature, and atmospheric inversions. Fourth, we review the platforms/sensors, methods, findings, and challenges in passive optical, microwave, and lidar remote sensing of biomass carbon stocks as well as remote sensing of soil organic carbon. Fifth, we review the progresses in remote sensing of disturbance impacts on the carbon cycle. Sixth, we also discuss the uncertainty and validation of the resulting carbon flux and stock estimates. Finally, we offer a forward-looking perspective and insights for future research and directions in remote sensing of th...

Xiao, J, Zhang, F, Tang, K, Li, X, Wang, D, Wang, Y, Liu, H, Wu, M & Wang, G 2019, 'Rational Design of a P2-Type Spherical Layered Oxide Cathode for High-Performance Sodium-Ion Batteries', ACS Central Science, vol. 5, no. 12, pp. 1937-1945.
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© 2019 American Chemical Society. Sodium-ion batteries (SIBs) have been regarded as the most promising candidates for the next-generation energy storage devices owing to their low price and high abundance. However, the development of SIBs is mainly hindered by the instability of cathode materials. Here, we report a new P2-type manganese-rich cathode material, Na0.66Li0.18Mn0.71Mg0.21Co0.08O2 (P2-NaLiMMCO) with uniform spherical structure prepared via a simple solvothermal method and subsequent solid-state reaction. This P2-NaLiMMCO cathode material with uniform microsize secondary spheres and nanosize primary crystalline particles delivers a high initial discharge capacity of 166 mA h g-1 and superior capacity retention, which are superior to most previously reported results. The improved stability of the cathode material was further investigated by the in situ X-ray diffraction technique, which suggests an enhanced reversibility of the cathode material during the desodiation/sodiation process. With the superior electrochemical performance and stable structures, this new P2-NaLiMMCO can serve as a practical cathode material for SIBs.

Xie, Q, Dash, J, Huete, A, Jiang, A, Yin, G, Ding, Y, Peng, D, Hall, CC, Brown, L, Shi, Y, Ye, H, Dong, Y & Huang, W 2019, 'Retrieval of crop biophysical parameters from Sentinel-2 remote sensing imagery', International Journal of Applied Earth Observation and Geoinformation, vol. 80, pp. 187-195.
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Xin, GLL, Khee, YP, Ying, TY, Chellian, J, Gupta, G, Kunnath, AP, Nammi, S, Collet, T, Hansbro, PM, Dua, K & Chellappan, DK 2019, 'Current Status on Immunological Therapies for Type 1 Diabetes Mellitus', Current Diabetes Reports, vol. 19, no. 5, p. 22.
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© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Purpose of Review: Type 1 diabetes (T1D) occurs when there is destruction of beta cells within the islets of Langerhans in the pancreas due to autoimmunity. It is considered a complex disease, and different complications can surface and worsen the condition if T1D is not managed well. Since it is an incurable disease, numerous treatments and therapies have been postulated in order to control T1D by balancing hyperglycemia control while minimizing hypoglycemic episodes. The purpose of this review is to primarily look into the current state of the available immunological therapies and their advantages for the treatment of T1D. Recent Findings: Over the years, immunological therapy has become the center of attraction to treat T1D. Immunomodulatory approaches on non-antigens involving agents such as cyclosporine A, mycophenolate mofetil, anti-CD20, cytotoxic T cells, anti-TNF, anti-CD3, and anti-thymocyte globulin as well as immunomodulative approaches on antigens such as insulin, glutamic acid decarboxylase, and heat shock protein 60 have been studied. Aside from these two approaches, studies and trials have also been conducted on regulatory T cells, dendritic cells, interleukin 2, interleukin 4, M2 macrophages, and rapamycin/interleukin 2 combination therapy to test their effects on patients with T1D. Many of these agents have successfully suppressed T1D in non-obese diabetic (NOD) mice and in human trials. However, some have shown negative results. Summary: To date, the insights into the management of the immune system have been increasing rapidly to search for potential therapies and treatments for T1D. Nevertheless, some of the challenges are still inevitable. A lot of work and effort need to be put into the investigation on T1D through immunological therapy, particularly to reduce complications to improve and enhance clinical outcomes.

Xing, J, Adnan, A, Rakha, A, Kasim, K, Noor, A, Xuan, J, Zhang, X, Yao, J, McNevin, D & Wang, B 2019, 'Genetic analysis of 12 X-STRs for forensic purposes in Liaoning Manchu population from China', Gene, vol. 683, pp. 153-158.
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X-chromosomal short tandem repeats (X-STRs) have been widely used in forensic practice involving complicated cases of kinship and also play an increasingly important role in population genetics. X-STRs have been studied in regional populations of China but there is a lack of data for the Manchu population. In this study, we have investigated the forensic genetic properties of 12 X-STRs in the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 772 Manchu (male = 514, female = 258) individuals from the Xiuyan and Huanren Manchu autonomous counties of Liaoning province. We observed a total of 166 alleles at 12 X-STR loci with allele frequencies ranging from 0.001295to 0.615285. The most polymorphic locus was DXS10135 with 24 alleles while DXS7423 was the least polymorphic locus with 5 alleles. We found significant linkage disequilibrium (LD) between the following pairs of markers for males: DXS10103/DXS10101, DXS10135/DXS10146, DXS10101/DXS10148, DXS10135/DXS10148, DXS7423/DXS10148 and DXS10079/DXS10148. For females, LD was only observed for DXS10103/DXS10101. The combined power of discrimination was 0.9999999979699 for males and 0.999999999999998 for females. The numbers of observed haplotypes in Manchu males were 310, 172, 182 and 172 in four linkage groups; LG1, LG2, LG3 and LG4, respectively, however, these linkage groups did not form stable haplotypes as indicated by linkage equilibrium (LE) of STRs within the groups and significant LD between the groups. This study represents an extensive report on X-STR marker variation in the Manchu population for forensic applications and population genetic studies.

Xiong, P, Zhang, X, Wan, H, Wang, S, Zhao, Y, Zhang, J, Zhou, D, Gao, W, Ma, R, Sasaki, T & Wang, G 2019, 'Interface Modulation of Two-Dimensional Superlattices for Efficient Overall Water Splitting', Nano Letters, vol. 19, no. 7, pp. 4518-4526.
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© 2019 American Chemical Society. Molecular-scale modulation of interfaces between different unilamellar nanosheets in superlattices is promising for efficient catalytic activities. Here, three kinds of superlattices from alternate restacking of any two of the three unilamellar nanosheets of MoS2, NiFe-layered double hydroxide (NiFe-LDH), and graphene are systematically investigated for electrocatalytic water splitting. The MoS2/NiFe-LDH superlattice exhibits a low overpotential of 210 and 110 mV at 10 mA cm-2 for oxygen evolution reaction (OER) and alkaline hydrogen evolution reaction (HER), respectively, superior than MoS2/graphene and NiFe-LDH/graphene superlattices. High activity and stability toward the overall water splitting are also demonstrated on the MoS2/NiFe-LDH superlattice bifunctional electrocatalyst, outperforming the commercial Pt/C-RuO2 couple. This outstanding performance can be attributed to optimal adsorption energies of both HER and OER intermediates on the MoS2/NiFe-LDH superlattice, which originates from a strong electronic coupling effect at the heterointerfaces. These results herald the interface modulation of superlattices providing a promising approach for designing advanced electrocatalysts.

Xu, J, Gulzar, A, Yang, P, Bi, H, Yang, D, Gai, S, He, F, Lin, J, Xing, B & Jin, D 2019, 'Recent advances in near-infrared emitting lanthanide-doped nanoconstructs: Mechanism, design and application for bioimaging', Coordination Chemistry Reviews, vol. 381, pp. 104-134.
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© 2018 Elsevier B.V. Lanthanide-doped nanoconstructs (LDNCs) have been widely studied in the biomedical field. Especially, LDNCs with near-infrared (NIR) fluorescence show great promise in biological imaging. The fluorescence in the NIR window (700–1700 nm) affords increased tissue penetration due to the reduced light absorption, photon scattering and autofluorescence. Actually, LDNCs with various lanthanide-dopings can emit ultraviolet (UV), visible (VIS) and NIR photons through upconversion (UC) and downconversion (DC) processes. Moreover, there are review papers introducing different aspects of bioimaging based on LDNCs. Nevertheless, there has not been a review that systematically summarizes NIR fluorescent LDNCs. Herein, we summarize the recent progress made on NIR fluorescence imaging by highlighting the increasingly developing trend of NIR emitting LDNCs. The NIR emission mechanism of LDNCs activated by different lanthanide ions was discussed in detail, and their advantages as NIR fluorescent probes will be systematically introduced. From the aspect of realizing multimodal imaging, the advances made by combining magnetic resonance imaging (MRI), computed tomography (CT) and so on with NIR optical imaging were summarized. Finally, we discuss the superiority of NIR-II (1000–1700 nm) emitting LDNCs when applied in biomedical imaging, with an emphasis on how to use them to realize imaging guided cancer therapy.

Xu, J, Li, T, Zhang, W, Wu, W, Jin, Y, Zhang, X, Su, D & Wang, G 2019, 'Propelling the polysulfide phase transformation of lithium–sulfur battery by VO2-rGO', Journal of Alloys and Compounds, vol. 804, pp. 549-553.
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© 2019 Elsevier B.V. Rather than preventing the dissolution and diffusion of polysulfides, promoting polysulfide conversion through improved polysulfide redox is another promising strategy to suppress the dissolution of polysulfides and enhance the cycle life of sulfur cathodes. We demonstrated that VO2-rGO not only facilities liquid-involving polysulfide redox (Li2S8→Li2S6→Li2S4), but also promotes the effective decompositions of lithium sulfide (Li2S). As evidenced by the visual experiments and DFT calculation, VO2-rGO has strong affinity for polysulfides species. With sulfur loading of 2.15 mg cm−2 and sulfur content of 76 wt%, the reversible capacity retained at 896 mAh g−1 after 200 cycles.

Xu, X, Wang, C, Fronzi, M, Liu, X, Bi, L & Zhao, XS 2019, 'Modification of a first-generation solid oxide fuel cell cathode with Co3O4 nanocubes having selectively exposed crystal planes', Materials for Renewable and Sustainable Energy, vol. 8, no. 3.
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AbstractCo3O4 nanocubes with exposed (001) planes were prepared and employed for use as first-generation Sr-doped LaMnO3 (LSM) cathodes in solid oxide fuel cells to improve the cell performance. Theoretical simulations suggest that the Co3O4 (001) plane has the smallest oxygen adsorption and oxygen dissociation energies compared with other planes, thus favouring cathode reactions in solid oxide fuel cells (SOFCs). Experimental studies consistently demonstrate that a cell using an LSM cathode made with Co3O4 nanocubes with selective (001) surfaces exhibits a peak power density of 500 mW cm−2 at 600 °C, while the power output for a cell using unselective (commercial) Co3O4 nanoparticles is only 179 mW cm−2 at the same temperature. The electrochemical study indicates that the use of Co3O4 nanoparticles with exposed (001) surfaces obviously accelerates the cathode reactions and thus decreases the polarisation resistance, which is the key to improving fuel cell performance. This study demonstrates the feasibility of using the crystal planes of metal oxides to improve the fuel cell performance and provides a new way to design SOFC cathodes.

Xu, X, Wang, H, Fronzi, M, Wang, X, Bi, L & Traversa, E 2019, 'Tailoring cations in a perovskite cathode for proton-conducting solid oxide fuel cells with high performance', Journal of Materials Chemistry A, vol. 7, no. 36, pp. 20624-20632.
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Tailoring cathode materials with cations enables an improved hydration ability and proton migration, leading to a high fuel cell performance.

Xu, X, Wang, H, Ma, J, Liu, W, Wang, X, Fronzi, M & Bi, L 2019, 'Impressive performance of proton-conducting solid oxide fuel cells using a first-generation cathode with tailored cations', Journal of Materials Chemistry A, vol. 7, no. 32, pp. 18792-18798.
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Tailoring the first-generation cathode La_0.5Sr_0.5FeO_3−δ with Pr-doping brings new life to the cathode for proton-conducting solid oxide fuel cells.

Xu, X, Zhou, Z, Liu, Y, Wen, S, Guo, Z, Gao, L & Wang, F 2019, 'Optimising passivation shell thickness of single upconversion nanoparticles using a time-resolved spectrometer', APL Photonics, vol. 4, no. 2, pp. 026104-026104.
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© 2019 Author(s). Lanthanide-doped upconversion nanoparticles (UCNPs) are the most efficient multi-photon probe that can be used for deep tissue bio-imaging, fluorescence microscopy, and single molecule sensing applications. Passivating UCNPs with inert shell has been demonstrated to be an effective method to significantly enhance their brightness. However, this method also increases the overall size of the nanoparticles, which limited their cellular applications. Current reports to optimise the thickness of the shell are based on the spectrum measurement of ensembles of UCNPs, which are less quantitative. The characterisation of single UCNPs would be desirable, but is limited by the sensitivity of conventional spectrometers. We developed an optical filter-based spectrometer coupled to a laser scanning microscopy system and achieved a high degree of sensitivity - seven times more than the traditional amount. Through highly controlled syntheses of a range Yb 3+ and Tm 3+ doped UCNPs with different shell thickness, quantitative characterization of the emission intensity and lifetime on single UCNPs were comprehensively studied using a home-made optical system. We found that the optimal shell thickness was 6.3 nm. We further demonstrated that the system was sensitive enough to measure the time-resolved spectrum from a single UCNP, which is significantly useful for a comprehensive study of the energy transfer process of UCNPs.

Xu, Y, Kim, I & Carroll, RJ 2019, 'A Hybrid Omnibus Test for Generalized Semiparametric Single-Index Models With High-Dimensional Covariate Sets', Biometrics, vol. 75, no. 3, pp. 757-767.
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Abstract Numerous statistical methods have been developed for analyzing high-dimensional data. These methods often focus on variable selection approaches but are limited for the purpose of testing with high-dimensional data. They are often required to have explicit-likelihood functions. In this article, we propose a “hybrid omnibus test” for high-dicmensional data testing purpose with much weaker requirements. Our hybrid omnibus test is developed under a semiparametric framework where a likelihood function is no longer necessary. Our test is a version of a frequentist-Bayesian hybrid score-type test for a generalized partially linear single-index model, which has a link function being a function of a set of variables through a generalized partially linear single index. We propose an efficient score based on estimating equations, define local tests, and then construct our hybrid omnibus test using local tests. We compare our approach with an empirical-likelihood ratio test and Bayesian inference based on Bayes factors, using simulation studies. Our simulation results suggest that our approach outperforms the others, in terms of type I error, power, and computational cost in both the low- and high-dimensional cases. The advantage of our approach is demonstrated by applying it to genetic pathway data for type II diabetes mellitus.

Xu, Z, Octavia, S, Luu, LDW, Payne, M, Timms, V, Tay, CY, Keil, AD, Sintchenko, V, Guiso, N & Lan, R 2019, 'Pertactin-Negative and Filamentous Hemagglutinin-Negative Bordetella pertussis, Australia, 2013–2017', Emerging Infectious Diseases, vol. 25, no. 6, pp. 1196-1199.
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During the 2008-2012 pertussis epidemic in Australia, pertactin (Prn)-negative Bordetella pertussis emerged. We analyzed 78 isolates from the 2013-2017 epidemic and documented continued expansion of Prn-negative ptxP3 B. pertussis strains. We also detected a filamentous hemagglutinin-negative and Prn-negative B. pertussis isolate.

Yan, K, Wang, J, Zhao, S, Zhou, D, Sun, B, Cui, Y & Wang, G 2019, 'Temperature‐Dependent Nucleation and Growth of Dendrite‐Free Lithium Metal Anodes', Angewandte Chemie, vol. 131, no. 33, pp. 11486-11490.
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AbstractIt is essential to develop a facile and effective method to enhance the electrochemical performance of lithium metal anodes for building high‐energy‐density Li‐metal based batteries. Herein, we explored the temperature‐dependent Li nucleation and growth behavior and constructed a dendrite‐free Li metal anode by elevating temperature from room temperature (20 °C) to 60 °C. A series of ex situ and in situ microscopy investigations demonstrate that increasing Li deposition temperature results in large nuclei size, low nucleation density, and compact growth of Li metal. We reveal that the enhanced lithiophilicity and the increased Li‐ion diffusion coefficient in aprotic electrolytes at high temperature are essential factors contributing to the dendrite‐free Li growth behavior. As anodes in both half cells and full cells, the compact deposited Li with minimized specific surface area delivered high Coulombic efficiencies and long cycling stability at 60 °C.

Yan, K, Wang, J, Zhao, S, Zhou, D, Sun, B, Cui, Y & Wang, G 2019, 'Temperature‐Dependent Nucleation and Growth of Dendrite‐Free Lithium Metal Anodes', Angewandte Chemie International Edition, vol. 58, no. 33, pp. 11364-11368.
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AbstractIt is essential to develop a facile and effective method to enhance the electrochemical performance of lithium metal anodes for building high‐energy‐density Li‐metal based batteries. Herein, we explored the temperature‐dependent Li nucleation and growth behavior and constructed a dendrite‐free Li metal anode by elevating temperature from room temperature (20 °C) to 60 °C. A series of ex situ and in situ microscopy investigations demonstrate that increasing Li deposition temperature results in large nuclei size, low nucleation density, and compact growth of Li metal. We reveal that the enhanced lithiophilicity and the increased Li‐ion diffusion coefficient in aprotic electrolytes at high temperature are essential factors contributing to the dendrite‐free Li growth behavior. As anodes in both half cells and full cells, the compact deposited Li with minimized specific surface area delivered high Coulombic efficiencies and long cycling stability at 60 °C.

Yang, J, Hu, X, Kong, X, Jia, P, Ji, D, Quan, D, Wang, L, Wen, Q, Lu, D, Wu, J, Jiang, L & Guo, W 2019, 'Photo-induced ultrafast active ion transport through graphene oxide membranes', Nature Communications, vol. 10, no. 1, p. 1171.
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AbstractLayered graphene oxide membranes (GOM) with densely packed sub-nanometer-wide lamellar channels show exceptional ionic and molecular transport properties. Mass and charge transport in existing materials follows their concentration gradient, whereas attaining anti-gradient transport, also called active transport, remains a great challenge. Here, we demonstrate a coupled photon-electron-ion transport phenomenon through the GOM. Upon asymmetric light illumination, cations are able to move thermodynamically uphill over a broad range of concentrations, at rates much faster than that via simple diffusion. We propose, as a plausible mechanism, that light irradiation reduces the local electric potential on the GOM following a carrier diffusion mechanism. When the illumination is applied to an off-center position, an electric potential difference is built that can drive the transport of ionic species. We further develop photonic ion switches, photonic ion diodes, and photonic ion transistors as the fundamental elements for active ion sieving and artificial photosynthesis on synthetic nanofluidic circuits.

Yang, L, Grofe, A, Reimers, J & Gao, J 2019, 'Multistate density functional theory applied with 3 unpaired electrons in 3 orbitals: The singdoublet and tripdoublet states of the ethylene cation', Chemical Physics Letters, vol. 736, pp. 136803-136803.
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© 2019 Elsevier B.V. Multistate density functional theory (MSDFT) is extended to facilitate treatment of situations involving more than two open-shell electrons. The method is applied to determine energies for the two doublet state (tripdoublet and singdoublet) and the quartet-state components that arise when two electrons of one spin type and one electron of the other singly occupy three orbitals. A test system, the (π,π*) excitation of the ethylene cation, is utilized, with MSDFT delivering energies that are numerically superior to those from time-dependent density-functional theory (TD-DFT) and states free from spin contamination.

Yang, L, Reimers, JR, Kobayashi, R & Hush, NS 2019, 'Competition between charge migration and charge transfer induced by nuclear motion following core ionization: Model systems and application to Li2+', The Journal of Chemical Physics, vol. 151, no. 12, pp. 124108-124108.
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Attosecond and femtosecond spectroscopies present opportunities for the control of chemical reaction dynamics and products, as well as for quantum information processing; we address the somewhat unique situation of core-ionization spectroscopy which, for dimeric chromophores, leads to strong valence charge localization and hence tightly paired potential-energy surfaces of very similar shape. Application is made to the quantum dynamics of core-ionized Li2+. This system is chosen as Li2 is the simplest stable molecule facilitating both core ionization and valence ionization. First, the quantum dynamics of some model surfaces are considered, with the surprising result that subtle differences in shape between core-ionization paired surfaces can lead to dramatic differences in the interplay between electronic charge migration and charge transfer induced by nuclear motion. Then, equation-of-motion coupled-cluster calculations are applied to determine potential-energy surfaces for 8 core-excited state pairs, calculations believed to be the first of their type for other than the lowest-energy core-ionized molecular pair. While known results for the lowest-energy pair suggest that Li2+ is unsuitable for studying charge migration, higher-energy pairs are predicted to yield results showing competition between charge migration and charge transfer. Central is a focus on the application of Hush’s 1975 theory for core-ionized X-ray photoelectron spectroscopy to understand the shapes of the potential-energy surfaces and hence predict key features of charge migration.

Yang, T, Liu, J, Zhang, M, Yang, D, Zheng, J, Ju, Z, Cheng, J, Zhuang, J, Liu, Y, Zhong, J, Liu, H, Wang, G, Zheng, R & Guo, Z 2019, 'Encapsulating MnSe Nanoparticles Inside 3D Hierarchical Carbon Frameworks with Lithium Storage Boosted by in Situ Electrochemical Phase Transformation', ACS Applied Materials & Interfaces, vol. 11, no. 36, pp. 33022-33032.
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© 2019 American Chemical Society. Electrode materials that act through the electrochemical conversion mechanism, such as metal selenides, have been considered as promising anode candidates for lithium-ion batteries (LIBs), although their fast capacity attenuation and inadequate electrical conductivity are impeding their practical application. In this work, these issues are addressed through the efficient fabrication of MnSe nanoparticles inside porous carbon hierarchical architectures for evaluation as anode materials for LIBs. Density functional theory simulations indicate that there is a completely irreversible phase transformation during the initial cycle, and the high structural reversibility of β-MnSe provides a low energy barrier for the diffusion of lithium ions. Electron localization function calculations demonstrate that the phase transformation leads to high charge transfer kinetics and a favorable lithium ion diffusion coefficient. Benefitting from the phase transformation and unique structural engineering, the MnSe/C chestnut-like structures with boosted conductivity deliver enhanced lithium storage performance (885 mA h g-1 at a current density of 0.2 A g-1 after 200 cycles), superior cycling stability (a capacity of 880 mA h g-1 at 1 A g-1 after 1000 cycles), and outstanding rate performance (416 mA h g-1 at 2 A g-1).

Yang, T, Liu, Y, Yang, D, Deng, B, Huang, Z, Ling, CD, Liu, H, Wang, G, Guo, Z & Zheng, R 2019, 'Bimetallic metal-organic frameworks derived Ni-Co-Se@C hierarchical bundle-like nanostructures with high-rate pseudocapacitive lithium ion storage', Energy Storage Materials, vol. 17, pp. 374-384.
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© 2018 Metal-organic frameworks and its derivates have attracted much attention for energy storage application. In this work, three-dimensional bimetallic metal-organic frameworks with novel hierarchical bundle-like micro/nanostructure were synthesized at room temperature for the first time. After initial carbonization and subsequent selenization, hierarchical porous Ni-Co-Se nanoparticles embedded in 3D carbon network with a high surface area that obviously inherited the original morphology of the bimetallic metal organic frameworks. The resulting materials demonstrated superior performance as the anode in lithium ion batteries (LIBs): they provide high reversible Li-storage capacity, excellent cyclability (2061 mA h/g after 300 cycles) and high rate performance (493 mA h/g at 8 A/g). The features of Ni-Co-Se@C electrode include the synergistic effect of two metal selenides species for Li-storage, well-designed hierarchical porous bundle-like structure, steady carbon network and as-formed size-reduced particles after initial cycle process. These features not only enhanced the electronic properties and alleviated the volume variation of metal selenides during the repeated cycles, but also produced more active sites for lithium storage and a shorter lithium diffusion pathway to expedite the fast charge transfer and preserve a stable SEI layer, resulting in outstanding lithium storage performance. In addition, the pseudocapacitive behaviour contributes much to the high energy storage of lithium ions. These results uncover a facile methodology for the design of well-organized MOFs and transition metal dichalcogenides with 3D hierarchical structures.

Yang, T, Yang, D, Mao, Q, Liu, Y, Bao, L, Chen, Y, Xiong, Q, Ji, Z, Ling, CD, Liu, H, Wang, G & Zheng, R 2019, 'In-situ synthesis of Ni–Co–S nanoparticles embedded in novel carbon bowknots and flowers with pseudocapacitance-boosted lithium ion storage', Nanotechnology, vol. 30, no. 15, pp. 155701-155701.
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© 2019 IOP Publishing Ltd. We design a facile approach to prepare a bimetallic transition-metal-sulphide-based 3D hierarchically-ordered porous electrode based on bimetallic metal-organic frameworks (Ni-Co-MOFs) by using confinement growth and in-situ sulphurisation techniques. In the novel resulting architectures, Ni-Co-S nanoparticles are confined in bowknot-like and flower-like carbon networks and are mechanically isolated but electronically well-connected, where the carbon networks with a honeycomb-like feature facilitate electron transfer with uninterrupted conductive channels from all sides. Moreover, these hierarchically-ordered porous structures together with internal voids can accommodate the volume expansion of the embedded Ni-Co-S nanoparticles. The pseudocapacitive behaviours displayed in the NCS@CBs and NCS@CFs occupied a significant portion in the redox processes. Because of these merits, both the as-built bowknot and flower networks show excellent electrochemical properties for lithium storage with superior rate capability and robust cycling stability (994 mAh g-1 for NCS@CBs and 888 mAh g-1 for NCS@CFs after 200 cycles). This unique 3D hierarchically-ordered structural design is believed to hold great potential applications in propagable preparation of carbon networks teamed up with sulphide nanocrystals for high energy storage.

Yasir, M, Dutta, D, Hossain, KR, Chen, R, Ho, KKK, Kuppusamy, R, Clarke, RJ, Kumar, N & Willcox, MDP 2019, 'Mechanism of Action of Surface Immobilized Antimicrobial Peptides Against Pseudomonas aeruginosa', Frontiers in Microbiology, vol. 10, p. 3053.
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Bacterial colonization and biofilm development on medical devices can lead to infection. Antimicrobial peptide-coated surfaces may prevent such infections. Melimine and Mel4 are chimeric cationic peptides showing broad-spectrum antimicrobial activity once attached to biomaterials and are highly biocompatible in animal models and have been tested in Phase I and II/III human clinical trials. These peptides were covalently attached to glass using an azidobenzoic acid linker. Peptide attachment was confirmed using X-ray photoelectron spectroscopy and amino acid analysis. Mel4 when bound to glass was able to adopt a more ordered structure in the presence of bacterial membrane mimetic lipids. The ability of surface bound peptides to neutralize endotoxin was measured along with their interactions with the bacterial cytoplasmic membrane which were analyzed using DiSC(3)-5 and Sytox green, Syto-9, and PI dyes with fluorescence microscopy. Leakage of ATP and nucleic acids from cells were determined by analyzing the surrounding fluid. Attachment of the peptides resulted in increases in the percentage of nitrogen by 3.0% and 2.4%, and amino acid concentrations to 0.237 nmole and 0.298 nmole per coverslip on melimine and Mel4 coated surfaces, respectively. The immobilized peptides bound lipopolysaccharide and disrupted the cytoplasmic membrane potential of Pseudomonas aeruginosa within 15 min. Membrane depolarization was associated with a reduction in bacterial viability by 82% and 63% for coatings melimine and Mel4, respectively (p < 0.001). Disruption of membrane potential was followed by leakage of ATP from melimine (1.5 ± 0.4 nM) or Mel4 (1.3 ± 0.2 nM) coated surfaces compared to uncoated glass after 2 h (p < 0.001). Sytox green influx started after 3 h incubation with either peptide. Melimine coatings yielded 59% and Mel4 gave 36% PI stained cells after 4 h. Release of the larger molecules (DNA/RNA) commenced after 4 h for melimine (1.8 ± 0.9 times more than co...

Yiu, BA, Booth, DJ, Fowler, AM & Feary, DA 2019, 'Macroalgal resource use differences across age and size classes in the dominant temperate herbivorous fish Aplodactylus lophodon (Aplodactylidae)', Marine and Freshwater Research, vol. 70, no. 4, pp. 531-531.
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Herbivorous fishes comprise a substantial proportion of temperate fish communities, although there is little understanding of their trophic resource use and whether this changes throughout post-settlement ontogeny. With increasing loss of macroalgal forests, understanding how temperate fishes use macroalgae will be vital in predicting future effects on temperate fish biodiversity. The Australian rock cale (Aplodactylus lophodon) is one of the most abundant herbivorous fish inhabiting shallow temperate south-eastern Australian reefs. We examined gastrointestinal contents throughout ontogeny and demonstrated that this species maintains a herbivorous diet through all life stages. Differences in algal taxa consumed were apparent through ontogeny, with the juvenile diet dominated by filamentous red and green algae and the adult diet dominated by brown and calcareous red algae. Relative gut length increased through ontogeny, potentially facilitating dietary transition to less digestible algae, but no concurrent increase in jaw power was observed. The results highlight the diversity of trophic resource use in a temperate marine herbivore, but the near-complete dominance of dietary algae throughout ontogeny indicates the reliance on primary producers across all life stages. Given the importance of fucoid resources in the adult diet, any loss of macroalgal forests within south-eastern Australia may affect foraging success and persistence.

Yu, X, Yu, Z-Y, Zhang, X-L, Zheng, Y-R, Duan, Y, Gao, Q, Wu, R, Sun, B, Gao, M-R, Wang, G & Yu, S-H 2019, '“Superaerophobic” Nickel Phosphide Nanoarray Catalyst for Efficient Hydrogen Evolution at Ultrahigh Current Densities', Journal of the American Chemical Society, vol. 141, no. 18, pp. 7537-7543.
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Copyright © 2019 American Chemical Society. The design of highly efficient non-noble-metal electrocatalysts for large-scale hydrogen production remains an ongoing challenge. We report here a Ni2P nanoarray catalyst grown on a commercial Ni foam substrate, which demonstrates an outstanding electrocatalytic activity and stability in basic electrolyte. The high catalytic activity can be attributed to the favorable electron transfer, superior intrinsic activity, and the intimate connection between the nanoarrays and their substrate. Moreover, the unique 'superaerophobic' surface feature of the Ni2P nanoarrays enables a remarkable capability to withstand internal and external forces and release the in situ generated H2 bubbles in a timely manner at large current densities (such as >1000 mA cm-2) where the hydrogen evolution becomes vigorous. Our results highlight that an aerophobic structure is essential to catalyze gas evolution for large-scale practical applications.

Zajaczkowski, P, Mazumdar, S, Conaty, S, Ellis, JT & Fletcher-Lartey, SM 2019, 'Epidemiology and associated risk factors of giardiasis in a peri-urban setting in New South Wales Australia', Epidemiology and Infection, vol. 147, pp. 1-9.
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AbstractGiardiasis is one of the most important non-viral causes of human diarrhoea. Yet, little is known about the epidemiology of giardiasis in the context of developed countries such as Australia and there is a limited information about local sources of exposure to inform prevention strategies in New South Wales. This study aimed to (1) describe the epidemiology of giardiasis and (2) identify potential modifiable risk factors associated with giardiasis that are unique to south-western Sydney, Australia. A 1:2 matched case-control study of 190 confirmed giardiasis cases notified to the South-Western Local Health District Public Health Unit from January to December 2016 was employed to investigate the risk factors for giardiasis. Two groups of controls were selected to increase response rate; Pertussis cases and neighbourhood (NBH) controls. A matched analysis was carried out for both control groups separately. Variables with a significant odds ratio (OR) in the univariate analysis were placed into a multivariable regression for each matched group, respectively. In the regression model with the NBH controls, age and sex were controlled as potential confounders. Identified risk factors included being under 5 years of age (aOR = 7.08; 95% confidence intervals (CI) 1.02–49.36), having a household member diagnosed with a gastrointestinal illness (aOR = 15.89; 95% CI 1.53–164.60) and having contact with farm animals, domestic animals or wildlife (aOR = 3.03; 95% CI 1.08–8.54). Cases that travelled overseas were at increased risk of infection (aOR = 19.89; 95% CI 2.00–197.37) when compared with Pertussis cases. This study provides an update on the epidemiology and associated risk factors of a neglected tropical disease, which can inform enhanced surveillance and prevention strategies in the developed metropolitan areas.

Zakarya, R, Adcock, I & Oliver, BG 2019, 'Epigenetic impacts of maternal tobacco and e-vapour exposure on the offspring lung', Clinical Epigenetics, vol. 11, no. 1.
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© 2019 The Author(s). In utero exposure to tobacco products, whether maternal or environmental, have harmful effects on first neonatal and later adult respiratory outcomes. These effects have been shown to persist across subsequent generations, regardless of the offsprings' smoking habits. Established epigenetic modifications induced by in utero exposure are postulated as the mechanism underlying the inherited poor respiratory outcomes. As e-cigarette use is on the rise, their potential to induce similar functional respiratory deficits underpinned by an alteration in the foetal epigenome needs to be explored. This review will focus on the functional and epigenetic impact of in utero exposure to maternal cigarette smoke, maternal environmental tobacco smoke, environmental tobacco smoke and e-cigarette vapour on foetal respiratory outcomes.

Zakria, M, Huynh, TT, Ling, FCC, Su, SC, Phillips, MR & Ton-That, C 2019, 'Highly Luminescent MgZnO/ZnO Multiple Quantum Wells for Photonics Devices', ACS Applied Nano Materials, vol. 2, no. 4, pp. 2574-2579.
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Copyright © 2019 American Chemical Society. Multiple quantum wells (MQWs) have enabled a myriad of technological applications; however, their optical emission is currently severely constrained by the presence of undesirable defects, which limit their performance in advanced photonic devices. Here, we present a new route to achieve highly luminescent oxide-based MQWs by rapid remote plasma annealing (RRPA) in hydrogen. We demonstrate that the optical emission from the MgZnO/ZnO MQWs can be enhanced substantially by this plasma method, with its emission intensity increased by more than 10 times after being treated for 40 s. Concurrently, the emissions associated with both basal stacking faults and point defects are completely quenched. Based on temperature- and excitation-density-dependent luminescence results, the enhancement of the MQW emission is attributed to the passivation of competitive recombination channels. Additionally, the exciton-optical phonon coupling strength, deduced from the temperature-dependent MQW spectral line width, shows clear evidence for significantly enhanced phonon coupling as a result of exciton screening effects. This rapid plasma procedure presents a versatile method to enhance the optical quality of oxide-based MQW structures and could open the door to high-efficiency photonic devices. ©

Zang, R, Li, P, Guo, X, Man, Z, Zhang, S, Wang, C & Wang, G 2019, 'Yolk–shell N-doped carbon coated FeS₂nanocages as a high-performance anode for sodium-ion batteries', Journal of Materials Chemistry A, vol. 7, no. 23, pp. 14051-14059.
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Rationally designed yolk–shell structured N-doped carbon coated FeS₂nanocages demonstrate superior high-rate and long-term cycling performance as anode materials for sodium-ion batteries.

Zapata, J, Meynard, A, Anguita, C, Espinoza, C, Alvear, P, Kumar, M & Contreras‐Porcia, L 2019, 'Non‐Random Distribution and Ecophysiological Differentiation of Pyropia Species (Bangiales, Rhodophyta) Through Environmental Gradients', Journal of Phycology, vol. 55, no. 5, pp. 1140-1153.
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Recently 18 Bangiales seaweed species were reported for the Chilean coast, including Pyropia orbicularis and Pyropia variabilis (large [LM] and green [GM] morphotypes). Porphyra/Pyropia spp. occur mainly in the upper intertidal where desiccation stress is triggered by tidal fluctuations. However, the influence of environmental and ecophysiological variables and seasonal differences on Porphyra/Pyropia (microhabitats) intertidal distributions is unknown. Accordingly, we determined (i) the effect of environmental variables (temperature [T], relative humidity [RH], and photosynthetically active radiation [PAR]) and season on distribution, and (ii) physiological (cellular activity and lipid peroxidation [LPX]) and molecular responses (antioxidant enzymes expression at biochemical and transcript level) to desiccation stress in both Pyropia species and morphotypes (common garden experiment, on flat rocky platforms). Multivariate analyses of coverage and abundance in relation to environmental variables revealed a significant effect of temperature on P. variabilis GM distribution, GM dominating almost exclusively on rocky walls (where lowest PAR and T values but maximum RH were registered). Conversely, Pyropia orbicularis

Zaslawski, C, Gadau, M, Zhang, SP, Wang, FC, Bangrazi, S, Li, W, Tan, YS, Berle, C & Razavy, S 2019, 'The effect of acupuncture on lateral elbow tendinopathy (LET): a multi-center international randomized controlled trial', Advances in Integrative Medicine, vol. 6, pp. S52-S52.
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Zavřel, T, Faizi, M, Loureiro, C, Poschmann, G, Stühler, K, Sinetova, M, Zorina, A, Steuer, R & Červený, J 2019, 'Quantitative insights into the cyanobacterial cell economy', eLife, vol. 8.
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Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

Zeng, X, Vonk, JM, van der Plaat, DA, Faiz, A, Paré, PD, Joubert, P, Nickle, D, Brandsma, C-A, Kromhout, H, Vermeulen, R, Xu, X, Huo, X, de Jong, K & Boezen, HM 2019, 'Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms', Environment International, vol. 122, pp. 263-269.
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Respiratory symptoms are important indicators of respiratory diseases. Both genetic and environmental factors contribute to respiratory symptoms development but less is known about gene-environment interactions. We aimed to assess interactions between single nucleotide polymorphisms (SNPs) and occupational exposures on respiratory symptoms cough, dyspnea and phlegm. As identification cohort LifeLines I (n = 7976 subjects) was used. Job-specific exposure was estimated using the ALOHA + job exposure matrix. SNP-by-occupational exposure interactions on respiratory symptoms were tested using logistic regression adjusted for gender, age, and current smoking. SNP-by-exposure interactions with a p-value <10-4 were tested for replication in two independent cohorts: LifeLines II (n = 5260) and the Vlagtwedde-Vlaardingen cohort (n = 1529). The interaction estimates of the replication cohorts were meta-analyzed using PLINK. Replication was achieved when the meta-analysis p-value was <0.05 and the interaction effect had the same direction as in the identification cohort. Additionally, we assessed whether replicated SNPs associated with gene expression by analyzing if they were cis-acting expression quantitative trait loci (eQTL) in lung tissue. In the replication meta-analysis, sixteen out of 477 identified SNP-by-occupational exposure interactions had a p-value <0.05 and 9 of these interactions had the same direction as in the identification cohort. Several identified loci were plausible candidates for respiratory symptoms, such as TMPRSS9, SERPINH1, TOX3, and ARHGAP18. Three replicated SNPs were cis-eQTLs for FCER1A, CHN1, and TIMM13 in lung tissue. Taken together, this genome-wide SNP-by-occupational exposure interaction study in relation to cough, dyspnea, and phlegm identified several suggestive susceptibility genes. Further research should determine if these genes are true susceptibility loci for respiratory symptoms in relation to occupational exposures.

Zeppel, MJB, Anderegg, WRL, Adams, HD, Hudson, P, Cook, A, Rumman, R, Eamus, D, Tissue, DT & Pacala, SW 2019, 'Embolism recovery strategies and nocturnal water loss across species influenced by biogeographic origin', Ecology and Evolution, vol. 9, no. 9, pp. 5348-5361.
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AbstractDrought‐induced tree mortality is expected to increase in future climates with the potential for significant consequences to global carbon, water, and energy cycles. Xylem embolism can accumulate to lethal levels during drought, but species that can refill embolized xylem and recover hydraulic function may be able to avoid mortality. Yet the potential controls of embolism recovery, including cross‐biome patterns and plant traits such as nonstructural carbohydrates (NSCs), hydraulic traits, and nocturnal stomatal conductance, are unknown. We exposed eight plant species, originating from mesic (tropical and temperate) and semi‐arid environments, to drought under ambient and elevated CO2 levels, and assessed recovery from embolism following rewatering. We found a positive association between xylem recovery and NSCs, and, surprisingly, a positive relationship between xylem recovery and nocturnal stomatal conductance. Arid‐zone species exhibited greater embolism recovery than mesic zone species. Our results indicate that nighttime stomatal conductance often assumed to be a wasteful use of water, may in fact be a key part of plant drought responses, and contribute to drought survival. Findings suggested distinct biome‐specific responses that partially depended on species climate‐of‐origin precipitation or aridity index, which allowed some species to recover from xylem embolism. These findings provide improved understanding required to predict the response of diverse plant communities to drought. Our results provide a framework for predicting future vegetation shifts in response to climate change.

Zhang, F, Xiong, P, Guo, X, Zhang, J, Yang, W, Wu, W, Liu, H & Wang, G 2019, 'A nitrogen, sulphur dual-doped hierarchical porous carbon with interconnected conductive polyaniline coating for high-performance sodium-selenium batteries', Energy Storage Materials, vol. 19, pp. 251-260.
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© 2019 Elsevier B.V. Sodium-selenium (Na-Se)battery has been emerging as a new rechargeable energy storage system with high capacity, low cost and high rate capability. However, the shuttling of polyselenides from the cathode to the anode causes dramatic capacity decay, severely impeding their practical applications. Herein, we report a combinational strategy of nitrogen and sulphur dual-doped hierarchical porous carbon with interconnected conductive polyaniline (PANI)coating to incorporate Se as stable cathodes (i-PANI@NSHPC/Se)for Na-Se batteries. Ex situ characterizations and density functional theory (DFT)calculations demonstrate that the i-PANI@NSHPC/Se cathode can provide both physical diffusion barrier and strong chemical affinity for polyselenides. In addition, the interconnected conductive polyaniline network enhances the conductivity for electrons and ions. With this strategy, the i-PANI@NSHPC/Se cathode delivered a high reversible capacity of 617 mAh g−1 after 200 cycles at 0.2C with a low capacity decay rate of 0.013% per cycle and an excellent rate capability at 20 C. Importantly, stable cycling performances were achieved with high capacities at different Se areal mass loadings (1.2, 2.3, 3.5 mg cm−2). This work could provide an efficient approach for developing Na-Se batteries with high active material mass loading, high rate capacity and long cycle life.

Zhang, H, Wang, B, Liu, DL, Zhang, M, Feng, P, Cheng, L, Yu, Q & Eamus, D 2019, 'Impacts of future climate change on water resource availability of eastern Australia: A case study of the Manning River basin', Journal of Hydrology, vol. 573, pp. 49-59.
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© 2019 Elsevier B.V. Hydrological responses of catchments to climate change require detailed examination to ensure sustainable management of both water resources and natural ecosystems. This study evaluated the impacts of climate change on water resource availability of a catchment in eastern Australia (i.e. the Manning River catchment) and analyzed climate-hydrology relationships. For this evaluation, the Xinanjiang (XAJ) model was used and validated to simulate monthly rainfall-runoff relationships of the catchment. Statistically downscaled climate data based on 28 global climate models (GCMs) under RCP8.5 scenarios were used to assess the impacts of climate changes on the Manning River catchment. Our results showed that the XAJ model was able to reproduce observed monthly rainfall-runoff relationships with an R 2 ≥ 0.94 and a Nash-Sutcliffe Efficiency ≥0.92. The median estimates from the ensemble of downscaled GCM projections showed a slight decrease in annual rainfall and runoff for the period 2021–2060 and an increase for the period 2061–2100. Annual actual evapotranspiration was projected to increase slightly, while annual soil moisture content was predicted to decrease in the future. Our results also demonstrated that future changes in seasonal and annual runoff, actual evapotranspiration and soil moisture are largely dominated by changes in rainfall, with a smaller influence arising from changes in temperature. An increase in the values of high runoffs and a decrease in the values of low runoffs predicted from the ensemble of the 28 GCMs suggest increased variability of water resources at monthly and seasonal time-scales in the future. A trend of decreasing values in winter runoff and soil moisture content in the future is likely to aggravate possible future reductions in water availability in eastern Australia. These results contribute to the development of adaptive strategies and future policy options for the sustainable management of water re...

Zhang, J, Sun, B, Zhao, Y, Tkacheva, A, Liu, Z, Yan, K, Guo, X, McDonagh, AM, Shanmukaraj, D, Wang, C, Rojo, T, Armand, M, Peng, Z & Wang, G 2019, 'A versatile functionalized ionic liquid to boost the solution-mediated performances of lithium-oxygen batteries', Nature Communications, vol. 10, no. 1.
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AbstractDue to the high theoretical specific energy, the lithium–oxygen battery has been heralded as a promising energy storage system for applications such as electric vehicles. However, its large over-potentials during discharge–charge cycling lead to the formation of side-products, and short cycle life. Herein, we report an ionic liquid bearing the redox active 2,2,6,6-tetramethyl-1-piperidinyloxy moiety, which serves multiple functions as redox mediator, oxygen shuttle, lithium anode protector, as well as electrolyte solvent. The additive contributes a 33-fold increase of the discharge capacity in comparison to a pure ether-based electrolyte and lowers the over-potential to an exceptionally low value of 0.9 V. Meanwhile, its molecule facilitates smooth lithium plating/stripping, and promotes the formation of a stable solid electrolyte interface to suppress side-reactions. Moreover, the proportion of ionic liquid in the electrolyte influences the reaction mechanism, and a high proportion leads to the formation of amorphous lithium peroxide and a long cycling life (> 200 cycles). In particular, it enables an outstanding electrochemical performance when operated in air.

Zhang, W, Liu, T, Ye, L, Ueland, M, Forbes, SL & Su, SW 2019, 'A novel data pre-processing method for odour detection and identification system', Sensors and Actuators A: Physical, vol. 287, pp. 113-120.
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© 2018 Elsevier B.V. This paper presents a novel electronic nose (E-nose) data pre-processing method, based on a recently developed non-parametric kernel-based modelling (KBM) approach. The proposed method is tested by an automated odour detection and classification system, named “NOS.E” developed by the NOS.E team in University of Technology Sydney. Experimental results show that when extracting the derivative-related features from signals collected by the NOS.E, the proposed non-parametric KBM odour data pre-processing method achieves more reliable and stable pre-processing results comparing with other pre-processing methods such as wavelet package correlation filter (WPCF), mean filter (MF), polynomial curve fitting (PCF) and locally weighted regression (LWR). Based on these derivative-related features, the NOS.E can achieve a 96.23% accuracy of classification with the popular Support Vector Machine (SVM) classifier.

Zhang, X, Ma, Y & Carroll, RJ 2019, 'MALMEM: Model Averaging in Linear Measurement Error Models', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 81, no. 4, pp. 763-779.
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SummaryWe develop model averaging estimation in the linear regression model where some covariates are subject to measurement error. The absence of the true covariates in this framework makes the calculation of the standard residual-based loss function impossible. We take advantage of the explicit form of the parameter estimators and construct a weight choice criterion. It is asymptotically equivalent to the unknown model average estimator minimizing the loss function. When the true model is not included in the set of candidate models, the method achieves optimality in terms of minimizing the relative loss, whereas, when the true model is included, the method estimates the model parameter with root n rate. Simulation results in comparison with existing Bayesian information criterion and Akaike information criterion model selection and model averaging methods strongly favour our model averaging method. The method is applied to a study on health.

Zhang, X, Pei, Z, Wang, C, Yuan, Z, Wei, L, Pan, Y, Mahmood, A, Shao, Q & Chen, Y 2019, 'Flexible Zinc‐Ion Hybrid Fiber Capacitors with Ultrahigh Energy Density and Long Cycling Life for Wearable Electronics', Small, vol. 15, no. 47, pp. 1903817-1903817.
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AbstractEmerging wearable electronics require flexible energy storage devices with high volumetric energy and power densities. Fiber‐shaped capacitors (FCs) offer high power densities and excellent flexibility but low energy densities. Zn‐ion capacitors have high energy density and other advantages, such as low cost, nontoxicity, reversible Faradaic reaction, and broad operating voltage windows. However, Zn‐ion capacitors have not been applied in wearable electronics due to the use of liquid electrolytes. Here, the first quasisolid‐state Zn‐ion hybrid FC (ZnFC) based on three rationally designed components is demonstrated. First, hydrothermally assembled high surface area and conductive reduced graphene oxide/carbon nanotube composite fibers serve as capacitor‐type positive electrodes. Second, graphite fibers coated with a uniform Zn layer work as battery‐type negative electrodes. Third, a new neutral ZnSO4‐filled polyacrylic acid hydrogel act as the quasisolid‐state electrolyte, which offers high ionic conductivity and excellent stretchability. The assembled ZnFC delivers a high energy density of 48.5 mWh cm−3 at a power density of 179.9 mW cm−3. Further, Zn dendrite formation that commonly happens under high current density is efficiently suppressed on the fiber electrode, leading to superior cycling stability. Multiple ZnFCs are integrated as flexible energy storage units to power wearable devices under different deformation conditions.

Zhang, X, Tian, R, Zhao, C, Birch, S, Lee, JA, Alraek, T, Bovey, M, Zaslawski, C, Robinson, N, Kim, T-H, Lee, MS & Bian, Z-X 2019, 'The use of pattern differentiation in WHO-registered traditional Chinese medicine trials – A systematic review', European Journal of Integrative Medicine, vol. 30, pp. 100945-100945.
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© 2019 Introduction: Pattern differentiation is a critical component for traditional Chinese medicine (TCM) diagnosis and treatment. However, the issue of whether pattern differentiation is appropriately applied in TCM interventional trials, including Chinese herbal medicine (CHM) interventions and non-herbal TCM interventions, is unclear. The aim of this study was to i) systematically review the current status of pattern differentiation used in WHO-registered clinical trials for different types of TCM interventions; and ii) provide suggestions for improving the use of pattern differentiation in future clinical trial design. Methods: The World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) database was searched for all TCM interventional trials registered up to 31 December 2017. In this systematic review trials with a TCM pattern differentiation in their design were included. Descriptive statistics were collated to demonstrate the characteristics of pattern differentiation applied for different TCM interventional trials. Results: Among 2955 TCM interventional trials registered during 1999–2017, 376 (12.7%) trials included pattern differentiation. Of 376 trials, the use of pattern differentiation was identified in; –the title (30.6%), objective (50.5%), participants inclusion (100%), outcomes (43.6%) and study background (12.5%). Further, 85.4% reported the specific name of the TCM intervention, 10.6% provided the intervention's targeted pattern, 83.8% reported the specific name of the TCM pattern, 7.2% presented diagnostic criteria for the pattern studied, and 19.1% adopted a pattern-related outcome as primary outcome for evaluation. Conclusion: The reporting and application of pattern differentiation in TCM trials were inadequate and confusing, which was mainly due to lack of clarity regarding study design, objectives, diagnostic criteria and outcomes.

Zhang, X, Wen, Q, Wang, L, Ding, L, Yang, J, Ji, D, Zhang, Y, Jiang, L & Guo, W 2019, 'Asymmetric Electrokinetic Proton Transport through 2D Nanofluidic Heterojunctions', ACS Nano, vol. 13, no. 4, pp. 4238-4245.
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Nanofluidic ion transport in nacre-like 2D layered materials attracts broad research interest due to subnanometer confined space and versatile surface chemistry for precisely ionic sieving and ultrafast water permeation. Currently, most of the 2D-material-based nanofluidic systems are homogeneous, and the investigations of proton conduction therein are restricted to symmetric transport behaviors. It remains a great challenge to endow the 2D nanofluidic systems with asymmetric proton transport characteristics and adaptive responsibilities. Herein, we report the asymmetric proton transport phenomena through a 2D nanofluidic heterojunction membrane under three different types of electrokinetic driving force, that is, the external electric field, the transmembrane concentration gradient, and the hydraulic pressure difference. The heterogeneous 2D nanofluidic membrane comprises of sequentially stacked negatively and positively charged graphene oxide (n-GO and p-GO) multilayers. We find that the preferential direction for proton transport is opposite under the three types of electrokinetic driving force. The preferential direction for electric-field-driven proton transport is from the n-GO multilayers to the p-GO multilayers, showing rectified behaviors. Intriguingly, when the transmembrane concentration difference and the hydraulic flow are used as the driving force, a preferred diffusive and streaming proton current is found in the reverse direction, from the p-GO to the n-GO multilayers. The asymmetric proton transport phenomena are explained in terms of asymmetric proton concentration polarization and difference in proton selectivity. The membrane-scale heterogeneous 2D nanofluidic devices with electrokinetically controlled asymmetric proton flow provide a facile and general strategy for potential applications in biomimetic energy conversion and chemical sensing.

Zhang, Y, Li, H, Keadle, SK, Matthews, CE & Carroll, RJ 2019, 'A Review of Statistical Analyses on Physical Activity Data Collected from Accelerometers', Statistics in Biosciences, vol. 11, no. 2, pp. 465-476.
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© 2019, International Chinese Statistical Association. Studies for the associations between physical activity and disease risk have been supported by newly developed wearable accelerometer-based devices. These devices record raw activity/movement information in real time on a second-by-second basis and the data can be converted to a variety of summary metrics, such as energy expenditure, sedentary time and moderate-vigorous intensity physical activity. Here we review some of the methods used to analyze the accelerometer data and the R packages that can generate activity related variables from raw data. We also discuss longitudinal data and functional data approaches to perform analyses for various research purposes.

Zhanghao, K, Chen, X, Liu, W, Li, M, Liu, Y, Wang, Y, Luo, S, Wang, X, Shan, C, Xie, H, Gao, J, Chen, X, Jin, D, Li, X, Zhang, Y, Dai, Q & Xi, P 2019, 'Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy', Nature Communications, vol. 10, no. 1, p. 4694.
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AbstractFluorescence polarization microscopy images both the intensity and orientation of fluorescent dipoles and plays a vital role in studying molecular structures and dynamics of bio-complexes. However, current techniques remain difficult to resolve the dipole assemblies on subcellular structures and their dynamics in living cells at super-resolution level. Here we report polarized structured illumination microscopy (pSIM), which achieves super-resolution imaging of dipoles by interpreting the dipoles in spatio-angular hyperspace. We demonstrate the application of pSIM on a series of biological filamentous systems, such as cytoskeleton networks and λ-DNA, and report the dynamics of short actin sliding across a myosin-coated surface. Further, pSIM reveals the side-by-side organization of the actin ring structures in the membrane-associated periodic skeleton of hippocampal neurons and images the dipole dynamics of green fluorescent protein-labeled microtubules in live U2OS cells. pSIM applies directly to a large variety of commercial and home-built SIM systems with various imaging modality.

Zhao, C, Pan, T, Dou, T, Liu, J, Liu, C, Ge, Y, Zhang, Y, Yu, X, Mitrovic, S & Lim, R 2019, 'Making global river ecosystem health assessments objective, quantitative and comparable', Science of The Total Environment, vol. 667, pp. 500-510.
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Assessing and comparing global river ecosystem health in an objective and quantitative way remains a major challenge. In this study the widely-used semi-quantitative methods Rapid Biological assessment Protocols (RBPs) was used to determine the health of rivers. The findings were then compared to the results derived from our new UAV (Unmanned aerial vehicles) orthophotographic imagery method. This method quantitatively and objectively assesses river ecosystem health. As a comparison, our method was used to quantitatively measure distance and areas of a range of hydrological and biological attributes thus improving the accuracy of distance- and area-related indices, consequently avoiding subjective errors in these estimations that is fraught in methods like the RBPs. To strengthen the objectivity of the assessment the weights of these indices were objectively determined using the entropy weighting method. This new method was then tested using 9551 UAV orthophotographs taken over six field campaigns. It performed satisfactorily, showing that in our study area the health status of mountain rivers was the best with the highest score of 0.94 out of 1.0. Temporally, the health of the river was better in summer (0.65) compared with that in autumn (0.40). Changes in river ecosystem health were driven by variations in biology and water quality. In contrast the outputs of RBPs, especially in relation to distance and area indices, had ~ 20% uncertainty due to visual errors and subjectivity in estimations by observers. The UAV orthophotographic imaging method proposed in this study can improve the ability to compare the health of rivers across different periods and regions throughout the globe.

Zhao, CS, Yang, Y, Yang, ST, Xiang, H, Zhang, Y, Wang, ZY, Chen, X & Mitrovic, SM 2019, 'Predicting future river health in a minimally influenced mountainous area under climate change', Science of The Total Environment, vol. 656, pp. 1373-1385.
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It has been shown that climate change impacts the overall health of a river's ecosystem. Although predicting river health under climate change would be useful for stakeholders to adapt to the change and better conserve river health, little research on this topic exists. This paper presents a methodology predicting river health under different climate change scenarios. First, a multi-source, distributed, time-variant gain hydrological model (MS-DTVGM) was used to predict the runoff from a mountainous river in eastern China using the data from three existing IPCC5 climate change models (RCP2.6, RCP4.5, and RCP8.4). Next, a model was developed to predict the river's water quality under these scenarios. Finally, a multidimensional response model utilizing hydrology, water quality, and biology was used to predict the river's biological status and ascertain the impact of climate change on its overall health. The river is in a mountainous area near Jinan City, one of China's first "pilot" cities recognized as a "healthy water ecological community." Our results predict that the overall health of the Yufu River, which is minimally influenced by human activities, will improve by 2030 due to the increased river flow due to an increase in rainfall frequency and subsequent peak runoff. However, the total nitrogen concentration is predicted to increase, which is a potential eutrophication risk. Therefore, effective control of nitrogen pollutants entering the river will be necessary. The increase in flow velocity (the annual average increase is ~0.5 m/s) is favorable for fish reproduction. Our methods and results will provide scientific guidance for policy makers and river managers and will help people to better understand how global climate change impacts river health.

Zhao, S, Yan, K, Munroe, P, Sun, B & Wang, G 2019, 'Construction of Hierarchical K_1.39Mn₃O₆ Spheres via AlF₃ Coating for High‐Performance Potassium‐Ion Batteries', Advanced Energy Materials, vol. 9, no. 10, pp. 1803757-1803757.
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AbstractPotassium‐ion batteries are attracting great interest for emerging large‐scale energy storage owing to their advantages such as low cost and high operational voltage. However, they are still suffering from poor cycling stability and sluggish thermodynamic kinetics, which inhibits their practical applications. Herein, the synthesis of hierarchical K1.39Mn3O6 microspheres as cathode materials for potassium‐ion batteries is reported. Additionally, an effective AlF3 surface coating strategy is applied to further improve the electrochemical performance of K1.39Mn3O6 microspheres. The as‐synthesized AlF3 coated K1.39Mn3O6 microspheres show a high reversible capacity (about 110 mA h g−1 at 10 mA g−1), excellent rate capability, and cycling stability. Galvanostatic intermittent titration technique results demonstrate that the increased diffusion kinetics of potassium‐ion insertion and extraction during discharge and charge processes benefit from both the hierarchical sphere structure and surface modification. Furthermore, ex situ X‐ray diffraction measurements reveal that the irreversible structure evolution can be significantly mitigated via surface modification. This work sheds light on rational design of high‐performance cathode materials for potassium‐ion batteries.

Zhao, Y, Wang, S, Liu, H, Guo, X, Zeng, X, Wu, W, Zhang, J & Wang, G 2019, 'Porous Mo2C nanorods as an efficient catalyst for the hydrogen evolution reaction', Journal of Physics and Chemistry of Solids, vol. 132, pp. 230-235.
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© 2019 Elsevier Ltd Generate hydrogen fuel from electrochemical water splitting has been considered as a promising approach. However, to obtain the low-cost and high performance catalysts towards hydrogen evolution reaction (HER)which can be applied in both alkaline and acid solution remains a challenge. Herein, we synthesized an active and stable HER catalyst composed of Mo2C nanocrystals embedded in the nanocarbon layers (Mo2C@C)by using MoO3 nanorods as precursor. Benefiting from the porous one dimensional structure and ultrafine Mo2C nanocrystals, Mo2C@C exhibits high HER catalytic activity for 10 mA cm−2 with the overpotential of 119 mV in 1 M KOH solution and 170 mV in 0.5 M H2SO4 solution, respectively. Moreover, Mo2C@C displays long durability during the HER process with almost no decay and maintains the porous one dimensional architecture after the HER stability test. This study offers the guideline for the further design and fabrication of the nanostructured HER electrocatalysts in wide pH range.

Zhong, H-J, Sun, H-H, Xue, L-F, McGowan, EM & Chen, Y 2019, 'Differential hepatic features presenting in Wilson disease-associated cirrhosis and hepatitis B-associated cirrhosis', World Journal of Gastroenterology, vol. 25, no. 3, pp. 378-387.
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© The Author(s) 2019. Published by Baishideng Publishing Group Inc. All rights reserved. BACKGROUND Cirrhosis is a chronic late stage liver disease associated with hepatitis viruses, alcoholism, and metabolic disorders, such as Wilson disease (WD). There are no clear markers or clinical features that define cirrhosis originating from these disparate origins. We hypothesized that cirrhosis is not one disease and cirrhosis of different etiology may have differential clinical hepatic features. AIM To delineate the liver features between WD-associated cirrhosis and hepatitis Bassociated cirrhosis in the Chinese population. METHODS In this observational study, we reviewed the medical data of consecutive inpatients who had WD-associated cirrhosis or hepatitis B-associated cirrhosis from January 2010 to August 2018, and excluded patients who had carcinoma, severe heart or pulmonary diseases, or other liver diseases. According to the etiology of cirrhosis, patients were divided into two groups: WD-associated cirrhosis group (60 patients) and hepatitis B-associated cirrhosis group (56 patients). The liver fibrosis degree, liver function indices, and portal hypertension features of these patients were compared between the two groups. RESULTS No inter-group differences were observed in the diagnostic liver fibrosis markers, however, clinical features clearly defined the origin of cirrhosis. WD-associated cirrhosis patients (16-29 years) had lower levels of alanine transaminase, aspartate transaminase, and bilirubin, lower prothrombin time, lower incidence of hepatic encephalopathy, and lower portal vein diameter (P < 0.05), compared to cirrhosis resulting from hepatitis B in older patients (45-62 years). Importantly, they had decreased risks of progression from Child-Pugh grade A to B (odds ratio = 0.046, 95% confidence interval: 0.006-0.387, P = 0.005) and of ascites (odds ratio = 0.08, 95% confidence interval: 0.01-0.48, P = 0.005). Conversely, WDassociated cirr...

Zhou, D, Tkacheva, A, Tang, X, Sun, B, Shanmukaraj, D, Li, P, Zhang, F, Armand, M & Wang, G 2019, 'Stable Conversion Chemistry‐Based Lithium Metal Batteries Enabled by Hierarchical Multifunctional Polymer Electrolytes with Near‐Single Ion Conduction', Angewandte Chemie International Edition, vol. 58, no. 18, pp. 6001-6006.
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AbstractThe low Coulombic efficiency and serious safety issues resulting from uncontrollable dendrite growth have severely impeded the practical applications of lithium (Li) metal anodes. Herein we report a stable quasi‐solid‐state Li metal battery by employing a hierarchical multifunctional polymer electrolyte (HMPE). This hybrid electrolyte was fabricated via in situ copolymerizing lithium 1‐[3‐(methacryloyloxy)propylsulfonyl]‐1‐(trifluoromethanesulfonyl)imide (LiMTFSI) and pentaerythritol tetraacrylate (PETEA) monomers in traditional liquid electrolyte, which is absorbed in a poly(3,3‐dimethylacrylic acid lithium) (PDAALi)‐coated glass fiber membrane. The well‐designed HMPE simultaneously exhibits high ionic conductivity (2.24×10−3 S cm−1 at 25 °C), near‐single ion conducting behavior (Li ion transference number of 0.75), good mechanical strength and remarkable suppression for Li dendrite growth. More intriguingly, the cation permselective HMPE efficiently prevents the migration of negatively charged iodine (I) species, which provides the as‐developed Li‐I batteries with high capacity and long cycling stability.

Zhou, D, Tkacheva, A, Tang, X, Sun, B, Shanmukaraj, D, Li, P, Zhang, F, Armand, M & Wang, G 2019, 'Stable Conversion Chemistry‐Based Lithium Metal Batteries Enabled by Hierarchical Multifunctional Polymer Electrolytes with Near‐Single Ion Conduction', Angewandte Chemie, vol. 131, no. 18, pp. 6062-6067.
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AbstractThe low Coulombic efficiency and serious safety issues resulting from uncontrollable dendrite growth have severely impeded the practical applications of lithium (Li) metal anodes. Herein we report a stable quasi‐solid‐state Li metal battery by employing a hierarchical multifunctional polymer electrolyte (HMPE). This hybrid electrolyte was fabricated via in situ copolymerizing lithium 1‐[3‐(methacryloyloxy)propylsulfonyl]‐1‐(trifluoromethanesulfonyl)imide (LiMTFSI) and pentaerythritol tetraacrylate (PETEA) monomers in traditional liquid electrolyte, which is absorbed in a poly(3,3‐dimethylacrylic acid lithium) (PDAALi)‐coated glass fiber membrane. The well‐designed HMPE simultaneously exhibits high ionic conductivity (2.24×10−3 S cm−1 at 25 °C), near‐single ion conducting behavior (Li ion transference number of 0.75), good mechanical strength and remarkable suppression for Li dendrite growth. More intriguingly, the cation permselective HMPE efficiently prevents the migration of negatively charged iodine (I) species, which provides the as‐developed Li‐I batteries with high capacity and long cycling stability.

Zhou, W, Jin, W, Wang, D, Lu, C, Xu, X, Zhang, R, Kuang, T, Zhou, Y, Wu, W, Jin, D, Mou, Y & Lou, W 2019, 'Laparoscopic versus open pancreaticoduodenectomy for pancreatic ductal adenocarcinoma: a propensity score matching analysis', Cancer Communications, vol. 39, no. 1, pp. 1-11.
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AbstractBackgroundA growing body of evidence supports the use of laparoscopic pancreaticoduodenectomy (LPD) as an efficient and feasible surgical technique. However, few studies have investigated its applicability in pancreatic ductal adenocarcinoma (PDAC), and the long‐term efficacy of LPD on PDAC remains unclear. This study aimed to compare the short‐ and long‐term outcomes between LPD and open pancreaticoduodenectomy (OPD) for PDAC.MethodsThe data of patients who had OPD or LPD for PDAC between January 2013 and September 2017 were retrieved. Their postoperative outcomes and survival were compared after propensity score matching.ResultsA total of 309 patients were included. After a 2:1 matching, 93 cases in the OPD group and 55 in the LPD group were identified. Delayed gastric emptying (DGE), particularly grade B/C DGE, occurred less frequently in the LPD group than in the OPD group (1.8% vs. 36.6%, P < 0.001; 1.8% vs. 22.6%, P = 0.001). The overall complication rates were significantly lower in the LPD group than in the OPD group (49.1% vs. 71.0%, P = 0.008), whereas the rates of major complications were similar (10.9% vs. 14.0%, P = 0.590). In addition, the median overall survival was comparable between the two groups (20.0 vs. 18.7 months, P = 0.293).ConclusionLPD was found to be technically feasible with efficacy similar to OPD for patients with PDAC.

Zhou, Y, Chen, Y, He, H, Liao, J, Duong, HTT, Parviz, M & Jin, D 2019, 'A homogeneous DNA assay by recovering inhibited emission of rare earth ions-doped upconversion nanoparticles', Journal of Rare Earths, vol. 37, no. 1, pp. 11-18.
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© 2018 Chinese Society of Rare Earths Robust and easy-to-use kits specific for a particular DNA sequence are desirable for early detection of diseases. However, the major challenge with these tests is often the background fluorescence artifacts arising from biological species due to employing UV and visible range of light. Here, we have reported a near-infrared (NIR) fluorescence “turn-on” kit based on rare earth ions doped nanoparticles, upconversion nanoparticles (UCNPs), and gold nanoparticles (AuNPs), which forms a fluorescence-quencher pair, brought together by a hairpin structure through the formation of double-stranded DNA (dsDNA), with quenched upconversion luminescence. In the presence of analytes, the molecular beacon opens to push AuNPs away from UCNPs, with a distance longer than the efficient quenching distance, so that the inhibited upconversion emission will be restored. We demonstrated that this assay provides a homogeneous, facile, simple and highly selective HIV-1 based DNA detection system with restore efficiency up to 85%, and the detection limit of 5 nm.

Zhu, Q, Yang, X, Yu, B, Tulau, M, McInnes‐Clarke, S, Nolan, RH, Du, Z & Yu, Q 2019, 'Estimation of event‐based rainfall erosivity from radar after wildfire', Land Degradation & Development, vol. 30, no. 1, pp. 33-48.
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AbstractRainfall erosivity impacts all stages of hillslope erosion processes and is an important factor (the ‘R factor’) in the Revised Universal Soil Loss Equation. It is estimated as the average annual value of the sum of all erosive events (EI30) over a period of many years. For each storm event, the EI30 value is the product of storm energy, E in MJ ha−1, and peak 30‐min rainfall intensity (I30, mm hr−1). Previous studies often focused on estimation of the R factor for prediction of mean annual or long‐term soil losses. However, many applications require EI30 values at much higher temporal resolution, such as postfire soil erosion monitoring, which requires a time step at storm events or on a daily basis. In this study, we explored the use of radar rainfall data to estimate the storm event‐based EI30 after a severe wildfire in Warrumbungle National Park in eastern Australia. The radar‐derived rainfall data were calibrated against 12 tipping bucket rain gauges across an area of 239 km2 and subsequently used to produce a time series of rainfall erosivity maps at daily intervals since the wildfire in January 2013. The radar‐derived daily rainfall showed good agreement with the gauge measurements (R2 > 0.70, Ec = 0.66). This study reveals great variation in EI30 values ranging from near zero to 826.76 MJ·mm·ha−1·hr−1 for a single storm event. We conclude that weather radar rainfall data can be used to derive tim...

Zhu, X, Rice, SA & Barraud, N 2019, 'Nitric Oxide and Iron Signaling Cues Have Opposing Effects on Biofilm Development in Pseudomonas aeruginosa', Applied and Environmental Microbiology, vol. 85, no. 3.
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Nitric oxide (NO), which induces biofilm dispersal, is a promising strategy for biofilm control in both clinical and industrial contexts. However, competing environmental signals may reduce the efficacy of NO. The results presented here suggest that the presence of iron represents one such environmental cue that antagonizes the activity of NO as a biofilm-dispersing agent. Based on this understanding, we developed a strategy to enhance dispersal by combining NO with an iron-scavenging agent. Overall, this study links two important environmental signals, iron and NO, with their roles in biofilm development and suggests new ways for improving the use of NO in biofilm control strategies.

Zhu, Y, Suggett, DJ, Liu, C, He, J, Lin, L, Le, F, Ishizaka, J, Goes, J & Hao, Q 2019, 'Primary Productivity Dynamics in the Summer Arctic Ocean Confirms Broad Regulation of the Electron Requirement for Carbon Fixation by Light-Phytoplankton Community Interaction', Frontiers in Marine Science, vol. 6.
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Ziklo, N, Huston, WM, Taing, K & Timms, P 2019, 'High expression of IDO1 and TGF-β1 during recurrence and post infection clearance with Chlamydia trachomatis, are independent of host IFN-γ response', BMC Infectious Diseases, vol. 19, no. 1.
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© 2019 The Author(s). Background: Chlamydia trachomatis infections in women continue to be a major public health concern due to their high prevalence and consequent reproductive morbidities. While antibiotics are usually efficient to clear the Chlamydia, repeat infections are common and may contribute to pathological outcomes. Interferon-gamma (IFN-γ)-mediated immunity has been suggested to be protective against reinfection, and represent an important anti-chlamydial agent, primarily via the induction of indoleamine-2,3 dioxygenase 1 (IDO1) enzyme. IDO1 catalyzes the degradation of tryptophan, which can eliminate C. trachomatis infection in vitro. Here, we sought to measure IDO1 expression levels and related immune markers during different C. trachomatis infection statuses (repeated vs single infection vs post antibiotic treatment), in vitro and in vivo. Methods: In this study, we measured the expression levels of IDO1 and immune regulatory markers, transforming growth factor β1 (TGF-β1) and forkhead box P3 (FoxP3), in vaginal swab samples of C. trachomatis-infected women, with either single or repeated infection. In addition, we used an in vitro co-culture model of endometrial carcinoma cell-line and peripheral blood mononuclear cells (PBMCs) to measure the same immune markers. Results: We found that in women with repeated C. trachomatis infections vaginal IDO1 and TGF-β1 expression levels were significantly increased. Whereas, women who cleared their infection post antibiotic treatment, had increased levels of IDO1 and TGF-β1, as well as FoxP3. Similarly, using the in vitro model, we found significant upregulation of IDO1 and TGF-β1 levels in the co-culture infected with C. trachomatis. Furthermore, we found that in PBMCs infected with C. trachomatis there was a significant upregulation in IDO1 levels, which was independent of IFN-γ. In fact, C. trachomatis infection in PBMCs failed to induce IFN-γ levels in comparison to the uninfected culture. Concl...

Zizka, A, Silvestro, D, Andermann, T, Azevedo, J, Duarte Ritter, C, Edler, D, Farooq, H, Herdean, A, Ariza, M, Scharn, R, Svantesson, S, Wengström, N, Zizka, V & Antonelli, A 2019, 'CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases', Methods in Ecology and Evolution, vol. 10, no. 5, pp. 744-751.
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AbstractSpecies occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.Here, we present CoordinateCleaner, an r‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils.We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3...