Publications

Ben-Nissan, B & Choi, AH 2017, 'Calcium Phosphate Nanocoatings: Production, Physical and Biological Properties, and Biomedical Applications' in Nanobioceramics for Healthcare Applications, WORLD SCIENTIFIC (EUROPE), pp. 105-149.
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Ben-Nissan, B, Choi, AH & Macha, I 2017, 'Advances in Bioglass and Glass Ceramics for Biomedical Applications' in Springer Series in Biomaterials Science and Engineering, Springer Berlin Heidelberg, Germany, pp. 133-161.
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� Springer-Verlag GmbH Germany 2017. Tissue engineering and advanced biomedical technologies have proved to be potential to improve the quality of human life. During the last four decades, the capability to engineer or repair new functional tissues has been a very effective approach to improve the quality of life of patients. Since its discovery by Hench and co-workers in the 1960s, bioglasses and glass ceramics have attracted considerable attention of many researchers because of their unique properties which can easily be tailored by manipulating its compositions and morphology. Over the years, many questions concerning its interactions with both hard and soft tissues have been answered with a multidisciplinary team of surgeons, scientists and engineers. Many clinical Bioglass� and other similar structures and compositions are being used for bone augmentation and restoration, in orthopaedic, dental and maxillofacial surgery and in general in the field of tissue engineering. They have proved to be efficient and effective, some with outperformance over other bioceramic and metal prostheses. It is our aim in this chapter to present the development of these important biomaterials focusing on the history, synthesis, properties, modern characterisation methods and the current development of nano- and biocomposite materials for clinical applications.

Ben-Nissan, B, Choi, AH, Latella, BA & Bendavid, A 2017, '3.8 Biomedical Thin Films: Mechanical Properties ☆' in Comprehensive Biomaterials II, Elsevier, pp. 128-143.
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© 2017 Elsevier Ltd All rights reserved. In materials applied for medical applications, thin film coatings (including micro- and nanocoatings) offer the possibility of modifying the surface properties of a range of surgical materials and implants such as hip or knee replacements. The essential requirement of any artificial implant is to prevent immune rejection or inflammatory responses. Metals, ceramic, and polymers have all been used for implants. High-quality metal alloys of titanium, vanadium, and chromium are commonly used for orthopedic prostheses in order to avoid toxicity. Coatings on these alloys are aimed at improving abrasion resistance, corrosion resistance, and ion release protection; increasing bioactivity; and improving environment and structure for new bone attachment. In turn, they improve reliability, performance, and longevity of a range of biomedical implants and devices. Industrial techniques for the production of micro- and nanocoatings are many, including physical vapor deposition, chemical vapor deposition, thermal and plasma spraying, and sol-gel processing. Micro- and nanocoatings are clinically used to improve bioactivity and improve bone-implant bonding, improve abrasion and wear resistance, and reduce metal ion release in a range of orthopedic and maxillofacial implants.

Booth, DJ, Feary, D, Kobayashi, D, Luiz, O & Nakamura, Y 2017, 'Tropical Marine Fishes and Fisheries and Climate Change' in Climate Change Impacts on Fisheries and Aquaculture A Global Analysis, Wiley, USA, pp. 875-896.
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Covers an array of critical topics and assesses reviews of climate change impacts on fisheries and aquaculture from many countries, including Japan, Mexico, South Africa, Australia, Chile, US, UK, New Zealand, Pacific Islands, India and ...

Booth, DJ, Poloczanska, E, Donelson, J, Molinos, J & Burrows, M 2017, 'Biodiversity and climate change in the oceans' in Phillips, B & Perez-Ramirez, M (eds), Climate Change Impacts on Fisheries and Aquaculture A Global Analysis, John Wiley & Sons, pp. 63-89.
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The ocean is a vast and varied habitat for organisms, and contains most of the known phyla and at least 250,000 species. Patterns of biodiversity vary by depth, habitat type and region, with numerous hotspots of diversity of particular taxa, such as fishes. Patterns of fish diversity globally, and their sensitivities to climate change, need to be understood to predict the future of biodiversity and fisheries. This chapter describes key climate change stressors that can affect fish populations, assemblages and therefore biodiversity at many scales. We describe how sea temperature, through fish physiological processes, may act as a selective agent, while pressures such as disease and changing habitat, which can also be related to climate change, can drive biodiversity loss. We describe and compare approaches to understanding changes in ocean biodiversity, including risk modeling and direct empirical observations. We end with a case study to illustrate how changes in ocean biodiversity and fisheries can be linked to climate change via a modeling approach

Bottomley, AL, Turnbull, L, Whitchurch, CB & Harry, EJ 2017, 'Immobilization Techniques of Bacteria for Live Super-resolution Imaging Using Structured Illumination Microscopy' in Pontus Nordenfelt and Mattias Collin (ed), Methods in Molecular Biology, Springer New York, pp. 197-209.
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© Springer Science+Business Media New York 2017. Advancements in optical microscopy technology have allowed huge progression in the ability to understand protein structure and dynamics in live bacterial cells using fluorescence microscopy. Paramount to high quality microscopy is good sample preparation to avoid bacterial cell movement that can result in motion blur during image acquisition. Here, we describe two techniques of sample preparation that reduce unwanted cell movement and are suitable for application to a number of bacterial species and imaging methods.

Bradfield, L, Morris, R & Balleine, BW 2017, 'OCD as a Failure to Integrate Goal-Directed and Habitual Action Control', Oxford University Press.
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This chapter discusses the considerable research that has identified distinct functional circuits linking frontal cortex with the basal ganglia in the control of goal-directed and habitual actions. OCD is characterized by hyperactivity in a circuit involving some of these regions. Recent accounts of the interaction of goal-directed actions and habits suggest that these control processes interact hierarchically, so one alternative to current theories is that OCD reflects a dysfunction in this interactive process resulting in dysregulated action selection, whether that selection is driven by the outcome itself or by cues predicting the outcome. Importantly, it appears that both sources of action selection depend on the OFC—outcome based retrieval on the medial OFC and cue-related retrieval on the lateral OFC. From this perspective, therefore, hyperactivity of the OFC could produce both elevated outcome retrieval and increased responsiveness to outcomes-related cues, resulting in dysregulated action selection and compulsive action initiation as a consequence.

Bradfield, LA & Balleine, BW 2017, 'The Learning and Motivational Processes Controlling Goal-Directed Action and Their Neural Bases' in Decision Neuroscience, Elsevier, pp. 71-80.
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© 2017 Elsevier Inc. All rights reserved. Research has made considerable progress in describing the learning and motivational processes controlling goal-directed action and their related neural circuitry. Broadly this circuitry spans various regions within the corticostriatal-thalamic loop, within which specific structures mediate differentiable aspects of goal-directed learning and performance. These aspects include the acquisition of action-outcome contingencies, the encoding and retrieval or incentive value, the matching of that value to specific outcome representations, and finally the integration of this information for action selection. Information from each of the structures that mediate these processes converges on the striatum, with the posterior dorsomedial striatum in particular hypothesized to represent the neural locus of goal-directed action. Here we discuss evidence from rodent studies regarding the neural circuits mediating each of these individual processes before considering how they are integrated within the striatum for successful goal-directed action selection.

Care, A, Bergquist, PL & Sunna, A 2017, 'Solid-Binding Peptides in Biomedicine' in Peptides and Peptide-based Biomaterials and their Biomedical Applications, Springer International Publishing, pp. 21-36.
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© Springer International Publishing AG 2017. Some peptides are able to bind to inorganic materials such as silica and gold. Over the past decade, Solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to a diverse range of inorganic surfaces e.g. metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers and minerals. They can be used in applications such as protein purification and synthesis, assembly and the functionalization of nanomaterials. They offer simple and versatile bioconjugation methods that can increase biocompatibility and also direct the immobilization and orientation of nanoscale entities onto solid supports without impeding their functionality. SBPs have been employed in numerous nanobiotechnological applications such as the controlled synthesis of nanomaterials and nanostructures, formation of hybrid biomaterials, immobilization of functional proteins and improved nanomaterial biocompatibility. With advances in nanotechnology, a multitude of novel nanomaterials have been designed and synthesized for diagnostic and therapeutic applications. New approaches have been developed recently to exert a greater control over bioconjugation and eventually, over the optimal and functional display of biomolecules on the surfaces of many types of solid materials. In this chapter we describe SBPs and highlight some selected examples of their potential applications in biomedicine.

Choi, AH & Ben-Nissan, B 2017, 'Calcium Phosphate Nanocomposites for Biomedical and Dental Applications: Recent Developments' in Handbook of Composites from Renewable Materials, Wiley, pp. 423-450.
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© 2017 Scrivener Publishing LLC. Interests in nanostructured materials for advanced technologies have been growing throughout the past decade, and the current emphasis is on the production of nanocomposites which are relevant to a number of biomedical applications such as tissue engineering and regeneration. It is possible through the use of the composite approach to engineer the strength of the nanocomposite scaffold to become close to those of human bone. At present, the most common biomaterials used in nanocomposites for clinical applications are those selected from a handful of available and well-characterized biocompatible ceramics such as calcium phosphate and various natural and synthetic polymers such as chitosan and polylactic acid. This chapter aims to give a brief introduction and recent developments in calcium phosphate nanocomposite coatings and nanocomposites or nanolaminates for tissue-engineering scaffolds and delivery vehicles for pharmaceutical and therapeutic substances.

Choi, AH, Macha, IJ, Akyol, S, Cazalbou, S & Ben-Nissan, B 2017, 'Nanostructured Calcium Phosphates for Drug, Gene, DNA and Protein Delivery and as Anticancer Chemotherapeutic Devices' in Clinical Applications of Biomaterials, Springer International Publishing, pp. 227-256.
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© Springer International Publishing AG 2017. During the past two decades, a number of materials and devices have been utilised in drug delivery applications. A range of biomaterials with different morphologies and pore sizes are currently utilised. For any given biomaterial or bioceramic, having an adequate control of the chemical composition as well as the critical pore sizes is important in terms of controlling the effectiveness when used to deliver drugs locally. In comparison to all currently known and used biomaterials, given the fact that it possesses chemical similarity to human bone, and most importantly its dissolution characteristics which allow for bone regeneration and growth, calcium phosphate holds a special consideration. Moreover, due to their interconnected pore structure, marine materials such as shells and coral exoskeletons show potential for applications in drug delivery due to their easy conversion to calcium phosphates with controllable dissolution rates. This chapter covers a range of current methods used specifically for natural materials that can be converted to calcium phosphates and mixed with polymeric materials as thin film or nanostructured drug, genes, protein and range of delivery and as anticancer chemotherapeutic devices.

Contreras-Porcia, L, López-Cristoffanini, C, Meynard, A & Kumar, M 2017, 'Tolerance Pathways to Desiccation Stress in Seaweeds' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 13-33.
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© Springer International Publishing AG 2017. Seaweeds are sessile organisms that inhabit coastal benthic systems and are key species for the equilibrium of marine communities. Rocky intertidal zone seaweeds are distributed in marked patterns determined by interactions between biotic and abiotic factors influenced by tide levels. It has been proposed that the distribution and abundance of organisms in the upper intertidal zones, with longer emersions, are mostly regulated by abiotic factors. Desiccation is a particularly noteworthy abiotic factor since, during low tide, algae of the upper intertidal zones can lose more than 90% of cellular water content, which can ultimately induce oxidative stress. Considering the necessary activation of several desiccation tolerance mechanisms, these algal species are ideal research models in ecophysiology. In fact, several studies using physiological, transcriptomic, and proteomic approaches have determined that desiccation tolerance mechanisms are expressed within a well-coordinated network that includes morphological and cell wall changes, photosynthetic activity diminishment, increased expression of desiccation-associated proteins, hormone accumulation, ROS scavenging by antioxidant enzymes and compounds, and osmolyte and protein synthesis. These mechanisms explain the permanence of tolerant algae species in the upper intertidal zone in comparison with lower intertidal species. Therefore, this chapter focuses on identifying tolerant algal species, and explaining the mechanisms underlying the high capacity of these species to cope with desiccation- induced oxidative stress.

Contreras-Porcia, L, Meynard, A, López-Cristoffanini, C, Latorre, N & Kumar, M 2017, 'Marine Metal Pollution and Effects on Seaweed Species' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 35-48.
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© Springer International Publishing AG 2017. Heavy metals are significant pollutants continuously released into the biosphere, both naturally and anthropogenically. Conceptually, metal speciation, bioavailability, and associated toxicity in marine organisms depend on a wide array of abiotic and biotic factors. Among these, pH variation is one of the most important environmental factors influencing metal speciation and toxicity. Due to this, ocean acidification is expected to modify metal speciation, altering the effects these nondegradable contaminants have on marine organisms, such as seaweeds. One clear effect of heavy metals on seaweeds is the rapid formation of reactive oxygen species (ROS). The production of ROS beyond the physiological tolerance threshold causes an oxidative stress condition that, if not attenuated, can irreversibly damage cellular constituents such as DNA/RNA, proteins, and lipids. To cope with heavy metal excess, several mechanisms exist in tolerant seaweed species, including the activation of an efficient ROS-scavenging system constituted by metal-binding compounds, antioxidant enzymes, and oxygenated polyunsaturated fatty acids, among others. Another adaptive mechanism involves the participation of ATP-binding cassette (ABC) transporter proteins in translocating a wide variety of compounds across cell membranes, including heavy metals. In contrast, an excessive heavy metal presence can inhibit photosynthesis, reduce pigment concentration and growth, induce cation losses, and disrupt gametophyte development in non-tolerant seaweed species. In a scenario of lowered ocean pH and increased heavy metal toxicity, the important roles played by non-tolerant seaweed species in structuring communities could be severely compromised, with unknown consequences for associated organisms. Therefore, in the upcoming decades, marine pollution could majorly shift and rearrange community compositions and the distributional ranges of species.

Godara, P & Milthorpe, B 2017, '7.37 Surgical Adhesion and Its Prevention' in Comprehensive Biomaterials II, Elsevier, pp. 733-745.
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Adhesion of freely moving tissues and organs due to surgical injury and trauma can be a serious postoperative complication. High rates of incidence due to surgical intervention, especially associated with abdominal procedures, have been reported. This chapter gives an introduction to the formation of adhesions, with particular focus on peritoneum, urinary and reproductive (female) systems, tendon, ligament, joint, and pericardium. A number of techniques, treatments, and materials have been proposed for the prevention/reduction of adhesion formation. Of these, barrier methods are considered the only effective method currently available. An overview of biomaterials currently used as barriers for postsurgical tissue adhesion is presented. Current clinical practice utilizes solid membranes/mechanical barriers, spray-on, and gel and liquid barriers. These barriers can be either resorbable, nonresorbable, or a combination of both. Complications of barrier films are examined, and design criteria for barrier membranes are presented. Adhesion formation can be beneficial in particular circumstances, such as for anchoring implants, and these uses are commented upon. Much advancement has been made in this area, thanks to the increasing knowledge and understanding regarding the events that control adhesion formation, but there is still a long way to go before an optimum solution to this problem is found.

Gupta, V, Jain, M & Reddy, CRK 2017, 'Macroalgal Functional Genomics: A Missing Area' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 3-12.
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Hare, DJ, Paul, B & Doble, PA 2017, 'Imaging Metals in the Brain by Laser Ablation–Inductively Coupled Plasma-Mass Spectrometry' in Metals in the Brain, Springer New York, pp. 33-50.
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© Springer Science+Business Media LLC 2017. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) has been an invaluable tool for accurate and precise measurement of metals in geological and environmental samples. However, like many advanced analytical techniques its versatility has seen its translation into several other disciplines, including neuroimaging. In this chapter, we discuss the principles of LA-ICP-MS technology and how it is applied to mesoscale imaging of metals in neurological tissue; evaluate the various approaches available for image construction and analysis; discuss the challenges and opportunities for quantitative metal imaging; and present a selection of applications demonstrating the power of this analytical technique as a tool for assessing both spatial distribution and absolute levels of essential metals in the brain.

Hocking, JS, Huston, WM & Chen, M 2017, 'Sexually Transmitted Infections in HIV-Infected Adults and Special Populations' in Bachmann, LH (ed), Sexually Transmitted Infections in HIV-Infected Adults and Special Populations A Clinical Guide, Springer International Publishing.
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This text is the only book to provide a comprehensive and state-of-the-art review of issues relevant to STI care in the HIV-infected adult, adolescent, and transgendered populations.

Kordzakhia, N & Novikov, A 2017, 'Bounds and Approximations for Distributions of Weighted Kolmogorov-Smirnov Tests' in From Statistics to Mathematical Finance, Springer International Publishing, pp. 235-250.
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© Springer International Publishing AG 2017. The paper is motivated by the use of weighted Kolmogorov-Smirnov (wKS) tests in Gene Set Enrichment Analysis where the key requirements are speed and accuracy of computations. We reduce the problem of finding of distributions of one-and two-sided wKS statistics to the nonlinear boundary crossing problem for a Brownian motion. Theoretical estimates of accuracy of the approximations using piecewise linear boundaries are derived. The approximations with 2-knot piecewise linear boundaries are discussed for the one-sided wKS. In the numerical example the estimates of tail probabilities obtained with the use of upper and lower bounds were validated using Monte-Carlo simulation.

Kumar, M, Kuzhiumparambil, U, Ralph, PJ & Contreras-Porcia, L 2017, 'Polyamines' in Algal Green Chemistry, Elsevier, pp. 243-255.
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© 2017 Elsevier B.V. All rights reserved. Marine macrophytes including seaweeds and sea grasses are the ecosystem engineers and experience constant threats from a wide range of anthropogenic stressors and climate fluctuations in their ecological niche. Marine macrophytes acclimate and/or tolerate these external perturbations by reprogramming their metabolite networks. Among the various metabolites that contribute to alleviate the stress, polyamines (PAs) are the nitrogenous metabolites that play a key role in plant growth, development, and biotic/abiotic stress protection in land plants. Their mode of action, signaling, and cross talk with diverse metabolic networks have been well studied in land plants; however, their functionality in marine macrophytes has merely scratched the window. In this brief chapter we attempt to summarize PA research in marine macrophytes in response to abiotic stress conditions. We emphasize to undertake futuristic efforts to explore PA involvement in stress response and to identify novel stress tolerance mechanism in marine macrophytes.

Kuzhiumparambil, U, Kumar, M & Ralph, P 2017, 'Gas and Liquid Chromatography-Mass Spectrometry-Based Metabolic Profiling of Marine Angiosperm Zostera muelleri (Alismatales, Zosteraceae)' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 189-203.
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© Springer International Publishing AG 2017. Seagrasses are monocotyledonous marine flowering plants that are considered lungs of the sea and are the most intense carbon sinks on the planet, delivering a range of ecologically and economically valuable biological services. In this study, we report the chemical fingerprint of Zostera muelleri using an untargeted metabolomic approach. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were performed to study the metabolic profile of Z. muelleri. A total of 98 metabolites belonging to various chemical classes including flavonoids, phenolics, lipids, fatty acids, sugar alcohols and amino acids were identified, including two characteristic marker compounds of the genus, zosteric acid and rosmarinic acid. Chromatographic profiling yield a comprehensive map for the chemical constituents of Z. muelleri, and this method can be used as an effective and convenient approach to gain insights into the chemical composition of other seagrasses.

Macha, IJ, Ben-Nissan, B, Choi, A & Cazalbou, S 2017, 'Development and In Vitro Analysis of a New Biodegradable PLA/Hydroxyapatite (HAp) Composite for Biomedical Applications' in Clinical Applications of Biomaterials, Springer International Publishing, pp. 411-423.
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© Springer International Publishing AG 2017. The development of new drugs or formulations for the treatments of different musculoskeletal disorders (MSDs) has now being a focus of pharmaceutical and scientific societies. Targeted and multidelivery of drug and key minerals to support bone repair and regeneration at the defect site, from flexible biodegradable devices at the rate within the therapeutic window, seem to be an effective strategy. However, the drug delivery vehicles available are neither flexible and degradable nor able to deliver both pharmaceutical drug and minerals effectively. The use of biodegradable polymer and bioceramic for composite development with enough flexibility and potential for slow in situ drug delivery for biomedical applications could be one of the real options to mitigate MSDs problem. In vitro analysis of the developed devices is a vital step towards clinical trial and commercialization of the implant. Different approach and results have been compared to draw guidelines for the development and testing of thin film composite applications as a slow drug delivery vehicle.

Mahmood, A, Tabassum, H & Zou, R 2017, 'Zeolitic Type Templated Porous Carbon Materials' in Comprehensive Supramolecular Chemistry II, Elsevier, pp. 89-108.
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Mohanty, M, Asghar, MR & Russello, G 2017, 'Preserving privacy in pre-classification volume ray-casting of 3D images' in Data Security in Cloud Computing, Institution of Engineering and Technology, pp. 45-64.
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Murrihy, RC, Burns, JR, Reinke, WM, Herman, KC & King, KR 2017, 'Evidence-Based Assessment and Intervention for Oppositional Defiant Disorder and Conduct Disorder in School Psychology' in Thielking, M & Terjesen, M (eds), Handbook of Australian School Psychology, Springer International Publishing, pp. 331-347.
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Disruptive behaviour disorders (DBD’s) are highly prevalent childhood psychological disorders associated with pervasive impairment. They can affect the individual’s social adjustment and educational achievement, disrupt family harmony, place strain on resource-limited learning environments, impact juvenile justice systems and challenge wider society. This chapter reviews, from an international perspective, the theoretical underpinnings of DBDs including diagnostic systems, aetiological factors and current controversies in the literature. Commonly used assessment measures are discussed for both universal and selective screening of at-risk school populations and individual assessment of indicated youth. This is followed by a synopsis of evidence-based interventions, which are considered the gold standard in treating youth with externalising disorders in schools. The chapter concludes with a case study illustrating some of the challenges associated with the implementation of these types of interventions.

R. Cardoso, B, Hare, DJ & Bush, AI 2017, 'The Role of Selenium in Neurodegenerative Diseases' in Biometals in Neurodegenerative Diseases, Elsevier, pp. 35-49.
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© 2017 Elsevier Inc. All rights reserved. Selenium is an essential micronutrient, imparting a biological function as a key component of the 21st amino acid, selenocysteine. To date, 25 selenoproteins have been discovered within the human proteome, which can be classified according to a range of functions. Although these proteins are in low abundance in the brain, studies have reported their relevance to normal neurological function, primarily due to antioxidant activity and mechanisms that modulate mitochondrial function. Selenium has also been identified as playing a role in several neurodegenerative disorders, including Alzheimer's and Parkinson's disease, and recent research has suggested possible association with other diseases as multiple sclerosis, amyotrophic lateral sclerosis, and Huntington's disease. This chapter will discuss the emerging role of selenium in neurodegenerative processes, highlighting the rapidly growing interest in this often-overlooked essential element.

Reimers, JR, Li, M, Wan, D, Gould, T & Ford, MJ 2017, 'Chapter 13 Surface Adsorption' in Non-Covalent Interactions in Quantum Chemistry and Physics, pp. 387-416.
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Reimers, JR, Li, M, Wan, D, Gould, T & Ford, MJ 2017, 'Surface Adsorption' in Non-Covalent Interactions in Quantum Chemistry and Physics, Elsevier, pp. 387-416.
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© 2017 Elsevier Inc. All rights reserved. Practical aspects are considered that users need to know in choosing computational methods and conceptual ideas for understanding surface adsorption embodying some degree of van der Waals dispersive attractions. Emphasized is the unique chemistry that results when these forces are strong and mix with traditional covalent or ionic bonding mechanisms to control chemical outcomes. Indeed, many methods are being developed to provide accurate descriptions of surface adsorption, including those based on ab initio and density-functional-theory (DFT) approaches. Accurate methods like coupled-cluster theory (CC), the random-phase approximation (RPA), and time-dependent DFT (TDDFT) are demanded when the critical interactions are weak, but these methods are computationally expensive, scaling formally at least as order n6 in system size (though efficient modern algorithms can reduce that to, e.g., order n4logn or even to linear scaling). How such methods can be applied to large systems is discussed, but more focus is given to more approximate, faster approaches, especially: the empirical pairwise additive D3 correction of Grimme et al., the van der Waals density functional approach of Dion et al. (vdW-DF), and the new semiempirical many-body dispersion (MBD) method of Tkatchenko et al. Fundamental understanding of all methods is provided by describing the way they behave in the very short range (unified atom) and very long range asymptotic limits, using Dobson's classification scheme. How simple computational methods can give realistic adsorption energies and structures for close-contact interactions whilst providing very poor descriptions of these asymptotic limits is examined. Four strong-interaction test systems are considered: the adsorption of benzene on coinage metals, the adsorption of 1,10-phenanthroline (PHEN) on Au(111), the adsorption of large tetraalkylporphyrin molecules on graphite from organic solution, and t...

Robertson, J & Roux, C 2017, 'Preface to the third edition' in Forensic Examination of Fibre, Taylor and Francis, USA, pp. xi-xi.
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Robertson, J, Roux, C & Wiggins, KG 2017, 'Forensic Examination of Fibres, Third Edition' in Forensic Examination of Fibres: Third Edition, CRC Press, 3rd, pp. 345-425.
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This edition also highlights the critical role of quality assurance in ensuring the reliability of the technical observations and results, and, in doing so, looks at the implications of supervisory managers and labs in the accurate and ...

Rodgers, KJ, Samardzic, K & Main, BJ 2017, 'Toxic Nonprotein Amino Acids' in Plant Toxins, Springer Netherlands, pp. 263-285.
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Roux, C, Morison, R & Maynard, P 2017, 'Other instrumental approaches to fibre examination' in Roux, C, Robertson, J & Wiggins, K (eds), Forensic Examination of Fibres: Third Edition, CRC Press, USA, pp. 309-344.
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The objectives of a typical forensic analysis of fibres are (1) to identify the fibre type and (2) to compare one or several fibres of an unknown origin to fibres from a known source to determine if they could share a common origin. Collectively, the pool of techniques employed should fulfil the needs for accurate identification and a high degree of discrimination between similar fibres. In a particular case, choosing appropriate techniques from the wide range available will depend on several factors including the quantity of material available, the exact circumstances of the case under investigation and the instrumental techniques available to the laboratory. As described earlier, a number of techniques are well established and commonly used in forensic science laboratories worldwide. Examples include microscopic (Chapter 5) and microspectrometric (Chapter 6) examinations, infrared (IR) spectroscopy (Chapter 7) and Raman spectroscopy (Chapter 8). While these techniques meet the requirements expressed above in general casework, the context of the case, the nature of the fibre specimens and the questions being asked sometimes justify the application of other techniques. In parallel, new potential techniques are constantly being developed by the broad analytical scientific field and ought to be presented to the forensic fibre examiner. This chapter discusses instrumental approaches that are not presented elsewhere. It is not meant to be comprehensive and does not include all ‘exotic’ techniques, but the discussion will focus on the techniques that have been shown to have practical value or the ones with the best potential to add value to a typical forensic examination of fibres. For the ease of presentation, they will be classified as follows: Techniques primarily focusing on the fibre: • Pyrolysis techniques • Elemental and micro-structural analysis • Isotope ratio mass spectrometry Techniques primarily focusing on the fibre dyes: • High-performance liquid chromat...

Stuart, BH & Ueland, M 2017, 'Decomposition in Aquatic Environments' in Taphonomy of Human Remains Forensic Analysis of the Dead and the Depositional Environment, Wiley, pp. 235-250.
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A truly interdisciplinary approach to this core subject within Forensic Science Combines essential theory with practical crime scene work Includes case studies Applicable to all time periods so has relevance for conventional archaeology, ...

Stuart, BH & Ueland, M 2017, 'Degradation of Clothing in Depositional Environments' in Taphonomy of Human Remains Forensic Analysis of the Dead and the Depositional Environment, Wiley, pp. 120-133.
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A truly interdisciplinary approach to this core subject within Forensic Science Combines essential theory with practical crime scene work Includes case studies Applicable to all time periods so has relevance for conventional archaeology, ...

Varkey, DR & Doblin, MA 2017, 'Application of ‘Omics’ Approaches to Microbial Oceanography' in Systems Biology of Marine Ecosystems, Springer International Publishing, pp. 223-233.
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Viruses, bacteria, archaea and single celled eukaryotes, collectively known as microbes, dominate the biomass and metabolism of ocean ecosystems. Marine microbes are highly abundant and critical to human survival, but the vast majority of taxa have not yet been cultured. The use of environmental nucleic acid sequencing as a cultivation-independent approach to microbial oceanography has therefore significantly expanded our understanding of the diversity, evolution, biogeography and important biogeochemical roles of marine microorganisms. Here we provide illustrative examples of how genomic, transcriptomic and proteomic approaches have been applied to marine microbes to advance our understanding of their ecology. A remaining challenge is the need to link phenotypes to their environment, requiring a better understanding of genomic features that influence transcription (e.g. promoters and methylation) as well as post-translational modifications, and how such regulatory processes are impacted by extracellular abiotic and biotic processes. In addition, the expansion of available protein and taxonomic databases will greatly increase our capacity to link microbial function to specific taxa.

Wiwanitkit, V 2017, 'Application of Finite Element Analysis for Nanobiomedical Study' in Musa, SM (ed), Computational Finite Element Methods in Nanotechnology, CRC Press, United States, pp. 401-421.
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'Nanostructured materials' refer to certain materials that have delicate structures and sizes that fall within the range of 1100 nm. As a consequence of this size, an extensive development of nanotechnology has taken place in the !elds of materials science and engineering in the past decade. Yet, such developments have not come as a surprise, when it is appreciated that these nanostructured materials have the ability to be adapted and integrated into biomedical devices. This is possible because most biological systems, including viruses, membranes and protein complexes, exhibit natural nanostructures.

Abboud, M, Rybchyn, MS, Liu, J, Ning, Y, Gordon-Thomson, C, Brennan-Speranza, TC, Cole, L, Greenfield, H, Fraser, DR & Mason, RS 2017, 'The effect of parathyroid hormone on the uptake and retention of 25-hydroxyvitamin D in skeletal muscle cells', The Journal of Steroid Biochemistry and Molecular Biology, vol. 173, pp. 173-179.
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Data from our studies, and those of others, support the proposal that there is a role for skeletal muscle in the maintenance of vitamin D status. We demonstrated that skeletal muscle is able to internalise extracellular vitamin D binding protein, which then binds to actin in the cytoplasm, to provide high affinity binding sites which accumulate 25-hydroxyvitamin D3 (25(OH)D3) [1]. This study investigated the concentration- and time-dependent effects of parathyroid hormone (PTH) on the capacity of muscle cells to take up and release 3H-25(OH)D3. Uptake and retention studies for 3H-25(OH)D3 were carried out with C2C12 cells differentiated into myotubes and with primary mouse muscle fibers as described [1]. The presence of PTH receptors on mouse muscle fibers was demonstrated by immunohistochemistry and PTH receptors were detected in differentiated myotubes, but not myoblasts, and on muscle fibers by Western blot. Addition of low concentrations of vitamin D binding protein to the incubation media did not alter uptake of 25(OH)D3. Pre-incubation of C2 myotubes or primary mouse muscle fibers with PTH (0.1 to 100 pM) for 3h resulted in a concentration-dependent decrease in 25(OH)D3 uptake after 4 or 16h. These effects were significant at 0.1 or 1pM PTH (p<0.001) and plateaued at 10pM, with 25(OH)D3 uptake reduced by over 60% (p<0.001) in both cell types. In C2 myotubes, retention of 25(OH)D3 was decreased after addition of PTH (0.1 to 100pM) in a concentration-dependent manner by up to 80% (p<0.001) compared to non-PTH treated-C2 myotubes. These data show that muscle uptake and retention of 25(OH)D3 are modulated by PTH, a physiological regulator of mineral homeostasis, but the cell culture model may not be a comprehensive reflection of vitamin D homeostatic mechanisms in whole animals.

Abdo, AI, Rayner, BS, van Reyk, DM & Hawkins, CL 2017, 'Low-density lipoprotein modified by myeloperoxidase oxidants induces endothelial dysfunction', Redox Biology, vol. 13, pp. 623-632.
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Low-density lipoprotein (LDL) modified by hypochlorous acid (HOCl) produced by myeloperoxidase (MPO) is present in atherosclerotic lesions, where it is implicated in the propagation of inflammation and acceleration of lesion development by multiple pathways, including the induction of endothelial dysfunction. Thiocyanate (SCN-) ions are utilised by MPO to produce the oxidant hypothiocyanous acid (HOSCN), which reacts with LDL in a different manner to HOCl. Whilst the reactivity of HOCl-modified LDL has been previously studied, the role of HOSCN in the modification of LDL in vivo is poorly defined, although emerging evidence suggests that these particles have distinct biological properties. This is important because elevated plasma SCN- is linked with both the propagation and prevention of atherosclerosis. In this study, we demonstrate that both HOSCN- and HOCl-modified LDL inhibit endothelium-mediated vasorelaxation ex vivo in rat aortic ring segments. In vitro experiments with human coronary artery endothelial cells show that HOSCN-modified LDL decreases in the production of nitric oxide (NO•) and induces the loss of endothelial nitric oxide synthase (eNOS) activity. This occurs to a similar extent to that seen with HOCl-modified LDL. In each case, these effects are related to eNOS uncoupling, rather than altered expression, phosphorylation or cellular localisation. Together, these data provide new insights into role of MPO and LDL modification in the induction of endothelial dysfunction, which has implications for both the therapeutic use of SCN- within the setting of atherosclerosis and for smokers, who have elevated plasma levels of SCN-, and are more at risk of developing cardiovascular disease.

Abu Saleh, D, Shimoni, O & Sosnik, A 2017, 'Novel core-corona hybrid nanomaterials based on the conjugation of amphiphilic polymeric diblocks to the surface of multifunctional nanodiamond anchors', Materials Today Chemistry, vol. 3, pp. 15-26.
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© 2017 Elsevier Ltd The poor aqueous solubility and the physicochemical instability of many marketed drugs and new chemical entities is one of the most challenging issues in pharmaceutical research and development. Polymeric micelles (PMs) are produced by the self-assembly of polymeric amphiphiles and they represent one of the most extensively investigated nanotechnology platforms for encapsulation, delivery and targeting of hydrophobic drugs. However, a main challenge is preventing their disassembly under extreme dilution in the body fluids, which leads to uncontrolled release of the encapsulated cargo. In this work, we developed an amphiphilic nanomaterial that resembles the core-corona architecture of a PM with superior stability in the body fluids. Specifically, we utilized carboxylated nanodiamonds (cNDs) as particulate anchors to covalently link amphiphilic diblock copolymers consisting of poly(epsilon-caprolactone) (PCL) and poly(ethylene glycol) monomethyl ether (PEG) as hydrophobic and hydrophilic components, respectively. We confirmed a successful core-corona nanostructure using various characterization techniques. In addition, TEM revealed the presence of a thin polymeric layer. Then, the cell compatibility was evaluated in Caco2 cell monolayers, an in vitro model of the intestinal epithelium. Finally, the encapsulation of the hydrophobic anti-helmintic drug nitazoxanide was studied. Cargoes as high as 17.5% w/w were achieved and the sustained release of the cargo according to the Korsmeyer-Peppas model demonstrated in vitro. Overall, preliminary results highlight the potential of this novel approach to extend the applicability of PMs in drug delivery.

Agius, A, Jones, K, Epple, R, Morelato, M, Moret, S, Chadwick, S & Roux, C 2017, 'The use of handwriting examinations beyond the traditional court purpose', Science & Justice, vol. 57, no. 5, pp. 394-400.
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© 2017 The Chartered Society of Forensic Sciences Traditionally, forensic science has predominantly focused its resources and objectives on addressing court related questions. However, this view restricts the contribution of forensic science to one function and results in lost opportunities as investigative and intelligence roles are often overlooked. A change of perspective and expansion of the contributions of forensic science is required to take advantage of the benefits of abductive and inductive thought processes throughout the investigative and intelligence functions. One forensic discipline that has the potential to broaden its traditional focus is handwriting examination. Typically used in investigations that are focused on both criminal and civil cases, the examination procedure and outcome are time consuming and subjective, requiring a detailed study of the features of the handwriting in question. Traditionally, the major handwriting features exploited are characteristics that are often considered individual (or at least highly polymorphic) and habitual. However, handwriting can be considered as an information vector in an intelligence framework. One such example is the recognition of key elements related to the author's native language. This paper discusses the traditional method generally used around the world and proposes a theoretical approach to expand the application of handwriting examination towards gaining additional information for intelligence purposes. This concept will be designed and tested in a future research project.

Aguilar, C, Raina, J-B, Motti, CA, Fôret, S, Hayward, DC, Lapeyre, B, Bourne, DG & Miller, DJ 2017, 'Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals', BMC Genomics, vol. 18, no. 1, pp. 1-14.
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© 2017 The Author(s). Background: Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific bacteria can also produce this compound. Corals are major sources of DMSP, but the molecular basis for its biosynthesis is unknown in these organisms. Results: Here we used salinity stress, which is known to trigger DMSP production in other organisms, in conjunction with transcriptomics to identify coral genes likely to be involved in DMSP biosynthesis. We focused specifically on both adults and juveniles of the coral Acropora millepora: after 24 h of exposure to hyposaline conditions, DMSP concentrations increased significantly by 2.6 fold in adult corals and 1.2 fold in juveniles. Concomitantly, candidate genes enabling each of the necessary steps leading to DMSP production were up-regulated. Conclusions: The data presented strongly suggest that corals use an algal-like pathway to generate DMSP from methionine, and are able to rapidly change expression of the corresponding genes in response to environmental stress. However, our data also indicate that DMSP is unlikely to function primarily as an osmolyte in corals, instead potentially serving as a scavenger of ROS and as a molecular sink for excess methionine produced as a consequence of proteolysis and osmolyte catabolism in corals under hypo-osmotic conditions.

Agwa, AJ, Lawrence, N, Deplazes, E, Cheneval, O, Chen, RM, Craik, DJ, Schroeder, CI & Henriques, ST 2017, 'Corrigendum to “Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNaV1.7” [Biochim. Biophys. Acta 1859(5) (2017) 835–844]', Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1859, no. 11, pp. 2277-2277.
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Agwa, AJ, Lawrence, N, Deplazes, E, Cheneval, O, Chen, RM, Craik, DJ, Schroeder, CI & Henriques, ST 2017, 'Spider peptide toxin HwTx-IV engineered to bind to lipid membranes has an increased inhibitory potency at human voltage-gated sodium channel hNa V 1.7', Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1859, no. 5, pp. 835-844.
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The human voltage-gated sodium channel sub-type 1.7 (hNaV1.7) is emerging as an attractive target for the development of potent and sub-type selective novel analgesics with increased potency and fewer side effects than existing therapeutics. HwTx-IV, a spider derived peptide toxin, inhibits hNaV1.7 with high potency and is therefore of great interest as an analgesic lead. In the current study we examined whether engineering a HwTx-IV analogue with increased ability to bind to lipid membranes would improve its inhibitory potency at hNaV1.7. This hypothesis was explored by comparing HwTx-IV and two analogues [E1PyrE]HwTx-IV (mHwTx-IV) and [E1G,E4G,F6W,Y30W]HwTx-IV (gHwTx-IV) on their membrane-binding affinity and hNaV1.7 inhibitory potency using a range of biophysical techniques including computational analysis, NMR spectroscopy, surface plasmon resonance, and fluorescence spectroscopy. HwTx-IV and mHwTx-IV exhibited weak affinity for lipid membranes, whereas gHwTx-IV showed improved affinity for the model membranes studied. In addition, activity assays using SH-SY5Y neuroblastoma cells expressing hNaV1.7 showed that gHwTx-IV has increased activity at hNaV1.7 compared to HwTx-IV. Based on these results we hypothesize that an increase in the affinity of HwTx-IV for lipid membranes is accompanied by improved inhibitory potency at hNaV1.7 and that increasing the affinity of gating modifier toxins to lipid bilayers is a strategy that may be useful for improving their potency at hNaV1.7.

Aharonovich, I & Toth, M 2017, 'Quantum emitters in two dimensions', Science, vol. 358, no. 6360, pp. 170-171.
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Two-dimensional materials offer potential for developing integrated quantum technologies

Ahmad, M, Liu, S, Mahmood, N, Mahmood, A, Ali, M, Zheng, M & Ni, J 2017, 'Effects of porous carrier size on biofilm development, microbial distribution and nitrogen removal in microaerobic bioreactors', Bioresource Technology, vol. 234, pp. 360-369.
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Ahmad, M, Liu, S, Mahmood, N, Mahmood, A, Ali, M, Zheng, M & Ni, J 2017, 'Synergic Adsorption–Biodegradation by an Advanced Carrier for Enhanced Removal of High-Strength Nitrogen and Refractory Organics', ACS Applied Materials & Interfaces, vol. 9, no. 15, pp. 13188-13200.
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Aili, SR, Touchard, A, Petitclerc, F, Dejean, A, Orivel, J, Padula, MP, Escoubas, P & Nicholson, GM 2017, 'Combined Peptidomic and Proteomic Analysis of Electrically Stimulated and Manually Dissected Venom from the South American Bullet Ant Paraponera clavata', Journal of Proteome Research, vol. 16, no. 3, pp. 1339-1351.
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© 2017 American Chemical Society. Ants have evolved venoms rich in peptides and proteins used for predation, defense, and communication. However, they remain extremely understudied due to the minimal amount of venom secreted by each ant. The present study investigated the differences in the proteome and peptidome of the venom from the bullet ant, Paraponera clavata. Venom samples were collected from a single colony either by manual venom gland dissection or by electrical stimulation and were compared using proteomic methods. Venom proteins were separated by 2D-PAGE and identified by nanoLC-ESI-QTOF MS/MS. Venom peptides were initially separated using C18 reversed-phase high-performance liquid chromatography, then analyzed by MALDI-TOF MS. The proteomic analysis revealed numerous proteins that could be assigned a biological function (total 94), mainly as toxins, or roles in cell regulation and transport. This investigation found that ca. 73% of the proteins were common to venoms collected by the two methods. The peptidomic analysis revealed a large number of peptides (total 309) but with <20% shared by the two collection methods. There was also a marked difference between venoms obtained by venom gland dissection from different ant colonies. These findings demonstrate the rich composition and variability of P. clavata venom.

Ali, H, Zaman, S, Majeed, I, Kanodarwala, FK, Nadeem, MA, Stride, JA & Nadeem, MA 2017, 'Porous Carbon/rGO Composite: An Ideal Support Material of Highly Efficient Palladium Electrocatalysts for the Formic Acid Oxidation Reaction', ChemElectroChem, vol. 4, no. 12, pp. 3126-3133.
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AbstractCatalyst support materials play an important role in the electrochemical performance of the catalyst in fuel cells. Herein, we present a synergistic effect of surface area and electronic conductivity on the efficiency of a carbon support material towards its application in direct formic acid fuel cells. A composite of reduced graphene oxide (rGO) and metal organic framework (MOF‐5) derived porous carbon (PC) was used as a novel support material for a high dispersion of palladium nanoparticles. The rGO1‐C1 electrocatalyst, which consists of an equal ratio of PC and rGO, was found to be the most effective for the formic acid electro‐oxidation reaction. The obtained mass specific activity for Pd/rGO1‐C1 (969.76 mA mg−1) is 1.52 times higher than for Pd/rGO (639.5 mA mg−1) and 2.63 times higher than Pd/C (368.73 mA mg−1) synthesized under the same conditions and at given onset peak potentials. The Pd/rGO1‐C1 electrocatalyst was also found to be much more stable than other catalysts as evidenced by chronoamperometric measurements for up to 3000 s. The high activity and stability of the catalyst fabricated over the composite carbon support is due to a synergism between the Pd metal and the composite support toward charge transfer, where highly porous carbon provides a high surface area and the rGO is highly conductive, thereby boosting the electrical properties of the catalyst.

Ali, MK, Kim, RY, Karim, R, Mayall, JR, Martin, KL, Shahandeh, A, Abbasian, F, Starkey, MR, Loustaud-Ratti, V, Johnstone, D, Milward, EA, Hansbro, PM & Horvat, JC 2017, 'Role of iron in the pathogenesis of respiratory disease', The International Journal of Biochemistry & Cell Biology, vol. 88, pp. 181-195.
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© 2017 Elsevier Ltd Iron is essential for many biological processes, however, too much or too little iron can result in a wide variety of pathological consequences, depending on the organ system, tissue or cell type affected. In order to reduce pathogenesis, iron levels are tightly controlled in throughout the body by regulatory systems that control iron absorption, systemic transport and cellular uptake and storage. Altered iron levels and/or dysregulated homeostasis have been associated with several lung diseases, including chronic obstructive pulmonary disease, lung cancer, cystic fibrosis, idiopathic pulmonary fibrosis and asthma. However, the mechanisms that underpin these associations and whether iron plays a key role in the pathogenesis of lung disease are yet to be fully elucidated. Furthermore, in order to survive and replicate, pathogenic micro-organisms have evolved strategies to source host iron, including freeing iron from cells and proteins that store and transport iron. To counter these microbial strategies, mammals have evolved immune-mediated defence mechanisms that reduce iron availability to pathogens. This interplay between iron, infection and immunity has important ramifications for the pathogenesis and management of human respiratory infections and diseases. An increased understanding of the role that iron plays in the pathogenesis of lung disease and respiratory infections may help inform novel therapeutic strategies. Here we review the clinical and experimental evidence that highlights the potential importance of iron in respiratory diseases and infections.

Ali, MM, Al-Ani, A, Eamus, D & Tan, DKY 2017, 'Leaf nitrogen determination using non-destructive techniques–A review', Journal of Plant Nutrition, vol. 40, no. 7, pp. 928-953.
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The optimisation of plant nitrogen-use-efficiency (NUE) has a direct impact on increasing crop production by optimising use of nitrogen fertiliser. Moreover, it protects environment from negative effects of nitrate leaching and nitrous oxide production. Accordingly, nitrogen (N) management in agriculture systems has been major focus of many researchers. Improvement of NUE can be achieved through several methods including more accurate measurement of foliar N contents of crops during different growth phases. There are two types of methods to diagnose foliar N status: destructive and non-destructive. Destructive methods are expensive and time-consuming as they require tissue sampling and subsequent laboratory analysis. Thus, many farmers find destructive methods to be less attractive. Non-destructive methods are rapid and less expensive but are usually less accurate. Accordingly, improving the accuracy of non-destructive N estimations has become a common goal of many researchers, and various methods varying in complexity and optimality have been proposed for this purpose. This paper reviews various commonly used non-destructive methods for estimating foliar N status of plants.

AL-Kouba, J, Wilkinson, AN, Starkey, MR, Rudraraju, R, Werder, RB, Liu, X, Law, S-C, Horvat, JC, Brooks, JF, Hill, GR, Davies, JM, Phipps, S, Hansbro, PM & Steptoe, RJ 2017, 'Allergen-encoding bone marrow transfer inactivates allergic T cell responses, alleviating airway inflammation', JCI Insight, vol. 2, no. 11.
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Memory Th2 cell responses underlie the development and perpetuation of allergic diseases. Because these states result from immune dysregulation, established Th2 cell responses represent a significant challenge for conventional immunotherapies. New approaches that overcome the detrimental effects of immune dysregulation are required. We tested whether memory Th2 cell responses were silenced using a therapeutic approach where allergen expression in DCs is transferred to sensitized recipients using BM cells as a vector for therapeutic gene transfer. Development of allergen-specific Th2 responses and allergen-induced airway inflammation was blocked by expression of allergen in DCs. Adoptive transfer studies showed that Th2 responses were inactivated by a combination of deletion and induction of T cell unresponsiveness. Transfer of BM encoding allergen expression targeted to DCs terminated, in an allergen-specific manner, Th2 responses in sensitized recipients. Importantly, when preexisting airway inflammation was present, there was effective silencing of Th2 cell responses, airway inflammation was alleviated, and airway hyperreactivity was reversed. The effectiveness of DC-targeted allergen expression to terminate established Th2 responses in sensitized animals indicates that exploiting cell-intrinsic T cell tolerance pathways could lead to development of highly effective immunotherapies.

Alonso‐Peral, MM, Trigueros, M, Sherman, B, Ying, H, Taylor, JM, Peacock, WJ & Dennis, ES 2017, 'Patterns of gene expression in developing embryos of Arabidopsis hybrids', The Plant Journal, vol. 89, no. 5, pp. 927-939.
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SummaryHybrids between the Arabidopsis ecotypes C24 and Ler have high levels of hybrid vigour, or heterosis, in both biomass and seed yield. Heterosis can be detected throughout the development of the plant and in different tissues. We examined developing embryos and seeds of C24/Ler reciprocal hybrids with the aim of detecting the earliest time at which heterotic gene activity occurs. In the transcriptomes of 4‐dap (days after pollination; dermatogen to globular) and 6‐dap (heart) embryos from both parents and hybrids, 95% of expressed genes were at the mid parent value (MPV) and 95% of the genes with single nucleotide polymorphisms between C24 and Ler retained the same relative allelic expression levels in the hybrids as existed in the parents. This included loci that had equivalent levels of transcription in the two parents, together with loci which had different levels of expression in the parents. Amongst the genes which did not have MPV expression levels in the hybrids (non‐additively expressed genes), approximately 40 in the globular embryo stage and 89 in the heart embryo stage had altered levels of transcription in both reciprocal hybrids; these genes could contribute to the heterotic phenotype of the hybrid embryo. Many of the non‐additively expressed genes had expression levels that were shifted towards maternal levels of transcription, and these differed in the reciprocal hybrids. Allelic expression analysis indicated that most genes with altered allelic contributions in the hybrids had an increase in the expression level of the hybrid's maternal allele. Consistent with the maternal pattern of gene expression, embryo and seed also show maternally influenced phenotypes.

Alvarado, R, To, J, Lund, ME, Pinar, A, Mansell, A, Robinson, MW, O'Brien, BA, Dalton, JP & Donnelly, S 2017, 'The immune modulatory peptide FhHDM‐1 secreted by the helminth Fasciola hepatica prevents NLRP3 inflammasome activation by inhibiting endolysosomal acidification in macrophages', The FASEB Journal, vol. 31, no. 1, pp. 85-95.
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The NLRP3 inflammasome is a multimeric protein complex that controls the production of IL-1b, a cytokine that influences the development of both innate and adaptive immune responses. Helminth parasites secrete molecules that interact with innate immune cells, modulating their activity to ultimately determine the phenotype of differentiated T cells, thus creating an immune environment that is conducive to sustaining chronic infection. We show that one of these molecules, FhHDM-1, a cathelicidin-like peptide secreted by the helminth parasite, Fasciola hepatica, inhibits the activation of the NLRP3 inflammasome resulting in reduced secretion of IL-1β by macrophages. FhHDM-1 had no effect on the synthesis of pro-IL-1β. Rather, the inhibitory effect was associatedwith the capacity of the peptide to prevent acidification of the endolysosome. The activation of cathepsin B protease by lysosomal destabilization was prevented in FhHDM-1-treated macrophages. By contrast, peptide derivatives of FhHDM-1 that did not alter the lysosomal pH did not inhibit secretion of IL-1b. Wepropose a novel immunemodulatory strategy usedby F. hepatica,whereby secretion of theFhHDM-1 peptide impairs the activation of NLRP3 by lysosomal cathepsin B protease, which prevents the downstream production of IL-1b and the development of protective T helper 1 type immune responses that are detrimental to parasite survival.-Alvarado,R., To, J., Lund, M. E., Pinar, A., Mansell, A., Robinson, M. W., O'Brien, B. A., Dalton, J. P., Donnelly, S. The immune modulatory peptide FhHDM-1 secreted by the helminth Fasciola hepatica prevents NLRP3 inflammasome activation by inhibiting endolysosomal acidification in macrophages. FASEB J. 31, 85-95 (2017). www.fasebj.org.

Anderson, C & Ryan, L 2017, 'A Comparison of Spatio-Temporal Disease Mapping Approaches Including an Application to Ischaemic Heart Disease in New South Wales, Australia', International Journal of Environmental Research and Public Health, vol. 14, no. 2, pp. 146-146.
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© 2017 by the authors; licensee MDPI, Basel, Switzerland. The field of spatio-temporal modelling has witnessed a recent surge as a result of developments in computational power and increased data collection. These developments allow analysts to model the evolution of health outcomes in both space and time simultaneously. This paper models the trends in ischaemic heart disease (IHD) in New South Wales, Australia over an eight-year period between 2006 and 2013. A number of spatio-temporal models are considered, and we propose a novel method for determining the goodness-of-fit for these models by outlining a spatio-temporal extension of the Moran’s I statistic. We identify an overall decrease in the rates of IHD, but note that the extent of this health improvement varies across the state. In particular, we identified a number of remote areas in the north and west of the state where the risk stayed constant or even increased slightly.

Andersson, J, Knobloch, JJ, Perkins, MV, Holt, SA & Köper, I 2017, 'Synthesis and Characterization of Novel Anchorlipids for Tethered Bilayer Lipid Membranes', Langmuir, vol. 33, no. 18, pp. 4444-4451.
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Tethered bilayer lipid membranes are versatile solid-supported model membrane systems. Core to these systems is an anchorlipid that covalently links a lipid bilayer to a support. The molecular structure of these lipids can have a significant impact on the properties of the resulting bilayer. Here, the synthesis of anchorlipids containing ester groups in the tethering part is described. The lipids are used to form bilayer membranes, and the resulting structures are compared with membranes formed using conventional anchorlipids or sparsely tethered membranes. All membranes showed good electrical sealing properties; the disulphide-terminated anchorlipids could be used in a sparsely tethered system without significantly reducing the sealing properties of the lipid bilayers. The sparsely tethered systems also allowed for higher ion transport across the membrane, which is in good correlation with higher hydration of the spacer region as seen by neutron scattering.

Angelini, M, Coupland, M, Schuck, S & Prescott, A 2017, 'Maths Inside: a Project to Raise Interest in Mathematics', MERGA Conference Proceedings.

Anthony, K, Bay, LK, Costanza, R, Firn, J, Gunn, J, Harrison, P, Heyward, A, Lundgren, P, Mead, D, Moore, T, Mumby, PJ, van Oppen, MJH, Robertson, J, Runge, MC, Suggett, DJ, Schaffelke, B, Wachenfeld, D & Walshe, T 2017, 'New interventions are needed to save coral reefs', Nature Ecology & Evolution, vol. 1, no. 10, pp. 1420-1422.
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Archer, MS & Wallman, JF 2017, 'The development of forensic entomology in Australia and New Zealand: an overview of casework practice, quality control and standards', Australian Journal of Forensic Sciences, vol. 49, no. 2, pp. 125-133.
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Ardekani, SM, Dehghani, A, Hassan, M, Kianinia, M, Aharonovich, I & Gomes, VG 2017, 'Two-photon excitation triggers combined chemo-photothermal therapy via doped carbon nanohybrid dots for effective breast cancer treatment', Chemical Engineering Journal, vol. 330, pp. 651-662.
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© 2017 Elsevier B.V. Remotely triggered drug delivery using nanoparticles is an area of great interest for targeted therapy to fight cancer. In this work, we synthesized photoresponsive nanoparticles to remotely initiate the delivery of doxorubicin (DOX) to 3D cultured human breast cancer cells (MCF-7) via NIR two-photon excitation (TPE) using nitrogen-doped and surface passivated (PEG 200 ) carbon nanohybrid dots (CNDs). On-demand drug delivery relies on bio-compatible, photo-responsive nano-carriers with high quantum yields. A facile (5 min synthesis) one-pot hot plate method was used to synthesize functionalized and surface passivated carbon nanohybrid dots (CND-P) having 53% quantum yield (QY). Compared to CNDs prepared from citric acid (CND-C) and citric acid plus urea (CND-N), CND-P had QY enhanced by factors of 12.6 and 4.4, respectively. The up-converted emission intensity of CND-P was strengthened by a factor of 4.5 over that of CND-N from nitrogen doped CNDs for similar test conditions (wavelength, excitation power and concentration). The drug loading capacity of CND-P was measured to be 0.98 w/w with the ability to release DOX via two-photon excitation (TPE). Intense green luminescence was observed under both 360 and 780 nm lasers using single and two-photon excitations. The highly biocompatible CND-P showed 88% cell viability at concentrations as high as 1100 µg/mL. The combined chemo- and photothermal therapeutic effect of the DOX-loaded CND-P (CND-P@DOX) complex resulted in the death of 78% of the MCF-7 cells compared to 59% with DOX alone.

Arscott, E, Morgan, R, Meakin, G & French, J 2017, 'Understanding forensic expert evaluative evidence: A study of the perception of verbal expressions of the strength of evidence', Science & Justice, vol. 57, no. 3, pp. 221-227.
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Verbal expressions of evidential strength are routinely used when presenting forensic expert evaluative evidence. The degree to which these verbal expressions are interpreted uniformly among different individuals requires further empirical study. This study focussed on groups of individuals with different roles within the criminal justice system and individuals with varying degrees of expertise and knowledge. Three groups of individuals were identified: laypeople, legal professionals and those with some forensic or investigative knowledge. The participants in the study (n=230) were provided with a case summary to which a verbal expression of the strength of evidence was randomly assigned. Participants were subsequently invited to indicate their perception of the strength of the evidence on a scale that was provided. Generally, across the study groups, the trend was one of increased perceived strength of evidence as the intended strength of the verbal expression was increased, with some notable exceptions. In general, there was good concordance between the groups in the way the different expressions were perceived. It was found that participants performed poorly when it came to differentiating between expressions at the 'strong' end of the scale ('strong', 'very strong' and 'extremely strong'). The findings resonate with calls for validated and robust communication frameworks for evaluative opinions. Further empirical research in this area is warranted and that such research can represent an important contribution towards improving the communication and presentation of forensic evidence.

Arzt, J, Brito, B, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Vu, PP, Stenfeldt, C, Rodriguez, LL, Long, NT & Dung, DH 2017, 'Genome Sequence of Foot-and-Mouth Disease Virus Serotype O Lineage Ind-2001d Collected in Vietnam in 2015', Genome Announcements, vol. 5, no. 18, pp. 1-2.
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ABSTRACT In 2015, foot-and-mouth disease (FMD) virus lineage Ind-2001 was detected for the first time in Southeast Asia. This report contains the first near-complete genome sequence of a viral isolate from this lineage collected from an outbreak in Vietnam. This novel incursion has substantial implications for regional FMD control measures.

Atarashi, K, Suda, W, Luo, C, Kawaguchi, T, Motoo, I, Narushima, S, Kiguchi, Y, Yasuma, K, Watanabe, E, Tanoue, T, Thaiss, CA, Sato, M, Toyooka, K, Said, HS, Yamagami, H, Rice, SA, Gevers, D, Johnson, RC, Segre, JA, Chen, K, Kolls, JK, Elinav, E, Morita, H, Xavier, RJ, Hattori, M & Honda, K 2017, 'Ectopic colonization of oral bacteria in the intestine drives T _H 1 cell induction and inflammation', Science, vol. 358, no. 6361, pp. 359-365.
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Gut reasons to brush your teeth Some gut conditions, such as inflammatory bowel disease (IBD), ulcerative colitis, and Crohn's disease (CD), are associated with imbalances in the gut microbe community. The causes of these intractable diseases have been difficult to discern. Atarashi et al. took samples from the mouths of IBD and CD patients and inoculated the extracted bacteria into germ-free mice (see the Perspective by Cao). Some of the inoculated mice showed strong proliferation of T helper 1 cells associated with the establishment of oral Klebsiella species in the colon. Klebsiella can be resistant to multiple antibiotics and are able to replace normal colon microbes after antibiotic therapy. Now we know that they probably originate from the mouth and could potentially contribute to bowel disease. Science , this issue p. 359 ; see also p. 308

Au, PCK, Dennis, ES & Wang, M-B 2017, 'Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation', Genes, vol. 8, no. 8, pp. 198-198.
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© 2017 by the authors. Licensee MDPI, Basel, Switzerland. RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA. Comparison of these lncRNAs with gene expression data of RdDM mutants identified novel RdDM target genes. Surprisingly, a large proportion of these target genes were repressed in RdDM mutants suggesting that they are normally activated by RdDM. These RdDM-activated genes are more enriched for gene body lncRNA than the RdDM-repressed genes. Histone modification and RNA analyses of several RdDM-activated stress response genes detected increased levels of active histone mark and short RNA transcript in the lncRNA-overlapping gene body regions in the ago4 mutant despite the repressed expression of these genes. These results suggest that RdDM, or AGO4, may play a role in maintaining or activating stress response gene expression by directing gene body chromatin modification preventing cryptic transcription.

Bala, K, Wadhwa, R & Bohra, R 2017, '“ISOLATION AND CHARACTERIZATION OF LACTOSE AND NON- LACTOSE FERMENTING BACTERIA FROM TERTIARY CARE HOSPITAL AND THEIR ANTIMICROBIAL SUSCEPTIBILITY TEST”', Asian Journal of Pharmaceutical and Clinical Research, vol. 10, no. 2, pp. 201-201.
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Objective: The purpose of the present study was to identify the fermenting and non-fermenting gram negative bacteria from the tertiary care hospital.Methods: The conventional method of identification by biochemical analysis and antibiotic susceptibility test was performed by Kirby-Bauer disc diffusion method. Furthermore, analysis of microbes was done by Vitek-2.Results: 424strains of lactose fermenting and non-lactose fermenting gram negative bacilli were isolated from 3097 clinical samples. From the total lactose fermenting bacteria Escherichia coli was the predominant isolate accounting for 50.94% specimens, followed by Klebsiella pneumonia 27.59% and Enterobacter 0.47%. From the total non-lactose fermenting gram negative bacilli Acinetobacter baumannii was the predominant isolate accounting for 12.73% specimens followed by Pseudomonas aeroginosa 6.13%, other isolates were Stenotrophomonas maltophilia 1.17% , Burkholderia cepacia 0.94%. In the present study male were more infected than female. The study also showed that lactose fermenting bacteria were more infectious than non lactose-fermenting bacteria and isolates were from urine samples.Conclusion: Both Non-Lactose Fermenting Gram Negative Bacilli and Lactose Fermenting Gram Negative Bacilli were found to be major contaminants, and are important pathogenic bacteria causing wide range of infections in the tertiary care hospital.Keywords: Lactose fermenting gram negative bacteria, Vitek-2, Tertiary Care Hospital, Kirby-Bauer Disc Diffusion, Lactose non-fermenting gram negative bacteria  

Bao, W, Xie, X, Xu, J, Guo, X, Song, J, Wu, W, Su, D & Wang, G 2017, 'Confined Sulfur in 3 D MXene/Reduced Graphene Oxide Hybrid Nanosheets for Lithium–Sulfur Battery', Chemistry – A European Journal, vol. 23, no. 51, pp. 12613-12619.
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AbstractThree‐dimensional metal carbide MXene/reduced graphene oxide hybrid nanosheets are prepared and applied as a cathode host material for lithium–sulfur batteries. The composite cathodes are obtained through a facile and effective two‐step liquid‐phase impregnation method. Owing to the unique 3 D layer structure and functional 2 D surfaces of MXene and reduced graphene oxide nanosheets for effective trapping of sulfur and lithium polysulfides, the MXene/reduced graphene oxide/sulfur composite cathodes deliver a high initial capacity of 1144.2 mAh g−1 at 0.5 C and a high level of capacity retention of 878.4 mAh g−1 after 300 cycles. It is demonstrated that hybrid metal carbide MXene/reduced graphene oxide nanosheets could be a promising cathode host material for lithium–sulfur batteries.

Barratt, J, Kaufer, A, Peters, B, Craig, D, Lawrence, A, Roberts, T, Lee, R, McAuliffe, G, Stark, D & Ellis, J 2017, 'Isolation of Novel Trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) Provides Support for a Gondwanan Origin of Dixenous Parasitism in the Leishmaniinae', PLOS Neglected Tropical Diseases, vol. 11, no. 1, pp. e0005215-e0005215.
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© 2017 Barratt et al. The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais; a significant albeit neglected tropical disease. Leishmaniasis has afflicted humans for millennia, but how ancient is Leishmania and where did it arise? These questions have been hotly debated for decades and several theories have been proposed. One theory suggests Leishmania originated in the Palearctic, and dispersed to the New World via the Bering land bridge. Others propose that Leishmania evolved in the Neotropics. The Multiple Origins theory suggests that separation of certain Old World and New World species occurred due to the opening of the Atlantic Ocean. Some suggest that the ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia evolved on Gondwana between 90 and 140 million years ago. In the present study a detailed molecular and morphological characterisation was performed on a novel Australian trypanosomatid following its isolation in Australia’s tropics from the native black fly, Simulium (Morops) dycei Colbo, 1976. Phylogenetic analyses were conducted and confirmed this parasite as a sibling to Zelonia costaricensis, a close relative of Leishmania previously isolated from a reduviid bug in Costa Rica. Consequently, this parasite was assigned the name Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis diverged when Australia and South America became completely separated, their divergence occurred between 36 and 41 million years ago at least. Using this vicariance event as a calibration point for a phylogenetic time tree, the common ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia appeared in Gondwana approximately 91 million years ago. Ultimately, this study contributes to our understanding of trypanosomatid diversity, and of Leishmania origins by providing support for a Gondwanan origin of dixenous parasitism in the Leishmaniinae.

Barraza, V, Restrepo-Coupe, N, Huete, A, Grings, F, Beringer, J, Cleverly, J & Eamus, D 2017, 'Estimation of latent heat flux over savannah vegetation across the North Australian Tropical Transect from multiple sensors and global meteorological data', AGRICULTURAL AND FOREST METEOROLOGY, vol. 232, pp. 689-703.
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© 2016 Elsevier B.V. Latent heat flux (LE) and corresponding water loss in non-moisture-limited ecosystems are well correlated to radiation and temperature. By contrast, in savannahs and arid and semi-arid lands LE is mostly driven by available water and the vegetation exerts a strong control over the rate of transpiration. Therefore, LE models that use optical vegetation indices (VIs) to represent the vegetation component (transpiration as a function of surface conductance, Gs) generally overestimate water fluxes in water-limited ecosystems. In this study, we evaluated and compared optical and passive microwave index based retrievals of Gs and LE derived using the Penman-Monteith (PM) formulation over the North Australian Tropical Transect (NATT). The methodology was evaluated at six eddy covariance (EC) sites from the OzFlux network. To parameterize the PM equation for retrievals of LE (PM-Gs), a subset of Gs values was derived from meteorological and EC flux observations and regressed against individual and combined satellite indices, from (1) MODIS AQUA: the Normalized Difference Water Index (NDWI) and the Enhanced Vegetation Index (EVI); and from (2) AMSR-E passive microwave: frequency index (FI), polarization index (PI), vegetation optical depth (VOD) and soil moisture (SM) products. Similarly, we combined optical and passive microwave indices (multi-sensor model) to estimate weekly Gs values, and evaluated their spatial and temporal synergies. The multi-sensor approach explained 40–80% of LE variance at some sites, with root mean square errors (RMSE) lower than 20 W/m2 and demonstrated better performance to other satellite-based estimates of LE. The optical indices represented potential Gs associated with the phenological status of the vegetation (e.g. leaf area index, chlorophyll content) at finer spatial resolution. The microwave indices provided information about water availability and moisture stress (e.g. water content in leaves and shallow ...

Bat‐Erdene, M, Batmunkh, M, Tawfik, SA, Fronzi, M, Ford, MJ, Shearer, CJ, Yu, L, Dadkhah, M, Gascooke, JR, Gibson, CT & Shapter, JG 2017, 'Efficiency Enhancement of Single‐Walled Carbon Nanotube‐Silicon Heterojunction Solar Cells Using Microwave‐Exfoliated Few‐Layer Black Phosphorus', Advanced Functional Materials, vol. 27, no. 48, pp. 1704488-1704488.
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AbstractCarbon nanotube‐silicon (CNT‐Si)‐based heterojunction solar cells (HJSCs) are a promising photovoltaic (PV) system. Herein, few‐layer black phosphorus (FL‐BP) sheets are produced in N‐methyl‐2‐pyrrolidone (NMP) using microwave‐assisted liquid‐phase exfoliation and introduced into the CNTs‐Si‐based HJSCs for the first time. The NMP‐based FL‐BP sheets remain stable after mixing with aqueous CNT dispersion for device fabrication. Due to their unique 2D structure and p‐type dominated conduction, the FL‐BP/NMP incorporated CNT‐Si devices show an impressive improvement in the power conversion efficiency from 7.52% (control CNT‐Si cell) to 9.37%. Our density‐functional theory calculation reveals that lowest unoccupied molecular orbital (LUMO) of FL‐BP is higher in energy than that of single‐walled CNT. Therefore, we observed a reduction in the orbitals localized on FL‐BP upon highest occupied molecular orbital to LUMO transition, which corresponds to an improved charge transport. This study opens a new avenue in utilizing 2D phosphorene nanosheets for next‐generation PVs.

Bazett, M, Biala, A, Huff, RD, Zeglinksi, MR, Hansbro, PM, Bosiljcic, M, Gunn, H, Kalyan, S & Hirota, JA 2017, 'Attenuating immune pathology using a microbial-based intervention in a mouse model of cigarette smoke-induced lung inflammation', Respiratory Research, vol. 18, no. 1, pp. 1-11.
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© 2017 The Author(s). Background: Cigarette smoke exposure is the major risk factor for developing COPD. Presently, available COPD treatments focus on suppressing inflammation and providing bronchodilation. However, these options have varying efficacy in controlling symptoms and do not reverse or limit the progression of COPD. Treatments strategies using bacterial-derived products have shown promise in diseases characterized by inflammation and immune dysfunction. This study investigated for the first time whether a novel immunotherapy produced from inactivated Klebsiella (hereafter referred to as KB) containing all the major Klebsiella macromolecules, could attenuate cigarette smoke exposure-induced immune responses. We hypothesized that KB, by re-directing damaging immune responses, would attenuate cigarette smoke-induced lung inflammation and bronchoalveolar (BAL) cytokine and chemokine production. Methods: KB was administered via a subcutaneous injection prophylactically before initiating a 3-week acute nose-only cigarette smoke exposure protocol. Control mice received placebo injection and room air. Total BAL and differential cell numbers were enumerated. BAL and serum were analysed for 31 cytokines, chemokines, and growth factors. Lung tissue and blood were analysed for Ly6CHI monocytes/macrophages and neutrophils. Body weight and clinical scores were recorded throughout the experiment. Results: We demonstrate that KB treatment attenuated cigarette smoke-induced lung inflammation as shown by reductions in levels of BAL IFNγ, CXCL9, CXCL10, CCL5, IL-6, G-CSF, and IL-17. KB additionally attenuated the quantity of BAL lymphocytes and macrophages. In parallel to the attenuation of lung inflammation, KB induced a systemic immune activation with increases in Ly6CHI monocytes/macrophages and neutrophils. Conclusions: This is the first demonstration that subcutaneous administration of a microbial-based immunotherapy can attenuate cigarette smoke-induced l...

Beck, HJ, Feary, DA, Nakamura, Y & Booth, DJ 2017, 'Temperate macroalgae impacts tropical fish recruitment at forefronts of range expansion', Coral Reefs, vol. 36, no. 2, pp. 639-651.
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© 2017, Springer-Verlag Berlin Heidelberg. Warming waters and changing ocean currents are increasing the supply of tropical fish larvae to temperature regions where they are exposed to novel habitats, namely temperate macroalgae and barren reefs. Here, we use underwater surveys on the temperate reefs of south-eastern (SE) Australia and western Japan (~33.5°N and S, respectively) to investigate how temperate macroalgal and non-macroalgal habitats influence recruitment success of a range of tropical fishes. We show that temperate macroalgae strongly affected recruitment of many tropical fish species in both regions and across three recruitment seasons in SE Australia. Densities and richness of recruiting tropical fishes, primarily planktivores and herbivores, were over seven times greater in non-macroalgal than macroalgal reef habitat. Species and trophic diversity (K-dominance) were also greater in non-macroalgal habitat. Temperate macroalgal cover was a stronger predictor of tropical fish assemblages than temperate fish assemblages, reef rugosities or wave exposure. Tropical fish richness, diversity and density were greater on barren reef than on reef dominated by turfing algae. One common species, the neon damselfish (Pomacentrus coelestis), chose non-macroalgal habitat over temperate macroalgae for settlement in an aquarium experiment. This study highlights that temperate macroalgae may partly account for spatial variation in recruitment success of many tropical fishes into higher latitudes. Hence, habitat composition of temperate reefs may need to be considered to accurately predict the geographic responses of many tropical fishes to climate change.

Bell, BA, Wang, K, Solntsev, AS, Neshev, DN, Sukhorukov, AA & Eggleton, BJ 2017, 'Spectral photonic lattices with complex long-range coupling', Optica, vol. 4, no. 11, pp. 1433-1433.
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© 2017 Optical Society of America. Photonic systems such as arrays of coupled waveguides are well suited to emulating quantum mechanics with periodic lattice potentials, allowing the investigation of many physical phenomena in a convenient experimental setting. Usually, photons will “hop” only between neighboring lattice sites at a rate given by a purely real coupling coefficient, thus limiting the rich physics enabled by long-range coupling with complex coupling coefficients. Here we suggest and experimentally realize a spectral photonic lattice that can be configured to realize a wide variety of complex-valued coupling parameters over arbitrary lattice separations. In this system, a weak signal propagates across discrete frequency channels, driven by nonlinear interaction from stronger pump lasers. Our approach allows the experimental investigation of new discrete lattice physics-as an example, we demonstrate two novel instances of the discrete Talbot effect.

Bellgrove, A, van Rooyen, A, Weeks, AR, Clark, JS, Doblin, MA & Miller, AD 2017, 'New resource for population genetics studies on the Australasian intertidal brown alga, Hormosira banksii: isolation and characterization of 15 polymorphic microsatellite loci through next generation DNA sequencing', Journal of Applied Phycology, vol. 29, no. 3, pp. 1721-1727.
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© 2016, Springer Science+Business Media Dordrecht. The Australasian fucoid, Hormosira banksii, commonly known as ‘Neptune’s necklace’ or ‘bubbleweed’ is regarded as an autogenic ecosystem engineer with no functional equivalents. Population declines resulting from climate change and other anthropogenic disturbances pose significant threats to intertidal biodiversity. For effective conservation strategies, patterns of gene flow and population genetic structure across the species distribution need to be clearly understood. We developed a suite of 15 polymorphic microsatellite markers using next generation sequencing of 53–55 individuals from two sites (south-western Victoria and central New South Wales, Australia) and a replicated spatially hierarchical sampling design. We observed low to moderate genetic variation across most loci (mean number of alleles per locus =3.26; mean expected heterozygosity =0.38) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Independent spatial autocorrelation analyses were performed for each site using multilocus genotypes and different relatedness measures. Both analyses indicated no significant patterns between relatedness and geographic distance, complemented by non-significant Hardy-Weinberg estimates (P  <  0.05), suggesting that individuals from each site represent a randomly mating, outcrossing population. A preliminary investigation of population structure indicates that gene flow among sites is limited (F ST  = 0.49), however more comprehensive sampling is needed to determine the extent of population structure across the species range ( > 10,000 km). The genetic markers described provide a valuable resource for future population genetic assessments that will help guide conservation planning for H. banksii and the associated intertidal communities.

Bennett, D, Knight, E, Divan, A, Kuchel, L, Horn, J, van Reyk, D & Burke da Silva, K 2017, 'How do research-intensive universities portray employability strategies? A review of their websites', Australian Journal of Career Development, vol. 26, no. 2, pp. 52-61.
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Employability development is a strategic priority for universities across advanced western economies. Despite this, there is no systematic study of employability development approaches internationally. In this study, we considered how universities portray employability on the public pages of their websites. We undertook website content analysis of 107 research-intensive universities in Australia, Canada, the United Kingdom and the United States. Following Farenga and Quinlan, we classified these strategies as Portfolio, Hands-off, Award and Non-embedded. Portfolio or Award strategies were the most common across all four locations; Hands-off and Non-embedded strategies were more common to US universities; and Award was more common in the United Kingdom. Universities focused on either possessional or positional approaches to employability. We advocate for a pedagogical shift towards processual approaches in which responsibility for employability development is shared.

Bennett, VM, McNevin, D, Roffey, P & Gahan, ME 2017, 'Characterization of Yersinia species by protein profiling using automated microfluidic capillary electrophoresis', Forensic Science, Medicine, and Pathology, vol. 13, no. 1, pp. 10-19.
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Ben-Nissan, B & Vance, L 2017, 'Editorial', Journal of the Australian Ceramic Society, vol. 53, no. 1, pp. 1-1.
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Benson, N, Oliveira Dos Santos, R, Griffiths, K, Cole, N, Doble, P, Roux, C & Blanes, L 2017, 'The development of a stabbing machine for forensic textile damage analysis', Forensic Science International, vol. 273, pp. 132-139.
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© 2017 This article describes the development of a horizontal stabbing machine with an interchangeable knife holder to simulate stab events. The machine consists of a motorised arm with a pneumatic system designed to deliver 60 unique stabbing positions. The mechanics were robust and the positioning system highly reproducible with standard deviations of less than 1.0 mm in the x-axis and 2.3 mm in the y-axis for a given stab position. The force of the instrument may be varied by the operator to a maximum of approximately 221 N. The suitability of the instrument for simulating stab events was evaluated by measuring the severance length and textile damage from stab delivered from four different knives and nine penetrating angles.

Berhane, AM, Jeong, K, Bodrog, Z, Fiedler, S, Schröder, T, Triviño, NV, Palacios, T, Gali, A, Toth, M, Englund, D & Aharonovich, I 2017, 'Bright Room‐Temperature Single‐Photon Emission from Defects in Gallium Nitride', Advanced Materials, vol. 29, no. 12, pp. 1605092-1605092.
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Researchers report room-temperature (RT), bright, stable single-photon emitters (SPEs) in GaN films that do not require any post-growth sample treatments. The emitters are defects that are optically active in the visible/near-infrared spectral range, and the zero-phonon lines (ZPL) span a wide range of wavelengths. They are found in five GaN wafers that have different doping types and levels, and are grown on various substrates using metal organic chemical vapor deposition various substrates using metal organic chemical vapor deposition (MOCVD), the most common commercially viable technique for the growth of device-grade GaN.

Berhane, AM, Jeong, K, Bodrog, Z, Fiedler, S, Schröder, T, Triviño, NV, Palacios, T, Gali, A, Toth, M, Englund, D & Aharonovich, I 2017, 'Single‐Photon Emission: Bright Room‐Temperature Single‐Photon Emission from Defects in Gallium Nitride (Adv. Mater. 12/2017)', Advanced Materials, vol. 29, no. 12.
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Berry, IJ, Jarocki, VM, Tacchi, JL, Raymond, BBA, Widjaja, M, Padula, MP & Djordjevic, SP 2017, 'N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen', Scientific Reports, vol. 7, no. 1, pp. 1-17.
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AbstractProteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.

Bertrand, A, Legrand, C, Carroll, RJ, de Meester, C & Van Keilegom, I 2017, 'Inference in a survival cure model with mismeasured covariates using a simulation-extrapolation approach', Biometrika, vol. 104, no. 1, pp. asw054-asw054.
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© 2017 Biometrika Trust. In many situations in survival analysis, it may happen that a fraction of individuals will never experience the event of interest: They are considered to be cured. The promotion time cure model takes this into account. We consider the case where one or more explanatory variables in the model are subject to measurement error, which should be taken into account to avoid biased estimators. A general approach is the simulation-extrapolation algorithm, a method based on simulations which allows one to estimate the effect of measurement error on the bias of the estimators and to reduce this bias. We extend this approach to the promotion time cure model. We explain how the algorithm works, and we show that the proposed estimator is approximately consistent and asymptotically normally distributed, and that it performs well in finite samples. Finally, we analyse a database in cardiology: Among the explanatory variables of interest is the ejection fraction, which is known to be measured with error.

Bhan, M, Satija, S, Garg, C, Dureja, H & Garg, M 2017, 'A Novel Approach towards Green Extraction for Glycyrrhitinic Acid by Ionic Liquid Based Microwave Assisted Extraction and Optimization through Response Surface Methodology', Pharmacognosy Journal, vol. 9, no. 6, pp. 866-872.
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© 2017 Phcog.Net. Background: Extraction process plays an important role in extraction of herbal bioactive components. Ionic liquid based microwave assisted extraction (IL-MAE) has the potential to yield maximum analytes from the crude drugs in shorter time period with less solvent consumption and greater efficiency. Objective: The present study aimed to develop new protocol of Ionic Liquids based Microwave-Assisted Extraction (ILs-MAE) of glycyrrhetinic acid from licorice; optimization of the protocol through RSM and comparison of IL-MAE with conventional extraction techniques like maceration and soxhlation by HPTLC. Materials and Methods: A novel ionic liquid-based microwave assisted extraction (IL-MAE) method was carried out for glycyrrhitinic acid from Glycyrrhiza glabra using ionic liquid, 1-butyl-3-methyl-imidazolium chloride ([bmim]Cl) and optimized by response surface methodology. The variable microwave-Assisted extraction parameters selected were concentration of [bmim]Cl, extraction time and microwave power while solid-liquid ratio and extraction temperature were kept constant. Response surface methodology was applied for developing, improving and optimizing the whole process and comparison of IL-MAE with maceration and soxhlation by HPTLC. Results: The yield of glycyrrhitinic acid was found to be 0.48 % w/w in maceration in 7 days, 0.76 % in soxhlation in 3 h and 2.54 % w/w in IL-MAE in 4 min. Conclusion: IL-MAE of glycyrrhitinic acid from Glycyrrhiza glabra was proved to be better in respect of extraction efficiency, time and quantity of solvent used. Meanwhile, there was great reduction in the environmental pollution by using the green solvents/ ionic liquids (ILs), which is a great benefit to all.

Bhan, M, Satija, S, Garg, C, Dureja, H & Garg, M 2017, 'Optimization of ionic liquid-based microwave assisted extraction of a diterpenoid lactone-andrographolide from Andrographis paniculata by response surface methodology', Journal of Molecular Liquids, vol. 229, pp. 161-166.
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Bidny, S, Gago, K, Chung, P, Albertyn, D & Pasin, D 2017, 'Simultaneous Screening and Quantification of Basic, Neutral and Acidic Drugs in Blood Using UPLC-QTOF-MS', Journal of Analytical Toxicology, vol. 41, no. 3, pp. 181-195.
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An analytical method using ultra performance liquid chromatography (UPLC) quadrupole time-of-flight mass spectrometry (QTOF-MS) was developed and validated for the targeted toxicological screening and quantification of commonly used pharmaceuticals and drugs of abuse in postmortem blood using 100 µL sample. It screens for more than 185 drugs and metabolites and quantifies more than 90 drugs. The selected compounds include classes of pharmaceuticals and drugs of abuse such as: antidepressants, antipsychotics, analgesics (including narcotic analgesics), anti-inflammatory drugs, benzodiazepines, beta-blockers, amphetamines, new psychoactive substances (NPS), cocaine and metabolites. Compounds were extracted into acetonitrile using a salting-out assisted liquid-liquid extraction (SALLE) procedure. The extracts were analyzed using a Waters ACQUITY UPLC coupled with a XEVO QTOF mass spectrometer. Separation of the analytes was achieved by gradient elution using Waters ACQUITY HSS C18 column (2.1 mm x 150 mm, 1.8 μm). The mass spectrometer was operated in both positive and negative electrospray ionization modes. The high-resolution mass spectrometry (HRMS) data was acquired using a patented Waters MSE acquisition mode which collected low and high energy spectra alternatively during the same acquisition. Positive identification of target analytes was based on accurate mass measurements of the molecular ion, product ion, peak area ratio and retention times. Calibration curves were linear over the concentration range 0.05-2 mg/L for basic and neutral analytes and 0.1-6 mg/L for acidic analytes with the correlation coefficients (r2) > 0.96 for most analytes. The limits of detection (LOD) were between 0.001-0.05 mg/L for all analytes. Good recoveries were achieved ranging from 80% to 100% for most analytes using the SALLE method. The method was validated for sensitivity, selectivity, accuracy, precision, stability, carryover and matrix effects. The developed method was teste...

Bilokur, M, Gentle, A, Arnold, MD, Cortie, MB & Smith, GB 2017, 'High Temperature Spectrally Selective Solar Absorbers Using Plasmonic AuAl₂:AlN Nanoparticle Composites', Solar RRL, vol. 1, no. 10, pp. 1700092-1700092.
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Advanced solar energy collectors require the use of thermally stable and spectrally selective coatings in order to boost absorption of radiant energy. Here, it is shown that incorporation of plasmonically resonant Au and AuAl2 nanoparticles into multilayer coatings based on AlN provides strong and stable absorption across the solar spectrum at temperatures between RT and 500 °C. Optical properties at operating temperature are verified using in situ measurements. Solar absorptance of 92–97% is available in the as‐deposited films, which are comprised of layers of Al, Au:AlN, AlN, and SiO2. Annealing at the operating temperature of ∼500 °C causes the conversion of the elemental Au to the intermetallic compound AuAl2, but the good solar absorbing performance is retained. The additional Al that reacts with the Au nanoparticles to form the AuAl2 diffuses up from the reflective Al substrate used. Enhanced NIR solar absorptance post‐annealing is accompanied by a tolerable small rise in thermal emittance. Formation of AuAl2:AlN also prevents undesired Au nanoparticle agglomeration above 500 °C. This suggests that AuAl2:AlN nanoparticle composites are excellent candidates for solar thermal applications up to about 500 °C.

Bishop, DP, Blanes, L, Wilson, AB, Wilbanks, T, Killeen, K, Grimm, R, Wenzel, R, Major, D, Macka, M, Clarke, D, Schmid, R, Cole, N & Doble, PA 2017, 'Microfluidic high performance liquid chromatography-chip hyphenation to inductively coupled plasma–mass spectrometry', Journal of Chromatography A, vol. 1497, pp. 64-69.
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© 2017 Elsevier B.V. The Agilent Chip Cube Interface is a microfluidic chip-based technology originally designed for nanospray molecular mass spectrometry in which the sample enrichment, nano-column, tubing, connectors and spray tip were integrated into a single biocompatible chip. Here we describe the hyphenation of the Chip Cube Interface to ICP-MS via modification of the standard HPLC chip design and a new total consumption nebuliser suitable for flow rates as low as 300 nL min−1. The potential of the instrument to eliminate common nanoLC – ICP-MS shortcomings such as leaks, blockages and band-broadening was demonstrated via analysis of cyanocobalamin in equine plasma. The method was linear over three orders of magnitude with an r2 of 0.9999, the peak area repeatability was 1.9% (n = 7), and the detection limit was 14 ng mL−1. This novel configuration of the Chip Cube Interface coupled to ICP-MS is a suitable platform for the analysis of biomolecules associated with trace metals and speciation applications.

Bitto, NJ, Chapman, R, Pidot, S, Costin, A, Lo, C, Choi, J, D’Cruze, T, Reynolds, EC, Dashper, SG, Turnbull, L, Whitchurch, CB, Stinear, TP, Stacey, KJ & Ferrero, RL 2017, 'Bacterial membrane vesicles transport their DNA cargo into host cells', Scientific Reports, vol. 7, no. 1, pp. 1-11.
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AbstractBacterial outer membrane vesicles (OMVs) are extracellular sacs containing biologically active products, such as proteins, cell wall components and toxins. OMVs are reported to contain DNA, however, little is known about the nature of this DNA, nor whether it can be transported into host cells. Our work demonstrates that chromosomal DNA is packaged into OMVs shed by bacteria during exponential phase. Most of this DNA was present on the external surfaces of OMVs, with smaller amounts located internally. The DNA within the internal compartments of Pseudomonas aeruginosa OMVs were consistently enriched in specific regions of the bacterial chromosome, encoding proteins involved in virulence, stress response, antibiotic resistance and metabolism. Furthermore, we demonstrated that OMVs carry DNA into eukaryotic cells, and this DNA was detectable by PCR in the nuclear fraction of cells. These findings suggest a role for OMV-associated DNA in bacterial-host cell interactions and have implications for OMV-based vaccines.

Bordin, DM, Bettim, BB, Perdona, GC, de Campos, EG & De Martinis, BS 2017, 'Understanding alterations on blood and biochemical parameters in athletes that use dietary supplements, steroids and illicit drugs', Toxicology, vol. 376, pp. 75-82.
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Borovkov, K, Mishura, Y, Novikov, A & Zhitlukhin, M 2017, 'Bounds for expected maxima of Gaussian processes and their discrete approximations', Stochastics, vol. 89, no. 1, pp. 21-37.
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© 2015 Taylor & Francis The paper deals with the expected maxima of continuous Gaussian processes (Formula presented.) that are Hölder continuous in (Formula presented.)-norm and/or satisfy the opposite inequality for the (Formula presented.)-norms of their increments. Examples of such processes include the fractional Brownian motion and some of its “relatives” (of which several examples are given in the paper). We establish upper and lower bounds for (Formula presented.) and investigate the rate of convergence to that quantity of its discrete approximation (Formula presented.). Some further properties of these two maxima are established in the special case of the fractional Brownian motion.

Bossa, L, Kline, K, McDougald, D, Lee, BB & Rice, SA 2017, 'Urinary catheter-associated microbiota change in accordance with treatment and infection status', PLOS ONE, vol. 12, no. 6, pp. e0177633-e0177633.
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© 2017 Bossa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The use of long-term catheterisation to manage insensate bladders, often associated with spinal cord injury (SCI), increases the risk of microbial colonisation and infection of the urinary tract. Urinary tract infection (UTI) is typically diagnosed and treated based on the culturing of organisms from the urine, although this approach overlooks low titer, slow growing and non-traditional pathogens. Here, we present an investigation of the urinary tract microbiome in catheterised SCI individuals, using T-RFLP and metagenomic sequencing of the microbial community. We monitored three neurogenic patients over a period of 12 months, who were part of a larger study investigating the efficacy of probiotics in controlling UTIs, to determine how their urinary tract microbial community composition changed over time and in relation to probiotic treatment regimens. Bacterial biofilms adherent to urinary catheters were examined as a proxy for bladder microbes. The microbial community composition of the urinary tract differed significantly between individuals. Probiotic therapy resulted in a significant change in the microbial community associated with the catheters. The community also changed as a consequence of UTI and this shift in community composition preceded the clinical diagnosis of infection. Changes in the microbiota due to probiotic treatment or infection were transient, resolving to microbial communities similar to their pre-treatment communities, suggesting that the native community was highly resilient. Based on these results, we propose that monitoring a patient’s microbial community can be used to track the health of chronically catheterized patients and thus, can be used as part of a health-status mo...

Bottomley, AL, Liew, ATF, Kusuma, KD, Peterson, E, Seidel, L, Foster, SJ & Harry, EJ 2017, 'Coordination of Chromosome Segregation and Cell Division in Staphylococcus aureus', Frontiers in Microbiology, vol. 8, no. AUG.
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© 2017 Bottomley, Liew, Kusuma, Peterson, Seidel, Foster and Harry. Productive bacterial cell division and survival of progeny requires tight coordination between chromosome segregation and cell division to ensure equal partitioning of DNA. Unlike rod-shaped bacteria that undergo division in one plane, the coccoid human pathogen Staphylococcus aureus divides in three successive orthogonal planes, which requires a different spatial control compared to rod-shaped cells. To gain a better understanding of how this coordination between chromosome segregation and cell division is regulated in S. aureus, we investigated proteins that associate with FtsZ and the divisome. We found that DnaK, a well-known chaperone, interacts with FtsZ, EzrA and DivIVA, and is required for DivIVA stability. Unlike in several rod shaped organisms, DivIVA in S. aureus associates with several components of the divisome, as well as the chromosome segregation protein, SMC. This data, combined with phenotypic analysis of mutants, suggests a novel role for S. aureus DivIVA in ensuring cell division and chromosome segregation are coordinated.

Boudewijn, IM, Faiz, A, Steiling, K, van der Wiel, E, Telenga, ED, Hoonhorst, SJM, ten Hacken, NHT, Brandsma, C-A, Kerstjens, HAM, Timens, W, Heijink, IH, Jonker, MR, de Bruin, HG, Sebastiaan Vroegop, J, Pasma, HR, Boersma, WG, Wielders, P, van den Elshout, F, Mansour, K, Spira, A, Lenburg, ME, Guryev, V, Postma, DS & van den Berge, M 2017, 'Nasal gene expression differentiates COPD from controls and overlaps bronchial gene expression', Respiratory Research, vol. 18, no. 1.
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© 2017 The Author(s). Background: Nasal gene expression profiling is a promising method to characterize COPD non-invasively. We aimed to identify a nasal gene expression profile to distinguish COPD patients from healthy controls. We investigated whether this COPD-associated gene expression profile in nasal epithelium is comparable with the profile observed in bronchial epithelium. Methods: Genome wide gene expression analysis was performed on nasal epithelial brushes of 31 severe COPD patients and 22 controls, all current smokers, using Affymetrix Human Gene 1.0 ST Arrays. We repeated the gene expression analysis on bronchial epithelial brushes in 2 independent cohorts of mild-to-moderate COPD patients and controls. Results: In nasal epithelium, 135 genes were significantly differentially expressed between severe COPD patients and controls, 21 being up- and 114 downregulated in COPD (false discovery rate < 0.01). Gene Set Enrichment Analysis (GSEA) showed significant concordant enrichment of COPD-associated nasal and bronchial gene expression in both independent cohorts (FDRGSEA < 0.001). Conclusion: We identified a nasal gene expression profile that differentiates severe COPD patients from controls. Of interest, part of the nasal gene expression changes in COPD mimics differentially expressed genes in the bronchus. These findings indicate that nasal gene expression profiling is potentially useful as a non-invasive biomarker in COPD. Trial registration:ClinicalTrials.govregistration number NCT01351792(registration date May 10, 2011), ClinicalTrials.govregistration number NCT00848406(registration date February 19, 2009), ClinicalTrials.govregistration number NCT00807469(registration date December 11, 2008).

Boulais, D, Lal, S, Sztynda, T & Zaslawski, C 2017, 'Preserving lumbar spine physiology in the cleaning industry', Journal of Health, Safety and Environment, vol. 33, no. 3.
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Background: Lumbar spine disc breakdown may begin as early as the second decade of life. Peak bone mass occurs between the ages of 16 and 25 years and continuously decreases thereafter where bone loss occurs at a faster rate in females increasing throughout menopause. The objectives of this study were to examine the relationship of age and gender against lumbar or non-lumbar musculoskeletal disorder (MSD) diagnosis and post-injury recovery time. Methods: Records of 144 MSD-related incidents that were recorded between 2012 and 2016 (five years) were retrieved from the injury register of a large commercial cleaning organisation (n = 700 cleaners) for analysis. The mean age of the organisations workforce was 57 years of age and 62% of cleaners were female by payroll. Results: The overall non-lumbar related MSD was higher within the older age (>45 years) group (n = 53) as opposed to the younger age (<45 years) group (n = 34). Consequently, more lumbar spinerelated MSDs occurred in the younger age (<45 years) group (n = 33) than the older age (>45 years) group (n = 24). A strong relationship was identified between the age of a cleaner (greater than or less than 45 years) and the type of MSD (lumbar or non-lumbar) (p = 0.027). It was identified that that 110 (76.38%) of cleaners recovered from their MSD within four weeks. Of those in the younger age (<45 years) group then 16.42% (n = 11) took longer than four weeks to recover. Of those in the older age (>45 years) group then 29.87% (n = 23) took longer than four weeks to recover. A relationship between age and recovery time was identified at the 90% confidence interval (p = 0.058). Conclusions: It was identified that non-lumbar musculoskeletal injury is more likely to occur as one ages. Furthermore, it was identified that age may have an adverse effect upon injury recovery time. It was recommended that manual handling, return to work training programs and work schedules be periodically reviewed to strategical...

Boyjoo, Y, Cheng, Y, Zhong, H, Tian, H, Pan, J, Pareek, VK, Jiang, SP, Lamonier, J-F, Jaroniec, M & Liu, J 2017, 'From waste Coca Cola® to activated carbons with impressive capabilities for CO2 adsorption and supercapacitors', Carbon, vol. 116, pp. 490-499.
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We herein report the synthesis of heteroatoms doped, high surface area microporous activated carbons (AC) by utilisation of Coca Cola® as a potential source of waste biomass, for applications as CO2 adsorbent and electrodes of supercapacitors. N, S dual doped carbon spheres are firstly obtained by hydrothermal treatment of Coca Cola® and then thermally activated by either KOH or ZnCl2. The resulting KOH activated carbon material (CMC-3) exhibits extremely high adsorption capability for CO2 with 5.22 mmol g−1 at 25 °C and 1 atm, one of the highest values ever recorded for a carbonaceous material. On the other hand, ZnCl2 activated carbon material (CMC-2) performs excellently as an electrode for supercapacitor, exhibiting very high specific capacitance of 352.7 F g−1 at a current density of 1 A g−1 in 6 M KOH electrolyte, which again is one of the highest values recorded for a biomass derived AC. Coca Cola® has high content in carbon as sugars, provides in-situ doping of O, N and S and has constant composition, as opposed to other conventional biomass materials, making it an attractive and cheap alternative for synthesis of high performance AC for environmental and energy storage purposes.

Bradfield, LA & Balleine, BW 2017, 'Thalamic Control of Dorsomedial Striatum Regulates Internal State to Guide Goal-Directed Action Selection', The Journal of Neuroscience, vol. 37, no. 13, pp. 3721-3733.
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We (Bradfield et al., 2013) have demonstrated previously that parafascicular thalamic nucleus (PF)-controlled neurons in the posterior dorsomedial striatum (pDMS) are critical for interlacing new and existing action–outcome contingencies to control goal-directed action. Based on these findings, it was suggested that animals with a dysfunctional PF–pDMS pathway might suffer a deficit in creating or retrieving internal contexts or “states” on which such information could become conditional. To assess this hypothesis more directly, rats were given a disconnection treatment using contralateral cytotoxic lesions of the PF and pDMS (Group CONTRA) or ipsilateral control lesions (Group IPSI) and trained to press a right and left lever for sucrose and pellet outcomes, after which these contingencies were reversed. The rats were then given an outcome devaluation test (all experiments) and a test of outcome-specific reinstatement (Experiments 1 and 3). We found that devaluation performance was intact for both groups after training of initial contingencies, but impaired for Group CONTRA after reversal. However, performance was restored by additional reversal training. Furthermore, when tested a second time after reversal training, rats in both groups demonstrated responding in accordance with the original contingencies, providing direct evidence of modulation of action selection by state. Finally, we found that external context could substitute for internal state and so could rescue responding in Group CONTRA, but only in the reinstatement test. Together, these findings suggest that animals use internal state information to guide action selection and that this information is modulated by the PF–pDMS pathway.SIGNIFICANCE STATEMENTIndividuals with Parkinson's disease dementia often suffer a characteristic deficit in “cognitive flexibility.” It has been suggested that neurodegeneration in the pathway between the centrome...

Brakoulias, V & Rehn, S 2017, 'Does the severity of obsessive-compulsive symptoms reduce with age?', Journal of Affective Disorders, vol. 213, pp. 178-179.
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Brito, B, Pauszek, SJ, Eschbaumer, M, Stenfeldt, C, de Carvalho Ferreira, HC, Vu, LT, Phuong, NT, Hoang, BH, Tho, ND, Dong, PV, Minh, PQ, Long, NT, King, DP, Knowles, NJ, Dung, DH, Rodriguez, LL & Arzt, J 2017, 'Phylodynamics of foot-and-mouth disease virus O/PanAsia in Vietnam 2010–2014', Veterinary Research, vol. 48, no. 1, pp. 1-12.
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© 2017 The Author(s). Foot-and-mouth disease virus (FMDV) is endemic in Vietnam, a country that plays an important role in livestock trade within Southeast Asia. The large populations of FMDV-susceptible species in Vietnam are important components of food production and of the national livelihood. In this study, we investigated the phylogeny of FMDV O/PanAsia in Vietnam, reconstructing the virus' ancestral host species (pig, cattle or buffalo), clinical stage (subclinical carrier or clinically affected) and geographical location. Phylogenetic divergence time estimation and character state reconstruction analyses suggest that movement of viruses between species differ. While inferred transmissions from cattle to buffalo and pigs and from pigs to cattle are well supported, transmission from buffalo to other species, and from pigs to buffalo may be less frequent. Geographical movements of FMDV O/PanAsia virus appears to occur in all directions within the country, with the South Central Coast and the Northeast regions playing a more important role in FMDV O/PanAsia spread. Genetic selection of variants with changes at specific sites within FMDV VP1 coding region was different depending on host groups analyzed. The overall ratio of non-synonymous to synonymous nucleotide changes was greater in pigs compared to cattle and buffalo, whereas a higher number of individual amino acid sites under positive selection were detected in persistently infected, subclinical animals compared to viruses collected from clinically diseased animals. These results provide novel insights to understand FMDV evolution and its association with viral spread within endemic countries. These findings may support animal health organizations in their endeavor to design animal disease control strategies in response to outbreaks.

Brito, BP, Rodriguez, LL, Hammond, JM, Pinto, J & Perez, AM 2017, 'Review of the Global Distribution of Foot-and-Mouth Disease Virus from 2007 to 2014', Transboundary and Emerging Diseases, vol. 64, no. 2, pp. 316-332.
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Published (2015). This article is a U.S. Government work and is in the public domain in the USA. Foot-and-mouth disease (FMD) virus affects livestock worldwide. There are seven different serotypes, each with a diversity of topotypes, genetic lineages and strains. Some lineages have different properties that may contribute to sporadic spread beyond their recognized endemic areas. The objective of this study was to review the most significant FMD epidemiological events that took place worldwide between 2007 and 2014. Severe epidemics were caused by FMD virus (FMDV) lineage O/Asia/Mya-98 in Japan and South Korea in 2010, both previously free of disease. In India, where FMD is endemic, the most important event was the re-emergence of lineage O/ME-SA/Ind-2001 in 2008. Notably, this lineage, normally restricted to India, Bangladesh, Nepal and Bhutan, was also found in Saudi Arabia and Libya in 2013 and has caused several outbreaks in Tunisia and Algeria in 2014–2015. In January 2011, FMDV-positive wild boars were found in Bulgaria, where the disease last occurred in 1996, followed by 12 outbreaks in livestock infected with FMDV O/ME-SA/PanAsia2. In 2012, FMDV SAT2 caused outbreaks in Egypt and the Palestinian Autonomous Territories. Another significant event was the emergence of FMDV Asia1 Sindh-08 in the Middle East. In South America, one outbreak of FMDV serotype O, topotype Euro-SA was reported in Paraguay in 2011, which was recognized as FMD-free with vaccination at the time. Lessons learned from past events, point out the need for an integrated strategy that comprises coordinated global and regional efforts for FMDV control and surveillance. Specific local characteristics related to host, environment and virus that condition FMD occurrence should be carefully considered and incorporated to adapt appropriate strategies into local plans. In this review, we compiled relevant epidemiological FMD events to provide a global overview of the current situation. W...

Brodersen, KE, Hammer, KJ, Schrameyer, V, Floytrup, A, Rasheed, MA, Ralph, PJ, Kühl, M & Pedersen, O 2017, 'Sediment Resuspension and Deposition on Seagrass Leaves Impedes Internal Plant Aeration and Promotes Phytotoxic H2S Intrusion', Frontiers in Plant Science, vol. 8, pp. 1-13.
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© 2017 Brodersen, Hammer, Schrameyer, Floytrup, Rasheed, Ralph, Kühl and Pedersen. Anthropogenic activities leading to sediment re-suspension can have adverse effects on adjacent seagrass meadows, owing to reduced light availability and the settling of suspended particles onto seagrass leaves potentially impeding gas exchange with the surrounding water. We used microsensors to determine O2 fluxes and diffusive boundary layer (DBL) thickness on leaves of the seagrass Zostera muelleri with and without fine sediment particles, and combined these laboratory measurements with in situ microsensor measurements of tissue O2 and H2 S concentrations. Net photosynthesis rates in leaves with fine sediment particles were down to ∼20% of controls without particles, and the compensation photon irradiance increased from a span of 20–53 to 109–145 µmol photons m−2 s−1. An ∼2.5-fold thicker DBL around leaves with fine sediment particles impeded O2 influx into the leaves during darkness. In situ leaf meristematic O2 concentrations of plants exposed to fine sediment particles were lower than in control plants and exhibited long time periods of complete meristematic anoxia during night-time. Insufficient internal aeration resulted in H2 S intrusion into the leaf meristematic tissues when exposed to sediment resuspension even at relatively high night-time water-column O2 concentrations. Fine sediment particles that settle on seagrass leaves thus negatively affect internal tissue aeration and thereby the plants’ resilience against H2 S intrusion.

Brodersen, KE, Koren, K, Moßhammer, M, Ralph, PJ, Kühl, M & Santner, J 2017, 'Seagrass-Mediated Phosphorus and Iron Solubilization in Tropical Sediments', Environmental Science & Technology, vol. 51, no. 24, pp. 14155-14163.
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© 2017 American Chemical Society. Tropical seagrasses are nutrient-limited owing to the strong phosphorus fixation capacity of carbonate-rich sediments, yet they form densely vegetated, multispecies meadows in oligotrophic tropical waters. Using a novel combination of high-resolution, two-dimensional chemical imaging of O2, pH, iron, sulfide, calcium, and phosphorus, we found that tropical seagrasses are able to mobilize the essential nutrients iron and phosphorus in their rhizosphere via multiple biogeochemical pathways. We show that tropical seagrasses mobilize phosphorus and iron within their rhizosphere via plant-induced local acidification, leading to dissolution of carbonates and release of phosphate, and via local stimulation of microbial sulfide production, causing reduction of insoluble Fe(III) oxyhydroxides to dissolved Fe(II) with concomitant phosphate release into the rhizosphere porewater. These nutrient mobilization mechanisms have a direct link to seagrass-derived radial O2 loss and secretion of dissolved organic carbon from the below-ground tissue into the rhizosphere. Our demonstration of seagrass-derived rhizospheric phosphorus and iron mobilization explains why seagrasses are widely distributed in oligotrophic tropical waters.

Broséus, J, Morelato, M, Tahtouh, M & Roux, C 2017, 'Forensic drug intelligence and the rise of cryptomarkets. Part I: Studying the Australian virtual market', Forensic Science International, vol. 279, pp. 288-301.
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© 2017 Elsevier B.V. Analysing and understanding cryptomarkets is essential to become proactive in the fight against the illicit drug trade. Such a research seeks to combine a diversity of indicators related to the virtual (darknet markets) and physical (the traditional “offline” market) aspects of the illicit drug trade to provide information on the distribution and consumption as well as to assess similarities/differences between the virtual and physical markets. This study analysed data that had previously been collected on cryptomarkets from December 2013 to March 2015. In this article, the data was extracted from two marketplaces, Evolution and Silk Road 2, and analysed to evaluate the illicit drug trade of the Australian virtual market (e.g. information about the supply and demand, trafficking flows, prices of illicit drugs and market share) and highlight its specificities. The results revealed the domestic nature of the virtual Australian illicit drug trade (i.e. Australian sellers essentially ship their products to local customers). This may explain the coherence between supply and demand. Particularly, the virtual Australian illicit drug trade is dominated by amphetamine-type substances (ATS), mainly methamphetamine and 3,4-methylenedioxymethamphetamine (MDMA), and cannabis. Australia, as a shipping country, accounts for half of the methamphetamine offered and purchased on Silk Road 2. Moreover, it was observed that the online price fixed by Australian sellers for the considered illicit drugs is higher than for any other shipping countries, which is in line with previous studies. Understanding the virtual and physical drug market necessitates the integration and fusion of different perspectives to capture the dynamic nature of drug trafficking, monitor its evolution and finally improve our understanding of the phenomenon so policy makers can make informed decisions.

Budden, KF, Gellatly, SL, Wood, DLA, Cooper, MA, Morrison, M, Hugenholtz, P & Hansbro, PM 2017, 'Emerging pathogenic links between microbiota and the gut–lung axis', Nature Reviews Microbiology, vol. 15, no. 1, pp. 55-63.
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© 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. The microbiota is vital for the development of the immune system and homeostasis. Changes in microbial composition and function, termed dysbiosis, in the respiratory tract and the gut have recently been linked to alterations in immune responses and to disease development in the lungs. In this Opinion article, we review the microbial species that are usually found in healthy gastrointestinal and respiratory tracts, their dysbiosis in disease and interactions with the gut-lung axis. Although the gut-lung axis is only beginning to be understood, emerging evidence indicates that there is potential for manipulation of the gut microbiota in the treatment of lung diseases.

Busschaert, N, Park, S-H, Baek, K-H, Choi, YP, Park, J, Howe, ENW, Hiscock, JR, Karagiannidis, LE, Marques, I, Félix, V, Namkung, W, Sessler, JL, Gale, PA & Shin, I 2017, 'A synthetic ion transporter that disrupts autophagy and induces apoptosis by perturbing cellular chloride concentrations', Nature Chemistry, vol. 9, no. 7, pp. 667-675.
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Camlin, NJ, Jarnicki, AG, Vanders, RL, Walters, KA, Hansbro, PM, McLaughlin, EA & Holt, JE 2017, 'Grandmaternal smoke exposure reduces female fertility in a murine model, with great-grandmaternal smoke exposure unlikely to have an effect', Human Reproduction, vol. 32, no. 6, pp. 1270-1281.
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STUDY QUESTION: What effect does multigenerational (F2) and transgenerational (F3) cigarette smoke exposure have on female fertility in mice? SUMMARY ANSWER: Cigarette smoking has a multigenerational effect on female fertility. WHAT IS KNOWN ALREADY: It has been well established that cigarette smoking decreases female fertility. Furthermore, a growing body of evidence suggests that smoking during pregnancy decreases the fertility of daughters and increases cancer and asthma incidence in grandchildren and great-grandchildren. STUDY DESIGN, SIZE, DURATION: Six-week-old C57BL/6 female mice were exposed nasally to cigarette smoke or room air (controls) for 5 weeks prior to being housed with males. Females continued to be exposed to smoke throughout pregnancy and lactation until pups were weaned. A subset of F1 female pups born to these smoke and non-smoke exposed females were bred to create the F2 grandmaternal exposed generation (multigenerational). Finally, a subset of F2 females were bred to create the F3 great-grandmaternal exposed generation (transgenerational). The reproductive health of F2 and F3 females was examined at 8 weeks and 9 months. PARTICIPANTS/MATERIALS, SETTING, METHODS: Ovarian and oocyte quality was examined in smoke exposed and control animals. A small-scale fertility trial was performed before ovarian changes were examined using ovarian histology and immunofluorescence and/ or immunoblotting analysis of markers of apoptosis (TUNEL) and proliferation (proliferating cell nuclear antigen (PCNA) and anti-Mullerian hormone (AMH)). Oocyte quality was examined using immunocytochemistry to analyze the metaphase II spindle and ploidy status. Parthenogenetic activation of oocytes was used to investigate meiosis II timing and preimplantation embryo development. Finally, diestrus hormone serum levels (FSH and LH) were quantified. MAIN RESULTS AND THE ROLE OF CHANCE: F2 smoke exposed females had no detectable change in ovarian follicle quality at ...

Camp, EF, Dong, LF, Suggett, DJ, Smith, DJ, Boatman, TG, Crosswell, JR, Evenhuis, C, Scorfield, S, Walinjkar, A, Woods, J & Lawson, T 2017, 'A novel membrane inlet‐infrared gas analysis (MI‐IRGA) system for monitoring of seawater carbonate system', Limnology and Oceanography: Methods, vol. 15, no. 1, pp. 38-53.
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AbstractIncreased atmospheric CO2 concentrations are driving changes in ocean chemistry at unprecedented rates resulting in ocean acidification, which is predicted to impact the functioning of marine biota, in particular of marine calcifiers. However, the precise understanding of such impacts relies on an analytical system that determines the mechanisms and impact of elevated pCO2 on the physiology of organisms at scales from species to entire communities. Recent work has highlighted the need within experiments to control all aspects of the carbonate system to resolve the role of different inorganic carbon species on the physiological responses observed across taxa in real‐time. Presently however, there are limited options available for continuous quantification of physiological responses, coupled with real‐time calculation of the seawater carbonate chemistry system within microcosm environments. Here, we describe and characterise the performance of a novel pCO2 membrane equilibrium system (the Membrane Inlet Infra‐Red Gas Analyser, MI‐IRGA) integrated with a continuous pH and oxygen monitoring platform. The system can detect changes in the seawater carbonate chemistry and determine organism physiological responses, while providing the user with real‐time control over the microcosm system. We evaluate the systems control, response time and associated error, and demonstrate the flexibility of the system to operate under field conditions and within a laboratory. We use the system to measure physiological parameters (photosynthesis and respiration) for the corals Pocillipora damicornis and Porites cylindrica; in doing so we present a novel dataset examining the interactive role of temperature, light and pCO2 ...

Camp, EF, Nitschke, MR, Rodolfo-Metalpa, R, Houlbreque, F, Gardner, SG, Smith, DJ, Zampighi, M & Suggett, DJ 2017, 'Reef-building corals thrive within hot-acidified and deoxygenated waters', Scientific Reports, vol. 7, no. 1, pp. 2434-2434.
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AbstractCoral reefs are deteriorating under climate change as oceans continue to warm and acidify and thermal anomalies grow in frequency and intensity. In vitro experiments are widely used to forecast reef-building coral health into the future, but often fail to account for the complex ecological and biogeochemical interactions that govern reefs. Consequently, observations from coral communities under naturally occurring extremes have become central for improved predictions of future reef form and function. Here, we present a semi-enclosed lagoon system in New Caledonia characterised by diel fluctuations of hot-deoxygenated water coupled with tidally driven persistently low pH, relative to neighbouring reefs. Coral communities within the lagoon system exhibited high richness (number of species = 20) and cover (24–35% across lagoon sites). Calcification rates for key species (Acropora formosa, Acropora pulchra, Coelastrea aspera and Porites lutea) for populations from the lagoon were equivalent to, or reduced by ca. 30–40% compared to those from the reef. Enhanced coral respiration, alongside high particulate organic content of the lagoon sediment, suggests acclimatisation to this trio of temperature, oxygen and pH changes through heterotrophic plasticity. This semi-enclosed lagoon therefore provides a novel system to understand coral acclimatisation to complex climatic scenarios and may serve as a reservoir of coral populations already resistant to extreme environmental conditions.

Capistrano, S, van Reyk, D, Chen, H & Oliver, B 2017, 'Evidence of Biomass Smoke Exposure as a Causative Factor for the Development of COPD', Toxics, vol. 5, no. 4, pp. 36-36.
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© 2017 by the authors. Chronic obstructive pulmonary disease (COPD) is a progressive disease of the lungs characterised by chronic inflammation, obstruction of airways, and destruction of the parenchyma (emphysema). These changes gradually impair lung function and prevent normal breathing. In 2002, COPD was the fifth leading cause of death, and is estimated by theWorld Health Organisation (WHO) to become the third by 2020. Cigarette smokers are thought to be the most at risk of developing COPD. However, recent studies have shown that people with life-long exposure to biomass smoke are also at high risk of developing COPD. Most common in developing countries, biomass fuels such as wood and coal are used for cooking and heating indoors on a daily basis. Women and children have the highest amounts of exposures and are therefore more likely to develop the disease. Despite epidemiological studies providing evidence of the causative relationship between biomass smoke and COPD, there are still limited mechanistic studies on how biomass smoke causes, and contributes to the progression of COPD. This review will focus upon why biomass fuels are used, and their relationship to COPD. It will also suggest methodological approaches to model biomass exposure in vitro and in vivo.

Cardoso, BR, Hare, DJ, Bush, AI & Roberts, BR 2017, 'Glutathione peroxidase 4: a new player in neurodegeneration?', Molecular Psychiatry, vol. 22, no. 3, pp. 328-335.
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© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Glutathione peroxidase 4 (GPx4) is an antioxidant enzyme reported as an inhibitor of ferroptosis, a recently discovered non-apoptotic form of cell death. This pathway was initially described in cancer cells and has since been identified in hippocampal and renal cells. In this Perspective, we propose that inhibition of ferroptosis by GPx4 provides protective mechanisms against neurodegeneration. In addition, we suggest that selenium deficiency enhances susceptibility to ferroptotic processes, as well as other programmed cell death pathways due to a reduction in GPx4 activity. We review recent studies of GPx4 with an emphasis on neuronal protection, and discuss the relevance of selenium levels on its enzymatic activity.

Cardoso, BR, Hare, DJ, Bush, AI, Li, Q-X, Fowler, CJ, Masters, CL, Martins, RN, Ganio, K, Lothian, A, Mukherjee, S, Kapp, EA & Roberts, BR 2017, 'Selenium Levels in Serum, Red Blood Cells, and Cerebrospinal Fluid of Alzheimer’s Disease Patients: A Report from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL)', Journal of Alzheimer's Disease, vol. 57, no. 1, pp. 183-193.
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Selenium (Se) protects cells against oxidative stress damage through a range of bioactive selenoproteins. Increased oxidative stress is a prominent feature of Alzheimer's disease (AD), and previous studies have shown that Se deficiency is associated with age-related cognitive decline. In this study, we assessed Se status in different biofluids from a subgroup of participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing. As Se in humans can either be an active component of selenoproteins or inactive via non-specific incorporation into other proteins, we used both size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and tandem mass spectrometry to characterize selenoproteins in serum. We observed no differences in total Se concentration in serum or cerebrospinal fluid of AD subjects compared to mildly cognitively impairment patients and healthy controls. However, Se levels in erythrocytes were decreased in AD compared to controls. SEC-ICP-MS analysis revealed a dominant Se-containing fraction. This fraction was subjected to standard protein purification and a bottom-up proteomics approach to confirm that the abundant Se in the fraction was due, in part, to selenoprotein P. The lack of change in the Se level is at odds with our previous observations in a Brazilian population deficient in Se, and we attribute this to the Australian cohort being Se-replete.

Care, A, Petroll, K, Gibson, ESY, Bergquist, PL & Sunna, A 2017, 'Solid-binding peptides for immobilisation of thermostable enzymes to hydrolyse biomass polysaccharides', Biotechnology for Biofuels, vol. 10, no. 1.
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Castrillon, J, Huston, W & Bengtson Nash, S 2017, 'The blubber adipocyte index: A nondestructive biomarker of adiposity in humpback whales (Megaptera novaeangliae)', Ecology and Evolution, vol. 7, no. 14, pp. 5131-5139.
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AbstractThe ability to accurately evaluate the energetic health of wildlife is of critical importance, particularly under conditions of environmental change. Despite the relevance of this issue, currently there are no reliable, standardized, nonlethal measures to assess the energetic reserves of large, free‐roaming marine mammals such as baleen whales. This study investigated the potential of adipocyte area analysis and further, a standardized adipocyte index (AI), to yield reliable information regarding humpback whale (Megaptera novaeangliae) adiposity. Adipocyte area and AI, as ascertained by image analysis, showed a direct correlation with each other but only a weak correlation with the commonly used, but error prone, blubber lipid‐percent measure. The relative power of the three respective measures was further evaluated by comparing humpback whale cohorts at different stages of migration and fasting. Adipocyte area, AI, and blubber lipid‐percent were assessed by binary logistic regression revealing that adipocyte area had the greatest probability to predict the migration cohort with a high level of redundancy attributed to the AI given their strong linear relationship (r = −.784). When only AI and lipid‐percent were assessed, the performance of both predictor variables was significant but the power of AI far exceeded lipid‐percent. The sensitivity of adipocyte metrics and the rapid, nonlethal, and inexpensive nature of the methodology and AI calculation validate th...

Chadwick, S, Neskoski, M, Spindler, X, Lennard, C & Roux, C 2017, 'Effect of hand sanitizer on the performance of fingermark detection techniques', Forensic Science International, vol. 273, pp. 153-160.
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© 2017 Elsevier B.V. Hand sanitizers have seen a rapid increase in popularity amongst the general population and this increased use has led to the belief that hand sanitizers may have an effect on subsequent fingermark detection. Based on this hypothesis, three alcoholic and two non-alcoholic hand sanitizers were evaluated to determine the effect they had on the detection of fingermarks deposited after their use. The following fingermark detection methods were applied: 1,2-indanedione-zinc, ninhydrin, physical developer (porous substrate); and cyanoacrylate, rhodamine 6G, magnetic powder (non-porous substrate). Comparison between hand sanitized fingermarks and non-hand sanitized fingermarks showed that the alcohol-based hand sanitizers did not result in any visible differences in fingermark quality. The non-alcoholic hand sanitizers, however, improved the quality of fingermarks developed with 1,2-indanedione-zinc and ninhydrin, and marginally improved those developed with magnetic powder. Different parameters, including time since hand sanitizer application prior to fingermark deposition and age of deposited mark, were tested to determine the longevity of increased development quality. The non-alcoholic hand sanitized marks showed no decrease in quality when aged for up to two weeks. The time since sanitizer application was determined to be an important factor that affected the quality of non-alcoholic hand sanitized fingermarks. It was hypothesized that the active ingredient in non-alcoholic hand sanitizers, benzalkonium chloride, is responsible for the increase in fingermark development quality observed with amino acid reagents, while the increased moisture content present on the ridges resulted in better powdered fingermarks.

Chai, AB, Ammit, AJ & Gelissen, IC 2017, 'Examining the role of ABC lipid transporters in pulmonary lipid homeostasis and inflammation', Respiratory Research, vol. 18, no. 1, pp. 41-9.
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© The Author(s). 2017 Open Access Respiratory diseases including asthma and chronic obstructive pulmonary disease (COPD) are characterised by excessive and persistent inflammation. Current treatments are often inadequate for symptom and disease control, and hence new therapies are warranted. Recent emerging research has implicated dyslipidaemia in pulmonary inflammation. Three ATP-binding cassette (ABC) transporters are found in the mammalian lung - ABCA1, ABCG1 and ABCA3 - that are involved in movement of cholesterol and phospholipids from lung cells. The aim of this review is to corroborate the current evidence for the role of ABC lipid transporters in pulmonary lipid homeostasis and inflammation. Here, we summarise results from murine knockout studies, human diseases associated with ABC transporter mutations, and in vitro studies. Disruption to ABC transporter activity results in lipid accumulation and elevated levels of inflammatory cytokines in lung tissue. Furthermore, these ABC-knockout mice exhibit signs of respiratory distress. ABC lipid transporters appear to have a crucial and protective role in the lung. However, our knowledge of the underlying molecular mechanisms for these benefits requires further attention. Understanding the relationship between cholesterol and inflammation in the lung, and the role that ABC transporters play in this may illuminate new pathways to target for the treatment of inflammatory lung diseases.

Chan, YL, Saad, S, Al-Odat, I, Oliver, BG, Pollock, C, Jones, NM & Chen, H 2017, 'Maternal L-Carnitine Supplementation Improves Brain Health in Offspring from Cigarette Smoke Exposed Mothers', Frontiers in Molecular Neuroscience, vol. 10, pp. 1-15.
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© 2017 Chan, Saad, Al-Odat, Oliver, Pollock, Jones and Chen. Maternal cigarette smoke exposure (SE) causes detrimental changes associated with the development of chronic neurological diseases in the offspring as a result of oxidative mitochondrial damage. Maternal L-Carnitine administration has been shown to reduce renal oxidative stress in SE offspring, but its effect in the brain is unknown. Here, we investigated the effects of maternal L-Carnitine supplementation on brain markers of oxidative stress, autophagy, mitophagy and mitochondrial energy producing oxidative phosphorylation (OXPHOS) complexes in SE offspring. Female Balb/c mice (8 weeks) were exposed to cigarette smoke prior to mating, during gestation and lactation with or without L-Carnitine supplementation (1.5 mM in drinking water). In 1 day old male SE offspring, brain mitochondrial damage was suggested by increased mitochondrial fusion and reduced autophagosome markers; whereas at 13 weeks, enhanced brain cell damage was suggested by reduced fission and autophagosome markers, as well as increased apoptosis and DNA fragmentation markers, which were partially reversed by maternal L-Carnitine supplementation. In female SE offspring, enhanced mitochondrial regeneration was suggested by decreased fission and increased fusion markers at day 1. At 13 weeks, there was an increase in brain energy demand, oxidative stress and mitochondrial turnover, reflected by the protein changes of OXPHOS complex, fission and autophagosome markers, as well as the endogenous antioxidant, which were also partially normalized by maternal L-Carnitine supplementation. However, markers of apoptosis and DNA fragmentation were not significantly changed. Thus L-Carnitine supplementation may benefit the brain health of the offspring from smoking mothers.

Chan, YL, Saad, S, Machaalani, R, Oliver, BG, Vissel, B, Pollock, C, Jones, NM & Chen, H 2017, 'Maternal Cigarette Smoke Exposure Worsens Neurological Outcomes in Adolescent Offspring with Hypoxic-Ischemic Injury', Frontiers in Molecular Neuroscience, vol. 10, pp. 1-17.
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© 2017 Chan, Saad, Machaalani, Oliver, Vissel, Pollock, Jones and Chen. Hypoxic-ischemic (HI) encephalopathy occurs in approximately 6 per 1000 term newborns leading to devastating neurological consequences, such as cerebral palsy and seizures. Maternal smoking is one of the prominent risk factors contributing to HI injury. Mitochondrial integrity plays a critical role in neural injury and repair during HI. We previously showed that maternal cigarette smoke exposure (SE) can reduce brain mitochondrial fission and autophagosome markers in male offspring. This was accompanied by increased brain cell apoptosis (active caspase-3) and DNA fragmentation (TUNEL staining). Here, we aimed to investigate whether maternal SE leads to more severe neurological damage after HI brain injury in male offspring. Female BALB/c mice (8 weeks) were exposed to cigarette smoke prior to mating, during gestation, and lactation. At postnatal day 10, half of the pups from each litter underwent left carotid artery occlusion, followed by exposure to 8% oxygen (92% nitrogen). At postnatal day 40–44, maternal SE reduced grip strength in grip traction and foot fault tests, which were also reduced by HI injury to similar levels regardless of the maternal group. Limb coordination was impaired by maternal SE which was not worsened by HI injury. Maternal SE increased anxiety level in the offspring, which was normalized by HI injury. Apoptosis markers were increased in different brain regions by maternal SE, with the cortex having further increased TUNEL by HI injury, along with increased markers of inflammation and mitophagy. We conclude that maternal SE can worsen HI-induced cellular damage in male offspring well into adolescence.

Chen, H, Corboliou, V, Solntsev, AS, Choi, D-Y, Vincenti, MA, de Ceglia, D, de Angelis, C, Lu, Y & Neshev, DN 2017, 'Enhanced second-harmonic generation from two-dimensional MoSe2 on a silicon waveguide', Light: Science & Applications, vol. 6, no. 10, pp. e17060-e17060.
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Two-dimensional transition-metal dichalcogenides (TMDCs) with intrinsically broken crystal inversion symmetry and large second-order nonlinear responses have shown great promise for future nonlinear light sources. However, the sub-nanometer monolayer thickness of such materials limits the length of their nonlinear interaction with light. Here, we experimentally demonstrate the enhancement of the second-harmonic generation from monolayer MoSe2 by its integration onto a 220-nm-thick silicon waveguide. Such on-chip integration allows for a marked increase in the interaction length between the MoSe2 and the waveguide mode, further enabling phase matching of the nonlinear process. The demonstrated TMDC-silicon photonic hybrid integration opens the door to second-order nonlinear effects within the silicon photonic platform, including efficient frequency conversion, parametric amplification and the generation of entangled photon pairs.

Cheng, YY, Mok, E, Tan, S, Leygo, C, McLaughlin, C, George, AM & Reid, G 2017, 'SFRPTumour Suppressor Genes Are Potential Plasma-Based Epigenetic Biomarkers for Malignant Pleural Mesothelioma', Disease Markers, vol. 2017, pp. 1-10.
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Malignant pleural mesothelioma (MPM) is associated with asbestos exposure. Asbestos can induce chronic inflammation which in turn can lead to silencing of tumour suppressor genes. Wnt signaling pathway can be affected by chronic inflammation and is aberrantly activated in many cancers including colon and MPM.SFRPgenes are antagonists of Wnt pathway, andSFRPs are potential tumour suppressors in colon, gastric, breast, ovarian, and lung cancers and mesothelioma. This study investigated the expression and DNA methylation ofSFRPgenes in MPM cells lines with and without demethylation treatment. Sixty-six patient FFPE samples were analysed and have showed methylation ofSFRP2(56%) andSFRP5(70%) in MPM.SFRP2andSFRP5tumour-suppressive activity in eleven MPM lines was confirmed, and long-term asbestos exposure led to reduced expression of theSFRP1andSFRP2 genes in the mesothelium (MeT-5A) via epigenetic alterations. Finally, DNA methylation ofSFRPs is detectable in MPM patient plasma samples, with methylatedSFRP2andSFRP5showing a tendency towards greater abundance in patients. These data suggested thatSFRPgenes have tumour-suppresive activity in MPM and that methylated DNA fromSFRPgene promoters has the potential to serve as a biomarker for MPM patient plasma.

Cheung, EYY, Gahan, ME & McNevin, D 2017, 'Prediction of biogeographical ancestry from genotype: a comparison of classifiers', International Journal of Legal Medicine, vol. 131, no. 4, pp. 901-912.
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DNA can provide forensic intelligence regarding a donor's biogeographical ancestry (BGA) and other externally visible characteristics (EVCs). A number of algorithms have been proposed to assign individual human genotypes to a BGA using ancestry informative marker (AIM) panels. This study compares the BGA assignment accuracy of the population clustering program STRUCTURE and three generic classification approaches including a Bayesian algorithm, genetic distance, and multinomial logistic regression (MLR). A selection of 142 ancestry informative single nucleotide polymorphisms (SNPs) were chosen from existing marker panels (SNPforID 34-plex, Eurasiaplex, Seldin, and Kidd's AIM panels) to assess BGA classification at the continental level for Africans, Europeans, East Asians, and Amerindians. A training set of 1093 individuals with self-declared BGA from the 1000 Genomes phase 1 database was used by each classifier to predict BGA in a test set of 516 individuals from the HGDP-CEPH (Stanford) cell line panel. Tests were repeated with 0, 10, 50, 70, and 90% of the genotypes missing. Comparison of the area under the receiver operating characteristic curves (AUROCs) showed high accuracy in STRUCTURE and the generic Bayesian approach. The latter algorithm offers a computationally simpler alternative to STRUCTURE with little loss in accuracy and is suitable for phenotype prediction while STRUCTURE is not.

Chi, Q, Ford, MJ, Halder, A, Hush, NS, Reimers, JR & Ulstrup, J 2017, 'Sulfur ligand mediated electrochemistry of gold surfaces and nanoparticles: What, how, and why', Current Opinion in Electrochemistry, vol. 1, no. 1, pp. 7-15.
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© 2017 Gold surfaces are widely used in electrochemistry while gold nanoparticles have very many uses, with both the surfaces and the particles often being protected by sulfur-bound organic ligands. The ligands not only provide chemical stability but also directly participate in many desired processes. This review considers the diversity of known atomic structures for gold–sulfur interfaces, how these structures facilitate a diversity of mechanisms in electrochemical applications, and why this is possible based on recent advances in the basic understanding of the electronic structure of gold–sulfur bonds. Believed once to be Au(I)-thiolate in character and hence distinctly different to physisorbed thiols and disulfides, chemisorbed bonds are shown to be Au(0)-thiyls instead. A wide range of in situ STM electrochemical and other data is interpreted from this perspective.

Chikoidze, E, Fellous, A, Perez-Tomas, A, Sauthier, G, Tchelidze, T, Ton-That, C, Huynh, TT, Phillips, M, Russell, S, Jennings, M, Berini, B, Jomard, F & Dumont, Y 2017, 'P-type β-gallium oxide: A new perspective for power and optoelectronic devices', Materials Today Physics, vol. 3, pp. 118-126.
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© 2017 Elsevier Ltd Wide-bandgap semiconductors (WBG) are expected to be applied to solid-state lighting and power devices, supporting a future energy-saving society. Here we present evidence of p-type conduction in the undoped WBG β-Ga 2 O 3 . Hole conduction, established by Hall and Seebeck measurements, is consistent with findings from photoemission and cathodoluminescence spectroscopies. The ionization energy of the acceptor level was measured to be 1.1eV above the valence band edge. The gallium vacancy was identified as a possible acceptor candidate based on thermodynamic equilibrium Ga 2 O 3 (crystal) – O 2 (gas) system calculations (Kroger theory) which revealed a window without oxygen vacancy compensation. The possibility of fabricating large diameter wafers of β-Ga 2 O 3 of p and n type nature, provides new avenues for high power and deep UV-optoelectronic devices.

Chipperfield, J, Brown, J & Bell, P 2017, 'Estimating the Count Error in the Australian Census', Journal of Official Statistics, vol. 33, no. 1, pp. 43-59.
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Abstract In many countries, counts of people are a key factor in the allocation of government resources. However, it is well known that errors arise in Census counting of people (e.g., undercoverage due to missing people). Therefore, it is common for national statistical agencies to conduct one or more “audit” surveys that are designed to estimate and remove systematic errors in Census counting. For example, the Australian Bureau of Statistics (ABS) conducts a single audit sample, called the Post Enumeration Survey (PES), shortly after each Australian Population Census. This article describes the estimator used by the ABS to estimate the count of people in Australia. Key features of this estimator are that it is unbiased when there is systematic measurement error in Census counting and when nonresponse to the PES is nonignorable.

Chipperfield, J, Brown, JJ & Watson, N 2017, 'The Australian Census Longitudinal Dataset: using record linkage to create a longitudinal sample from a series of cross‐sections', Australian & New Zealand Journal of Statistics, vol. 59, no. 1, pp. 1-16.
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SummaryThe Australian Bureau of Statistics is creating a longitudinal sample, called the Australian Census Longitudinal Dataset (ACLD), by linking person records across its five‐yearly Census of Population and Housing. This paper proposes a Multi‐Panel framework for selecting and weighting records in the ACLD. This framework can be applied more generally to selecting longitudinal samples from a series of cross‐sectional administrative files. The proposed framework avoids some significant limitations of the popular ‘Top‐Up’ sampling approach to maintaining the cross‐sectional and longitudinal representativeness of a sample over time.

Choi, G, Karacan, I, Cazalbou, S, Evans, L, Sinutok, S & Ben-Nissan, B 2017, 'Conversion of Calcified Algae (<i>Halimeda </i>sp) and Hard Coral (<i>Porites </i>sp) to Hydroxyapatite', Key Engineering Materials, vol. 758, pp. 157-161.
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Calcium phosphate materials can be produced using a number of wet methods that are based on hydrothermal or co-precipitation methods that might use acidic or basic chemical environments. In our previously published works, we have investigated calcium phosphates such as monetite, hydroxyapatite, and whitlockite which were successfully produced by mechano-chemical methods and/or hydrothermal treatments from a range of marine shells and corals which were obtained from the Great Barrier Reef. The aim of the current work was to analyze and compare the mechanisms of conversion of one hard coral species and one calcified algae species from the Great Barrier Reef.

Choi, JP, Yang, X, Foley, M, Wang, X & Zheng, X 2017, 'Induction and Micro-CT Imaging of Cerebral Cavernous Malformations in Mouse Model', Journal of Visualized Experiments, vol. Sept, no. 127, pp. 1-5.
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Mutations in the CCM1 (aka KRIT1), CCM2, or CCM3 (aka PDCD10) gene cause cerebral cavernous malformation (CCM) in humans. Mouse models of CCM disease have been established by tamoxifen induced deletion of Ccm genes in postnatal animals. These mouse models provide invaluable tools to investigate molecular mechanism and therapeutic approaches for CCM disease. An accurate and quantitative method to assess lesion burden and progression is essential to harness the full value of these animal models. Here, we demonstrate the induction of CCM disease in a mouse model and the use of the contrast enhanced X-ray micro computed tomography (micro-CT) method to measure CCM lesion burden in mouse brains. At postnatal day 1 (P1), we used 4-hydroxytamoxifen (4HT) to activate Cre recombinase activity from the Cdh5-CreErt2 transgene to cleave the floxed allele of Ccm2. CCM lesions in mouse brains were analyzed at P8. For micro-CT, iodine based Lugol's solution was used to enhance contrast in brain tissue. We have optimized the scan parameters and utilized a voxel dimension of 9.5 µm, which lead to a minimum feature size of approximately 25 µm. This resolution is sufficient to measure CCM lesion volume and number globally and accurately, and provide high-quality 3-D mapping of CCM lesions in mouse brains. This method enhances the value of the established mouse models to study the molecular basis and potential therapies for CCM and other cerebrovascular diseases.

Choi, S, Rogers, DJ, Sandana, EV, Bove, P, Teherani, FH, Nenstiel, C, Hoffmann, A, McClintock, R, Razeghi, M, Look, D, Gentle, A, Phillips, MR & Ton-That, C 2017, 'Author Correction: Radiative recombination of confined electrons at the MgZnO/ZnO heterojunction interface', Scientific Reports, vol. 7, no. 1, pp. 15912-15912.
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A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Choi, S, Rogers, DJ, Sandana, EV, Bove, P, Teherani, FH, Nenstiel, C, Hoffmann, A, McClintock, R, Razeghi, M, Look, D, Gentle, A, Phillips, MR & Ton-That, C 2017, 'Radiative recombination of confined electrons at the MgZnO/ZnO heterojunction interface', Scientific Reports, vol. 7, no. 1, pp. 1-7.
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AbstractWe investigate the optical signature of the interface in a single MgZnO/ZnO heterojunction, which exhibits two orders of magnitude lower resistivity and 10 times higher electron mobility compared with the MgZnO/Al2O3 film grown under the same conditions. These impressive transport properties are attributed to increased mobility of electrons at the MgZnO/ZnO heterojunction interface. Depth-resolved cathodoluminescence and photoluminescence studies reveal a 3.2 eV H-band optical emission from the heterointerface, which exhibits excitonic properties and a localization energy of 19.6 meV. The emission is attributed to band-bending due to the polarization discontinuity at the interface, which leads to formation of a triangular quantum well and localized excitons by electrostatic coupling.

Choi, T-Y, Lee, MS, Kim, JI & Zaslawski, C 2017, 'Moxibustion for the treatment of osteoarthritis: An updated systematic review and meta-analysis', Maturitas, vol. 100, pp. 33-48.
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The aim of this study was to update previous reviews and examine recent evidence from randomised clinical trials (RCTs) of the use of moxibustion for osteoarthritis (OA). Twelve databases were searched from inception through to September 2016 with no language limits applied. Data extraction and risk-of-bias assessments were performed by two independent reviewers. A total of 19 RCTs met all inclusion criteria and were evaluated. Three RCTs compared the effects of moxibustion with those of sham moxibustion in patients with knee OA (KOA) and found favourable effects of moxibustion on pain reduction (n=305; SMD, -0.46; 95% CI: -0.86 to -0.06, P=0.02, I2=65%), including at follow-up (n=305; SMD, -0.36; 95% CI: -0.70 to -0.01, P=0.04, I2=54%). Eleven RCTs compared the effects of moxibustion with those of conventional oral drug therapies. Eight RCTs reported a total symptom score and the meta-analysis showed superior effects of moxibustion compared with drug therapies for this measure (n=691; SMD, -0.24; 95% CI: -0.78 to 0.29; P=0.37, I2=91%) and response rate (n=758 knees; RR, 1.10; 95% CI: 1.05-1.16, P <0.0001, I2=0%). Three RCTs found superior or equivalent effects of moxibustion on symptom score compared with intra-articular injection or topical drug therapy. The existing trial evidence is sufficiently convincing to suggest that moxibustion, compared with sham moxibustion and oral drugs, is effective for pain reduction and symptom management in KOA. The level of evidence is moderate, given the high risk of bias and small sample size.

Chotirmall, SH, Gellatly, SL, Budden, KF, Mac Aogáin, M, Shukla, SD, Wood, DLA, Hugenholtz, P, Pethe, K & Hansbro, PM 2017, 'Microbiomes in respiratory health and disease: An Asia‐Pacific perspective', Respirology, vol. 22, no. 2, pp. 240-250.
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ABSTRACTThere is currently enormous interest in studying the role of the microbiome in health and disease. Microbiome's role is increasingly being applied to respiratory diseases, in particular COPD, asthma, cystic fibrosis and bronchiectasis. The changes in respiratory microbiomes that occur in these diseases and how they are modified by environmental challenges such as cigarette smoke, air pollution and infection are being elucidated. There is also emerging evidence that gut microbiomes play a role in lung diseases through the modulation of systemic immune responses and can be modified by diet and antibiotic treatment. There are issues that are particular to the Asia‐Pacific region involving diet and prevalence of specific respiratory diseases. Each of these issues is further complicated by the effects of ageing. The challenges now are to elucidate the cause and effect relationships between changes in microbiomes and respiratory diseases and how to translate these into new treatments and clinical care. Here we review the current understanding and progression in these areas.

Chung, H-P, Huang, K-H, Wang, K, Yang, S-L, Yang, S-Y, Sung, C-I, Solntsev, AS, Sukhorukov, AA, Neshev, DN & Chen, Y-H 2017, 'Asymmetric adiabatic couplers for fully-integrated broadband quantum-polarization state preparation', Scientific Reports, vol. 7, no. 1, pp. 1-7.
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AbstractSpontaneous parametric down-conversion (SPDC) is a widely used method to generate entangled photons, enabling a range of applications from secure communication to tests of quantum physics. Integrating SPDC on a chip provides interferometric stability, allows to reduce a physical footprint, and opens a pathway to true scalability. However, dealing with different photon polarizations and wavelengths on a chip presents a number of challenging problems. In this work, we demonstrate an on-chip polarization beam-splitter based on z-cut titanium-diffused lithium niobate asymmetric adiabatic couplers (AAC) designed for integration with a type-II SPDC source. Our experimental measurements reveal unique polarization beam-splitting regime with the ability to tune the splitting ratios based on wavelength. In particular, we measured a splitting ratio of 17 dB over broadband regions (>60 nm) for both H- and V-polarized lights and a specific 50%/50% splitting ratio for a cross-polarized photon pair from the AAC. The results show that such a system can be used for preparing different quantum polarization-path states that are controllable by changing the phase-matching conditions in the SPDC over a broad band. Furthermore, we propose a fully integrated electro-optically tunable type-II SPDC polarization-path-entangled state preparation circuit on a single lithium niobate photonic chip.

Ciobanu, L, Elder, M & Ferov, M 2017, 'Applications of L systems to group theory', International Journal of Algebra and Computation, vol. 28, no. 2, pp. 309-329.
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L systems generalise context-free grammars by incorporating parallelrewriting, and generate languages such as EDT0L and ET0L that are strictlycontained in the class of indexed languages. In this paper we show that many ofthe languages naturally appearing in group theory, and that were known to beindexed or context-sensitive, are in fact ET0L and in many cases EDT0L. Forinstance, the language of primitives in the free group on two generators, theBridson-Gilman normal forms for the fundamental groups of 3-manifolds ororbifolds, and the co-word problem of Grigorchuk's group can be generated by Lsystems. To complement the result on primitives in free groups, we show thatthe language of primitives, and primitive sets, in free groups of rank higherthan two is context-sensitive. We also show the existence of EDT0L and ET0Llanguages of intermediate growth.

Cole, AJ, Zhu, Y, Dwight, T, Yu, B, Dickson, K-A, Gard, GB, Maidens, J, Valmadre, S, Gill, AJ, Clifton-Bligh, R & Marsh, DJ 2017, 'Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency', Scientific Data, vol. 4, no. 1, pp. 170120-170120.
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AbstractSomatic mutation of the tumor suppressor gene TP53 is reported in at least 50% of human malignancies. Most high-grade serous ovarian cancers (HGSC) have a mutant TP53 allele. Accurate detection of these mutants in heterogeneous tumor tissue is paramount as therapies emerge to target mutant p53. We used a Fluidigm Access Array™ System with Massively Parallel Sequencing (MPS) to analyze DNA extracted from 76 serous ovarian tumors. This dataset has been made available to researchers through the European Genome-phenome Archive (EGA; EGAS00001002200). Herein, we present analyses of this dataset using HaplotypeCaller and MuTect2 through the Broad Institute’s Genome Analysis Toolkit (GATK). We anticipate that this TP53 mutation dataset will be useful to researchers developing and testing new software to accurately determine high and low frequency variant alleles in heterogeneous aneuploid tumor tissue. Furthermore, the analysis pipeline we present provides a valuable framework for determining somatic variants more broadly in tumor tissue.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Ajith, P, Allen, B, Allen, G, Allocca, A, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Angelova, SV, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Atallah, DV, Aufmuth, P, Aulbert, C, AultONeal, K, Austin, C, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barkett, K, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Barthelmy, SD, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Bawaj, M, Bayley, JC, Bazzan, M, B'ecsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Bero, JJ, Berry, CPL, Bersanetti, D, Bertolini, A, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Biscoveanu, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonilla, E, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bossie, K, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canepa, M, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, a, MC, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Cerd'a-Dur'an, P, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chase, E, Chassande-Mottin, E, Chatterjee, D, Chatziioannou, K, Cheeseboro, BD, Chen, HY, Chen, X, Chen, Y, Cheng, H-P, Chia, H, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S & et al. 2017, 'GW170814: A Three-Detector Observation of Gravitational Waves from a Binary Black Hole Coalescence', Phys. Rev. Lett., vol. 119, p. 141101.
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On August 14, 2017 at 10:30:43 UTC, the Advanced Virgo detector and the twoAdvanced LIGO detectors coherently observed a transient gravitational-wavesignal produced by the coalescence of two stellar mass black holes, with afalse-alarm-rate of $\lesssim$ 1 in 27000 years. The signal was observed with athree-detector network matched-filter signal-to-noise ratio of 18. The inferredmasses of the initial black holes are $30.5_{-3.0}^{+5.7}$ Msun and$25.3_{-4.2}^{+2.8}$ Msun (at the 90% credible level). The luminosity distanceof the source is $540_{-210}^{+130}~\mathrm{Mpc}$, corresponding to a redshiftof $z=0.11_{-0.04}^{+0.03}$. A network of three detectors improves the skylocalization of the source, reducing the area of the 90% credible region from1160 deg$^2$ using only the two LIGO detectors to 60 deg$^2$ using all threedetectors. For the first time, we can test the nature of gravitational wavepolarizations from the antenna response of the LIGO-Virgo network, thusenabling a new class of phenomenological tests of gravity.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Ajith, P, Allen, B, Allen, G, Allocca, A, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Aufmuth, P, Aulbert, C, AultONeal, K, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Baune, C, Bawaj, M, Bazzan, M, B'ecsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Berry, CPL, Bersanetti, D, Bertolini, A, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Braginsky, VB, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brown, NM, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canepa, M, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, a, MC, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Baiardi, LC, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chassande-Mottin, E, Chatterjee, D, Chatziioannou, K, Cheeseboro, BD, Chen, HY, Chen, Y, Cheng, H-P, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S, Ciani, G, Ciolfi, R, Cirelli, CE, Cirone, A, Clara, F, Clark, JA, Cleva, F, Cocchieri, C, Coccia, E, Cohadon, P-F, Colla, A & et al. 2017, 'Upper Limits on Gravitational Waves from Scorpius X-1 from a Model-Based Cross-Correlation Search in Advanced LIGO Data', The Astrophysical Journal, 847:47 (14pp), 2017 September 20.
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We present the results of a semicoherent search for continuous gravitationalwaves from the low-mass X-ray binary Scorpius X-1, using data from the firstAdvanced LIGO observing run. The search method uses details of the modelled,parametrized continuous signal to combine coherently data separated by lessthan a specified coherence time, which can be adjusted to trade off sensitivityagainst computational cost. A search was conducted over the frequency rangefrom 25 Hz to 2000 Hz, spanning the current observationally-constrained rangeof the binary orbital parameters. No significant detection candidates werefound, and frequency-dependent upper limits were set using a combination ofsensitivity estimates and simulated signal injections. The most stringent upperlimit was set at 175 Hz, with comparable limits set across the most sensitivefrequency range from 100 Hz to 200 Hz. At this frequency, the 95 pct upperlimit on signal amplitude h0 is 2.3e-25 marginalized over the unknowninclination angle of the neutron star's spin, and 8.03e-26 assuming the bestorientation (which results in circularly polarized gravitational waves). Theselimits are a factor of 3-4 stronger than those set by other analyses of thesame data, and a factor of about 7 stronger than the best upper limits setusing initial LIGO data. In the vicinity of 100 Hz, the limits are a factor ofbetween 1.2 and 3.5 above the predictions of the torque balance model,depending on inclination angle, if the most likely inclination angle of 44degrees is assumed, they are within a factor of 1.7.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Ajith, P, Allen, B, Allen, G, Allocca, A, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Aufmuth, P, Aulbert, C, AultONeal, K, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Baune, C, Bawaj, M, Bazzan, M, B'ecsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Berry, CPL, Bersanetti, D, Bertolini, A, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Braginsky, VB, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brown, NM, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canepa, M, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, a, MC, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Baiardi, LC, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chassande-Mottin, E, Chatterjee, D, Cheeseboro, BD, Chen, HY, Chen, Y, Cheng, H-P, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S, Ciani, G, Ciolfi, R, Cirelli, CE, Cirone, A, Clara, F, Clark, JA, Cleva, F, Cocchieri, C, Coccia, E, Cohadon, P-F, Colla, A, Collette, CG & et al. 2017, 'Constraints on cosmic strings using data from the first Advanced LIGO observing run', Phys. Rev. D, vol. 97, p. 102002.
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Cosmic strings are topological defects which can be formed in GUT-scale phasetransitions in the early universe. They are also predicted to form in thecontext of string theory. The main mechanism for a network of Nambu-Goto cosmicstrings to lose energy is through the production of loops and the subsequentemission of gravitational waves, thus offering an experimental signature forthe existence of cosmic strings. Here we report on the analysis conducted tospecifically search for gravitational-wave bursts from cosmic string loops inthe data of Advanced LIGO 2015-2016 observing run (O1). No evidence of suchsignals was found in the data, and as a result we set upper limits on thecosmic string parameters for three recent loop distribution models. In thispaper, we initially derive constraints on the string tension $G\mu$ and theintercommutation probability, using not only the burst analysis performed onthe O1 data set, but also results from the previously published LIGO stochasticO1 analysis, pulsar timing arrays, cosmic microwave background and Big-Bangnucleosynthesis experiments. We show that these data sets are complementary inthat they probe gravitational waves produced by cosmic string loops during verydifferent epochs. Finally, we show that the data sets exclude large parts ofthe parameter space of the three loop distribution models we consider.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Ajith, P, Allen, B, Allen, G, Allocca, A, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Aufmuth, P, Aulbert, C, AultONeal, K, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Baune, C, Bawaj, M, Bazzan, M, Bécsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Berry, CPL, Bersanetti, D, Bertolini, A, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Braginsky, VB, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brown, NM, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canepa, M, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, Cavaglià, M, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Baiardi, LC, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chassande-Mottin, E, Chatterjee, D, Chatziioannou, K, Cheeseboro, BD, Chen, HY, Chen, Y, Cheng, H-P, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S, Ciani, G, Ciolfi, R, Cirelli, CE, Cirone, A, Clara, F, Clark, JA, Cleva, F, Cocchieri, C, Coccia, E, Cohadon, P-F & et al. 2017, 'GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2', Phys. Rev. Lett., 118(22):221101, 2017.
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We describe the observation of GW170104, a gravitational-wave signal producedby the coalescence of a pair of stellar-mass black holes. The signal wasmeasured on January 4, 2017 at 10:11:58.6 UTC by the twin advanced detectors ofthe Laser Interferometer Gravitational-Wave Observatory during their secondobserving run, with a network signal-to-noise ratio of 13 and a false alarmrate less than 1 in 70,000 years. The inferred component black hole masses are$31.2^{+8.4}_{-6.0}\,M_\odot$ and $19.4^{+5.3}_{-5.9}\,M_\odot$ (at the 90%credible level). The black hole spins are best constrained through measurementof the effective inspiral spin parameter, a mass-weighted combination of thespin components perpendicular to the orbital plane, $\chi_\mathrm{eff} =-0.12^{+0.21}_{-0.30}.$ This result implies that spin configurations with bothcomponent spins positively aligned with the orbital angular momentum aredisfavored. The source luminosity distance is $880^{+450}_{-390}~\mathrm{Mpc}$corresponding to a redshift of $z = 0.18^{+0.08}_{-0.07}$. We constrain themagnitude of modifications to the gravitational-wave dispersion relation andperform null tests of general relativity. Assuming that gravitons are dispersedin vacuum like massive particles, we bound the graviton mass to $m_g \le 7.7\times 10^{-23}~\mathrm{eV}/c^2$. In all cases, we find that GW170104 isconsistent with general relativity.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Allen, B, Allen, G, Allocca, A, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Angelova, SV, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Atallah, DV, Aufmuth, P, Aulbert, C, AultONeal, K, Austin, C, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barkett, K, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Bawaj, M, Bayley, JC, Bazzan, M, Bécsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Bero, JJ, Berry, CPL, Bersanetti, D, Bertolini, A, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Biscoveanu, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonilla, E, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bossie, K, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, Cavaglià, M, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Cerd'a-Dur'an, P, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chase, E, Chassande-Mottin, E, Chatterjee, D, Cheeseboro, BD, Chen, HY, Chen, X, Chen, Y, Cheng, H-P, Chia, H, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S, Ciani, G, Ciolfi, R, Cirelli, CE, Cirone, A, Clara, F & et al. 2017, 'First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data', Phys. Rev. D, vol. 96, p. 122006.
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Spinning neutron stars asymmetric with respect to their rotation axis arepotential sources of continuous gravitational waves for ground-basedinterferometric detectors. In the case of known pulsars a fully coherentsearch, based on matched filtering, which uses the position and rotationalparameters obtained from electromagnetic observations, can be carried out.Matched filtering maximizes the signal-to-noise (SNR) ratio, but a largesensitivity loss is expected in case of even a very small mismatch between theassumed and the true signal parameters. For this reason, {\it narrow-band}analyses methods have been developed, allowing a fully coherent search forgravitational waves from known pulsars over a fraction of a hertz and severalspin-down values. In this paper we describe a narrow-band search of elevenpulsars using data from Advanced LIGO's first observing run. Although we havefound several initial outliers, further studies show no significant evidencefor the presence of a gravitational wave signal. Finally, we have placed upperlimits on the signal strain amplitude lower than the spin-down limit for 5 ofthe 11 targets over the bands searched: in the case of J1813-1749 the spin-downlimit has been beaten for the first time. For an additional 3 targets, themedian upper limit across the search bands is below the spin-down limit. Thisis the most sensitive narrow-band search for continuous gravitational wavescarried out so far.

Collaboration, TLIGOS, Collaboration, TV, Abbott, BP, Abbott, R, Abbott, TD, Acernese, F, Ackley, K, Adams, C, Adams, T, Addesso, P, Adhikari, RX, Adya, VB, Affeldt, C, Afrough, M, Agarwal, B, Agatsuma, K, Aggarwal, N, Aguiar, OD, Aiello, L, Ain, A, Ajith, P, Allen, B, Allen, G, Allocca, A, Almoubayyed, H, Altin, PA, Amato, A, Ananyeva, A, Anderson, SB, Anderson, WG, Antier, S, Appert, S, Arai, K, Araya, MC, Areeda, JS, Arnaud, N, Arun, KG, Ascenzi, S, Ashton, G, Ast, M, Aston, SM, Astone, P, Aufmuth, P, Aulbert, C, AultONeal, K, Avila-Alvarez, A, Babak, S, Bacon, P, Bader, MKM, Bae, S, Baker, PT, Baldaccini, F, Ballardin, G, Ballmer, SW, Banagiri, S, Barayoga, JC, Barclay, SE, Barish, BC, Barker, D, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Bartos, I, Bassiri, R, Basti, A, Batch, JC, Baune, C, Bawaj, M, Bazzan, M, B'ecsy, B, Beer, C, Bejger, M, Belahcene, I, Bell, AS, Berger, BK, Bergmann, G, Berry, CPL, Bersanetti, D, Bertolini, A, Etienne, ZB, Betzwieser, J, Bhagwat, S, Bhandare, R, Bilenko, IA, Billingsley, G, Billman, CR, Birch, J, Birney, R, Birnholtz, O, Biscans, S, Bisht, A, Bitossi, M, Biwer, C, Bizouard, MA, Blackburn, JK, Blackman, J, Blair, CD, Blair, DG, Blair, RM, Bloemen, S, Bock, O, Bode, N, Boer, M, Bogaert, G, Bohe, A, Bondu, F, Bonnand, R, Boom, BA, Bork, R, Boschi, V, Bose, S, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, PR, Braginsky, VB, Branchesi, M, Brau, JE, Briant, T, Brillet, A, Brinkmann, M, Brisson, V, Brockill, P, Broida, JE, Brooks, AF, Brown, DA, Brown, DD, Brown, NM, Brunett, S, Buchanan, CC, Buikema, A, Bulik, T, Bulten, HJ, Buonanno, A, Buskulic, D, Buy, C, Byer, RL, Cabero, M, Cadonati, L, Cagnoli, G, Cahillane, C, Bustillo, JC, Callister, TA, Calloni, E, Camp, JB, Canepa, M, Canizares, P, Cannon, KC, Cao, H, Cao, J, Capano, CD, Capocasa, E, Carbognani, F, Caride, S, Carney, MF, Diaz, JC, Casentini, C, Caudill, S, a, MC, Cavalier, F, Cavalieri, R, Cella, G, Cepeda, CB, Baiardi, LC, Cerretani, G, Cesarini, E, Chamberlin, SJ, Chan, M, Chao, S, Charlton, P, Chassande-Mottin, E, Chatterjee, D, Cheeseboro, BD, Chen, HY, Chen, Y, Cheng, H-P, Chincarini, A, Chiummo, A, Chmiel, T, Cho, HS, Cho, M, Chow, JH, Christensen, N, Chu, Q, Chua, AJK, Chua, S, Chung, AKW, Chung, S, Ciani, G, Ciolfi, R, Cirelli, CE, Cirone, A, Clara, F, Clark, JA, Cleva, F, Cocchieri, C, Coccia, E, Cohadon, P-F, Colla, A & et al. 2017, 'Search for gravitational waves from Scorpius X-1 in the first Advanced LIGO observing run with a hidden Markov model', Phys. Rev. D, vol. 95, p. 122003.
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Results are presented from a semi-coherent search for continuousgravitational waves from the brightest low-mass X-ray binary, Scorpius X-1,using data collected during the first Advanced LIGO observing run (O1). Thesearch combines a frequency domain matched filter (Bessel-weighted$\mathcal{F}$-statistic) with a hidden Markov model to track wandering of theneutron star spin frequency. No evidence of gravitational waves is found in thefrequency range 60-650 Hz. Frequentist 95% confidence strain upper limits,$h_0^{95\%} = 4.0\times10^{-25}$, $8.3\times10^{-25}$, and $3.0\times10^{-25}$for electromagnetically restricted source orientation, unknown polarization,and circular polarization, respectively, are reported at 106 Hz. They are $\leq10$ times higher than the theoretical torque-balance limit at 106 Hz.

Colusso, AC, Cortie, MB, Dowd, A & McDonagh, AM 2017, 'Thermal stability of mesoscopic compounds of cetyltrimethylammonium and Keggin metatungstates', Dalton Transactions, vol. 46, no. 33, pp. 11053-11062.
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A hybrid surfactant/polyoxometalate compound was synthesized by combining isopolytungstate anions with the cationic surfactant cetyltrimethylammonium bromide (CTA-Br) to produce a hierarchical compound that we identify as (CTA)₇[H₂W₁₂O₄₀]Cl·2H₂O.

Comas, M, Gordon, CJ, Oliver, BG, Stow, NW, King, G, Sharma, P, Ammit, AJ, Grunstein, RR & Phillips, CL 2017, 'A circadian based inflammatory response – implications for respiratory disease and treatment', Sleep Science and Practice, vol. 1, no. 1, pp. 1-19.
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Circadian clocks regulate the daily timing of many of our physiological, metabolic and biochemical functions. The immune system also displays circadian oscillations in immune cell count, synthesis and cytokine release, clock gene expression in cells and organs of the immune system as well as clock-controlled genes that regulate immune function. Circadian disruption leads to dysregulation of immune responses and inflammation which can further disrupt circadian rhythms. The response of organisms to immune challenges, such as allergic reactions also vary depending on time of the day, which can lead to detrimental responses particularly during the rest and early active periods. This review evaluates what is currently known in terms of circadian biology of immune response and the cross-talk between circadian and immune system. We discuss the circadian pattern of three respiratory-related inflammatory diseases, chronic obstructive pulmonary disease, allergic rhinitis and asthma. Increasing our knowledge on circadian patterns of immune responses and developing chronotherapeutic studies in inflammatory diseases with strong circadian patterns will lead to preventive measures as well as improved therapies focussing on the circadian rhythms of symptoms and the daily variation of the patients’ responses to medication.

Commault, AS, Laczka, O, Siboni, N, Tamburic, B, Crosswell, JR, Seymour, JR & Ralph, PJ 2017, 'Electricity and biomass production in a bacteria- Chlorella based microbial fuel cell treating wastewater', Journal of Power Sources, vol. 356, pp. 299-309.
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© 2017 Elsevier B.V. The chlorophyte microalga Chlorella vulgaris has been exploited within bioindustrial settings to treat wastewater and produce oxygen at the cathode of microbial fuel cells (MFCs), thereby accumulating algal biomass and producing electricity. We aimed to couple these capacities by growing C. vulgaris at the cathode of MFCs in wastewater previously treated by anodic bacteria. The bioelectrochemical performance of the MFCs was investigated with different catholytes including phosphate buffer and anode effluent, either in the presence or absence of C. vulgaris. The power output fluctuated diurnally in the presence of the alga. The maximum power when C. vulgaris was present reached 34.2 ± 10.0 mW m −2 , double that observed without the alga (15.6 ± 9.7 mW m −2 ), with a relaxation of 0.19 gL −1  d −1 chemical oxygen demand and 5 mg L −1  d −1 ammonium also removed. The microbial community associated with the algal biofilm included nitrogen-fixing (Rhizobiaceae), denitrifying (Pseudomonas stutzeri and Thauera sp., from Pseudomonadales and Rhodocyclales orders, respectively), and nitrate-reducing bacteria (Rheinheimera sp. from the Alteromonadales), all of which likely contributed to nitrogen cycling processes at the cathode. This paper highlights the importance of coupling microbial community screening to electrochemical and chemical analyses to better understand the processes involved in photo-cathode MFCs.

Conickx, G, Avila Cobos, F, van den Berge, M, Faiz, A, Timens, W, Hiemstra, PS, Joos, GF, Brusselle, GG, Mestdagh, P & Bracke, KR 2017, 'microRNA profiling in lung tissue and bronchoalveolar lavage of cigarette smoke-exposed mice and in COPD patients: a translational approach', Scientific Reports, vol. 7, no. 1.
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AbstractChronic obstructive pulmonary disease (COPD) is characterized by a progressive airflow limitation and is associated with a chronic inflammatory response in both airways and lungs. microRNAs (miRNAs) are often highly conserved between species and have an intricate role within homeostatic conditions and immune responses. Also, miRNAs are dysregulated in smoking-associated diseases. We investigated the miRNA profile of 523 miRNAs by stem-loop RT-qPCR in lung tissue and cell-free bronchoalveolar lavage (BAL) supernatant of mice exposed to air or cigarette smoke (CS) for 4 or 24 weeks. After 24 weeks of CS exposure, 31 miRNAs were differentially expressed in lung tissue and 78 in BAL supernatant. Next, we correlated the miRNA profiling data to inflammation in BAL and lung, obtained by flow cytometry or ELISA. In addition, we surveyed for overlap with newly assessed miRNA profiles in bronchial biopsies and with previously assessed miRNA profiles in lung tissue and induced sputum supernatant of smokers with COPD. Several miRNAs showed concordant differential expression between both species including miR-31*, miR-155, miR-218 and let-7c. Thus, investigating miRNA profiling data in different compartments and both species provided accumulating insights in miRNAs that may be relevant in CS-induced inflammation and the pathogenesis of COPD.

Conickx, G, Mestdagh, P, Avila Cobos, F, Verhamme, FM, Maes, T, Vanaudenaerde, BM, Seys, LJM, Lahousse, L, Kim, RY, Hsu, AC, Wark, PA, Hansbro, PM, Joos, GF, Vandesompele, J, Bracke, KR & Brusselle, GG 2017, 'MicroRNA Profiling Reveals a Role for MicroRNA-218-5p in the Pathogenesis of Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 195, no. 1, pp. 43-56.
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Rationale: Aberrant expression of microRNAs (miRNAs) can have a detrimental role in disease pathogenesis. Objectives: To identify dysregulated miRNAs in lung tissue of patients with chronic obstructive pulmonary disease (COPD). Methods: We performed miRNA and mRNA profiling using high throughput stem-loop reverse-transcriptase quantitative polymerase chain reaction and mRNA microarray, respectively, on lung tissue of 30 patients (screening cohort) encompassing 8 never-smokers, 10 smokers without airflow limitation, and 12 smokers with COPD. Differential expression of miRNA-218-5p (miR-218-5p) was validated by reverse-transcriptase quantitative polymerase chain reaction in an independent cohort of 71 patients, an in vivo murine model of COPD, and primary human bronchial epithelial cells. Localization of miR-218-5p was assessed by in situ hybridization. In vitro and in vivo perturbation of miR-218-5p combined with RNA sequencing and gene set enrichment analysis was used to elucidate its functional role in COPD pathogenesis. Measurements and Main Results: Several miRNAs were differentially expressed among the different patient groups. Interestingly, miR-218-5p was significantly down-regulated in smokers without airflow limitation and in patients with COPD compared with never-smokers. Decreased pulmonary expression of miR-218-5p was validated in an independent validation cohort, in cigarette smoke-exposed mice, and in human bronchial epithelial cells. Importantly, expression of miR-218-5p strongly correlated with airway obstruction. Furthermore, cellular localization of miR-218-5p in human and murine lung revealed highest expression of miR-218-5p in the bronchial airway epithelium. Perturbation experiments with a miR-218-5p mimic or inhibitor demonstrated a protective role of miR-218-5p in cigarette smoke-induced inflammation and COPD. Conclusions: We highlight a role for miR-218-5p in the pathogenesis of COPD.

Cook, AR, Leslie, LM, Parsons, DB & Schaefer, JT 2017, 'The Impact of El Niño–Southern Oscillation (ENSO) on Winter and Early Spring U.S. Tornado Outbreaks', Journal of Applied Meteorology and Climatology, vol. 56, no. 9, pp. 2455-2478.
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AbstractIn recent years, the potential of seasonal outlooks for tornadoes has attracted the attention of researchers. Previous studies on this topic have focused mainly on the influence of global circulation patterns [e.g., El Niño–Southern Oscillation (ENSO), North Atlantic Oscillation, or Pacific decadal oscillation] on spring tornadoes. However, these studies have yielded conflicting results of the roles of these climate drivers on tornado intensity and frequency. The present study seeks to establish linkages between ENSO and tornado outbreaks over the United States during winter and early spring. These linkages are established in two ways: 1) statistically, by relating raw counts of tornadoes in outbreaks (defined as six or more tornadoes in a 24-h period in the United States east of the Rocky Mountains), and their destructive potential, to sea surface temperature anomalies observed in the Niño-3.4 region, and 2) qualitatively, by relating ENSO to shifts in synoptic-scale atmospheric phenomena that contribute to tornado outbreaks. The latter approach is critical for interpreting the statistical relationships, thereby avoiding the deficiencies in a few of the previous studies that did not provide physical explanations relating ENSO to shifts in tornado activity. The results suggest that shifts in tornado occurrence are clearly related to ENSO. In particular, La Niña conditions consistently foster more frequent and intense tornado activity in comparison with El Niño, particularly at higher latitudes. Furthermore, it is found that tornado activity changes are tied not only to the location and intensity of the subtropical jet during individual outbreaks but also to the positions of surface cyclones, low-level jet streams, and instability axes.

Cook, SJ, Blas, B, Carroll, RJ & Sinha, S 2017, 'Two Wrongs Make a Right: Addressing Underreporting in Binary Data from Multiple Sources', Political Analysis, vol. 25, no. 2, pp. 223-240.
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Media-based event data—i.e., data comprised from reporting by media outlets—are widely used in political science research. However, events of interest (e.g., strikes, protests, conflict) are often underreported by these primary and secondary sources, producing incomplete data that risks inconsistency and bias in subsequent analysis. While general strategies exist to help ameliorate this bias, these methods do not make full use of the information often available to researchers. Specifically, much of the event data used in the social sciences is drawn from multiple, overlapping news sources (e.g., Agence France-Presse, Reuters). Therefore, we propose a novel maximum likelihood estimator that corrects for misclassification in data arising from multiple sources. In the most general formulation of our estimator, researchers can specify separate sets of predictors for the true-event model and each of the misclassification models characterizing whether a source fails to report on an event. As such, researchers are able to accurately test theories on both the causes of and reporting on an event of interest. Simulations evidence that our technique regularly outperforms current strategies that either neglect misclassification, the unique features of the data-generating process, or both. We also illustrate the utility of this method with a model of repression using the Social Conflict in Africa Database.

Cooper, ER, McGrath, KCY, Li, X, Akram, O, Kasz, R, Kazlauskas, R, McLeod, MD, Handelsman, DJ & Heather, AK 2017, 'The use of tandem yeast and mammalian cell in vitro androgen bioassays to detect androgens in internet‐sourced sport supplements', Drug Testing and Analysis, vol. 9, no. 4, pp. 545-552.
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Sport supplements containing steroids never approved for therapeutic use have the potential for abuse by athletes. Most are marketed online and may contain undisclosed steroids yet are readily available despite lacking toxicological or pharmacological evaluation. In this study, 18 supplements purchased online underwent organic solvent extraction to isolate any steroids they contained. From the 18 supplements, 19 steroids were identified and for each, its intrinsic androgenic potency was determined by a yeast cell (Saccharomyces cerevisiae) androgen bioassay and its potential androgenic potency was determined by a liver (HuH7) cell androgen bioassay. The yeast bioassay showed that of the 19 steroids tested, 6 demonstrated strong intrinsic bioactivity, with 4 metabolically activated to even stronger androgens. Moreover, 4 steroids with moderate and 1 with intrinsically weak androgenic bioactivity were activated to more potent androgens. Finally, 8 steroids were metabolically inactivated or deactivated into weaker androgens. Our results show that Internet‐sourced sport supplements may contain intrinsically strong androgens, or precursors that can be metabolized to them. These potentially potent pharmacologically active steroids are being used without regulatory control or consumer awareness of their potential adverse effects. Copyright © 2016 John Wiley & Sons, Ltd.

Corporal-Lodangco, IL & Leslie, LM 2017, 'Defining Philippine Climate Zones Using Surface and High-Resolution Satellite Data', Procedia Computer Science, vol. 114, pp. 324-332.
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Corporal‐Lodangco, IL & Leslie, LM 2017, 'Climatology of Philippine tropical cyclone activity: 1945–2011', International Journal of Climatology, vol. 37, no. 9, pp. 3525-3539.
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ABSTRACTThe Philippine region occupies the southwestern western North Pacific (WNP) Ocean, between 5°–25°N and 115°–135°E. About 70% of WNP tropical cyclones (TCs) formed in or entered the Philippine region during 1945–2011. Here, a climatology of Philippine TC metrics is developed, including mean annual frequencies, landfalls, TC days, season lengths, season earliest and latest start and end dates, genesis locations, and tracks. Two distinct TC seasons, the less active season (LAS; 1 January–31 May) and more active season (MAS; 1 June–31 December), are evident. Philippine TC annual median LAS frequency is 2 [interquartile range (IQR) is 2], and median landfalling frequency is 1. The annual median MAS frequency is 15 (IQR is 4.5), and median landfalling frequency is 6. About 55% of Philippine TCs reach typhoon intensity. A quiescent (TC‐free) period occurs between LAS and MAS, ranging fr...

Craddock, M 2017, 'Fundamental solutions for the two dimensional affine group and Hn+1', Journal of Mathematical Analysis and Applications, vol. 445, no. 1, pp. 953-970.
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© 2016 Elsevier Inc. We derive the wave and heat kernels on the ax+b group, as well as the fundamental solution of the group Laplacian. We make particular use of the Kontorovich–Lebedev transform and a recent result of the author to produce new expressions for these kernels. Our results easily extend to the hyperbolic space H n+1 for any n and the explicit formulas are given in n dimensions.

Craddock, M & Yakubovich, S 2017, 'New classes of non-convolution integral equations arising from Lie symmetry analysis of hyperbolic PDEs', Journal of Differential Equations, vol. 263, no. 11, pp. 7412-7447.
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© 2017 Elsevier Inc. In this paper we consider some new classes of integral equations that arise from Lie symmetry analysis. Specifically, we consider the task of obtaining solutions of a Cauchy problem for some classes of second order hyperbolic partial differential equations. Our analysis leads to new integral equations of non-convolution type, which can be solved by classical methods. We derive solutions of these integral equations, which in turn lead to solutions of the associated Cauchy problems.

Cranfield, CG, Henriques, ST, Martinac, B, Duckworth, P, Craik, DJ & Cornell, B 2017, 'Kalata B1 and Kalata B2 Have a Surfactant-Like Activity in Phosphatidylethanolomine-Containing Lipid Membranes', Langmuir, vol. 33, no. 26, pp. 6630-6637.
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© 2017 American Chemical Society. Cyclotides are cyclic disulfide-rich peptides that are chemically and thermally stable and possess pharmaceutical and insecticidal properties. The activities reported for cyclotides correlate with their ability to target phosphatidylethanolamine (PE)-phospholipids and disrupt cell membranes. However, the mechanism by which this disruption occurs remains unclear. In the current study we examine the effect of the prototypic cyclotides, kalata B1 (kB1) and kalata B2 (kB2), on tethered lipid bilayer membranes (tBLMs) using swept frequency electrical impedance spectroscopy. We confirmed that kB1 and kB2 bind to bilayers only if they contain PE-phospholipids. We hypothesize that the increase in membrane conduction and capacitance observed upon addition of kB1 or kB2 is unlikely to result from ion channel like pores but is consistent with the formation of lipidic toroidal pores. This hypothesis is supported by the concentration dependence of effects of kB1 and kB2 being suggestive of a critical micelle concentration event rather than a progressive increase in conduction arising from increased channel insertion. Additionally, conduction behavior is readily reversible when the peptide is rinsed from the bilayer. Our results support a mechanism by which kB1 and kB2 bind to and disrupt PE-containing membranes by decreasing the overall membrane critical packing parameter, as would a surfactant, which then opens or increases the size of existing membrane defects. The cyclotides need not participate directly in the conductive pore but might exert their effect indirectly through altering membrane packing constraints and inducing purely lipidic conductive pores.

Cullen, A, Muller, AJ & Williams, DBG 2017, 'Protecting group-free use of alcohols as carbon electrophiles in atom efficient aluminium triflate-catalysed dehydrative nucleophilic displacement reactions', RSC Advances, vol. 7, no. 67, pp. 42168-42171.
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Catalysed dehydrative nucleophilic displacement of OH groups affords high yields and 100% atom efficiency, with water as by-product.

Czibula, O, Gu, H, Russell, A & Zinder, Y 2017, 'A multi-stage IP-based heuristic for class timetabling and trainer rostering', Annals of Operations Research, vol. 252, no. 2, pp. 305-333.
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© 2015 Springer Science+Business Media New York We consider a timetabling and rostering problem involving periodic retraining of large numbers of employees at an Australian electricity distributor. This problem is different from traditional high school and university timetabling problems studied in the literature in several aspects. We propose a three-stage heuristic consisting of timetable generation, timetable improvement, and trainer rostering. Large-scale integer linear programming models for both the timetabling and the rostering components are proposed, and several unique operational constraints are discussed. We show that this solution approach is able to produce good solutions in practically acceptable time.

Dahlan, NA, Veeramachineni, AK, Langford, SJ & Pushpamalar, J 2017, 'Developing of a magnetite film of carboxymethyl cellulose grafted carboxymethyl polyvinyl alcohol (CMC- g -CMPVA) for copper removal', Carbohydrate Polymers, vol. 173, pp. 619-630.
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Daulatabad, D, Sonthalia, S, Srivastava, A, Bhattacharya, SN, Kaul, S & Moyal, D 2017, 'Folie a deux and delusional disorder by proxy: an atypical presentation', Australasian Journal of Dermatology, vol. 58, no. 3.
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AbstractDelusion of parasitosis is a rare condition characterised by an individual harbouring the delusion of being infested with insects or parasites. We report a rare and interesting case of delusion of parasitosis presenting as folie a deux, that is, the delusion is shared by both the parents of an 18‐month‐old child, with proxy projection of parental delusion on the child. The case highlights the rare concomitant occurrence of two psychocutaneous disorders and emphasizes the importance of early recognition and appropriate intervention to safeguard the well‐being of the child.

Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A & Richardson, AJ 2017, 'Erratum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters', Scientific Data, vol. 4, no. 1, pp. 1-1.
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Scientific Data 3:160043 doi:10.1038/sdata.2016.43 (2016); Published 21 Jun 2016; Updated 11 April 2017 The authors regret that Sarah A. Pausina was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions of this Data Descriptor, as well as the accompanying Corrigendum.

Dayananda, B, Murray, BR & Webb, JK 2017, 'Hotter nests produce hatchling lizards with lower thermal tolerance', Journal of Experimental Biology, vol. 220, no. 12, pp. 2159-2165.
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ABSTRACT In many regions, the frequency and duration of summer heatwaves is predicted to increase in future. Hotter summers could result in higher temperatures inside lizard nests, potentially exposing embryos to thermally stressful conditions during development. Potentially, developmentally plastic shifts in thermal tolerance could allow lizards to adapt to climate warming. To determine how higher nest temperatures affect the thermal tolerance of hatchling geckos, we incubated eggs of the rock-dwelling velvet gecko, Amalosia lesueurii, at two fluctuating temperature regimes to mimic current nest temperatures (mean 23.2°C, range 10–33°C, ‘cold’) and future nest temperatures (mean 27.0°C, range 14–37°C, ‘hot’). Hatchlings from the hot incubation group hatched 27 days earlier and had a lower critical thermal maximum (CTmax 38.7°C) and a higher critical thermal minimum (CTmin 6.2°C) than hatchlings from cold incubation group (40.2 and 5.7°C, respectively). In the field, hatchlings typically settle under rocks near communal nests. During the hatching period, rock temperatures ranged from 13 to 59°C, and regularly exceeded the CTmax of both hot- and cold-incubated hatchlings. Because rock temperatures were so high, the heat tolerance of lizards had little effect on their ability to exploit rocks as retreat sites. Instead, the timing of hatching dictated whether lizards could exploit rocks as retreat sites; that is, cold-incubated lizards that hatched later encountered less thermally stressful environments than earlier hatching hot-incubated lizards. In conclusion, we found no evidence that CTmax can shift upwards in response to higher incubation temperatures, suggesting that hotter summers may increase the vulnerability of lizards to climate warming.

De Silva, KSB, Keast, VJ, Gentle, A & Cortie, MB 2017, 'Optical properties and oxidation ofα-phase Ag–Al thin films', Nanotechnology, vol. 28, no. 9, pp. 095202-095202.
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© 2017 IOP Publishing Ltd. We investigate a series of Ag-Al thin films containing up to 12 at% Al with the purpose of discovering whether these alloys would be a better choice for nanophotonic applications than pure Ag. Variable angle spectroscopic ellipsometry, AFM, x-ray diffraction and density functional theory are applied to explore and characterize the materials. Electromagnetic simulations of optical properties are used to place the results into a theoretical framework. We find that the increase in electron-to-atom ratio associated with the Al additions changes the optical properties: additions of the order of 1-2 at% Al are beneficial as they are associated with favorable changes in the dielectric function, but for greater additions of Al there is a flattening of the absorption edge and an increase in optical loss. In addition, contents of more than about 2 at% Al are associated with the onset of time-dependent intergranular oxidation, which causes a pronounced dip in the reflectance spectrum at about 2.3-2.4 eV (∼500-540 nm).

Dean, S, Foureur, M, Zaslawski, C, Newton-John, T, Yu, N & Pappas, E 2017, 'The effects of a structured mindfulness program on the development of empathy in healthcare students', NursingPlus Open, vol. 3, pp. 1-5.
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Dean, S, Peng, W, Zaslawski, C, Elliott, D, Newton-John, T, Campo, M & Pappas, E 2017, 'Mindfulness in Physical and Occupational Therapy Education and Practice: A scoping review', Physical Therapy Reviews, vol. 22, no. 5-6, pp. 221-228.
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© 2017 Informa UK Limited, trading as Taylor & Francis Group. Background: Mindfulness practices provide numerous benefits for individuals with a variety of health issues. Recent research has highlighted the benefits of mindfulness for health professionals. The potential benefits for physical and occupational therapists or students however, are currently unclear. Objectives: To perform a scoping review on the effects of mindfulness practices among physical (PT) and occupational therapists (OT) and students of those disciplines. Methods: Eligible published articles in English were identified through a literature search of MEDLINE, PsycINFO, Cochrane Library, and AMED from the inception of databases to November 2015. Titles, abstracts, and full-text articles were screened for the selection of relevant papers. Articles identified as editorials, correspondences, commentaries, case reports, abstracts alone, and review papers were excluded. Results: Six studies (two qualitative studies, one quantitative study, one mixed-method study, and two experimental studies) met the inclusion criteria. Three studies focused on PT/OT students, two on clinicians and one on current clinicians who had previously failed a course. These studies highlighted the potential benefits of mindfulness for physical and occupational therapists. They should be interpreted with caution however, due to the small number of relevant studies, high heterogeneity in mindfulness interventions and methodological limitations. Conclusions: There is a paucity of research on the effects of mindfulness among physical and occupational therapists and students of those disciplines. The lack of relevant studies makes a systematic review challenging but the findings of the current studies suggest potentially promising effects.

del Campo, J, Pombert, J-F, Šlapeta, J, Larkum, A & Keeling, PJ 2017, 'The ‘other’ coral symbiont: Ostreobium diversity and distribution', The ISME Journal, vol. 11, no. 1, pp. 296-299.
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Abstract Ostreobium is an endolithic algal genus thought to be an early-diverging lineage of the Bryopsidales (Ulvophyceae, Chlorophyta). Ostreobium can live in low-light conditions on calcium carbonate substrata in tropical conditions. It is best known as a symbiont of corals, where it lives deep within the animal skeleton and exchanges nitrogen and carbon, as well as providing nutrients and photoassimilates. In contrast to the relatively well-studied role of the photosynthetic zooxanthellae symbionts in coral (Symbiodinium), Ostreobium phylogeny, diversity and distribution are all poorly understood. Here, we describe the phylogenetic position and diversity of Ostreobium based on plastid 16S ribosomal DNA (rDNA), 18S rDNA and rbcL genes from a nuclear genome survey and complete plastid genome, and determined its environmental diversity and distribution by screening the publicly available environmental data for those genes. The results shed light on the phylogeny and the ecology of the ‘other’ coral symbiont.

Deng, K, Li, C, Huang, S, Xing, B, Jin, D, Zeng, Q, Hou, Z & Lin, J 2017, 'Recent Progress in Near Infrared Light Triggered Photodynamic Therapy', Small, vol. 13, no. 44, pp. 1702299-1702299.
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AbstractNowadays, photodynamic therapy (PDT) is under the research spotlight as an appealing modality for various malignant tumors. Compared with conventional PDT treatment activated by ultraviolet or visible light, near infrared (NIR) light‐triggered PDT possessing deeper penetration to lesion area and lower photodamage to normal tissue holds great potential for in vivo deep‐seated tumor. In this review, recent research progress related to the exploration of NIR light responsive PDT nanosystems is summarized. To address current obstacles of PDT treatment and facilitate the effective utilization, several innovative strategies are developed and introduced into PDT nanosystems, including the conjugation with targeted moieties, O2 self‐sufficient PDT, dual photosensitizers (PSs)‐loaded PDT nanoplatform, and PDT‐involved synergistic therapy. Finally, the potential challenges as well as the prospective for further development are also discussed.

Deplazes, E 2017, 'Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes', Molecules, vol. 22, no. 3, pp. 362-362.
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DEWYNNE, JN & EL-HASSAN, N 2017, 'THE VALUATION OF SELF-FUNDING INSTALMENT WARRANTS', International Journal of Theoretical and Applied Finance, vol. 20, no. 04, pp. 1750025-1750025.
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We present two models for the fair value of a self-funding instalment warrant. In both models we assume the underlying stock process follows a geometric Brownian motion. In the first model, we assume that the underlying stock pays a continuous dividend yield and in the second we assume that it pays a series of discrete dividend yields. We show that both models admit similarity reductions and use these to obtain simple finite-difference and Monte Carlo solutions. We use the method of multiple scales to connect these two models and establish the first-order correction term to be applied to the first model in order to obtain the second, thereby establishing that the former model is justified when many dividends are paid during the life of the warrant. Further, we show that the functional form of this correction may be expressed in terms of the hedging parameters for the first model and is, from this point of view, independent of the particular payoff in the first model. In two appendices we present approximate solutions for the first model which are valid in the small volatility and the short time-to-expiry limits, respectively, by using singular perturbation techniques. The small volatility solutions are used to check our finite-difference solutions and the small time-to-expiry solutions are used as a means of systematically smoothing the payoffs so we may use pathwise sensitivities for our Monte Carlo methods.

Dhar Shukla, S, Hansbro, P & Walters, E 2017, 'Blocking rhinoviral adhesion molecule (ICAM-1): potential to prevent COPD exacerbations', International Journal of Chronic Obstructive Pulmonary Disease, vol. Volume 12, pp. 1413-1414.
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Dixit, A, Tanaka, A, Greer, JM & Donnelly, S 2017, 'Novel Therapeutics for Multiple Sclerosis Designed by Parasitic Worms', International Journal of Molecular Sciences, vol. 18, no. 10, pp. 2141-2141.
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© 2017 by the authors. Licensee MDPI, Basel, Switzerland. The evolutionary response to endemic infections with parasitic worms (helminth) was the development of a distinct regulatory immune profile arising from the need to encapsulate the helminths while simultaneously repairing tissue damage. According to the old friend’s hypothesis, the diminished exposure to these parasites in the developed world has resulted in a dysregulated immune response that contributes to the increased incidence of immune mediated diseases such as Multiple Sclerosis (MS). Indeed, the global distribution of MS shows an inverse correlation to the prevalence of helminth infection. On this basis, the possibility of treating MS with helminth infection has been explored in animal models and phase 1 and 2 human clinical trials. However, the possibility also exists that the individual immune modulatory molecules secreted by helminth parasites may offer a more defined therapeutic strategy.

Don, EK, Formella, I, Badrock, AP, Hall, TE, Morsch, M, Hortle, E, Hogan, A, Chow, S, Gwee, SSL, Stoddart, JJ, Nicholson, G, Chung, R & Cole, NJ 2017, 'A Tol2 Gateway-Compatible Toolbox for the Study of the Nervous System and Neurodegenerative Disease', Zebrafish, vol. 14, no. 1, pp. 69-72.
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Donahoe, SL, Phalen, DN, McAllan, BM, O'Meally, D, McAllister, MM, Ellis, J & Šlapeta, J 2017, 'Differential Gamma Interferon- and Tumor Necrosis Factor Alpha-Driven Cytokine Response Distinguishes Acute Infection of a Metatherian Host with Toxoplasma gondii and Neospora caninum', Infection and Immunity, vol. 85, no. 6.
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ABSTRACT Toxoplasma gondii and Neospora caninum (both Apicomplexa) are closely related cyst-forming coccidian parasites that differ significantly in their host ranges and ability to cause disease. Unlike eutherian mammals, Australian marsupials (metatherian mammals) have long been thought to be highly susceptible to toxoplasmosis and neosporosis because of their historical isolation from the parasites. In this study, the carnivorous fat-tailed dunnart ( Sminthopsis crassicaudata ) was used as a disease model to investigate the immune response and susceptibility to infection of an Australian marsupial to T. gondii and N. caninum . The disease outcome was more severe in N. caninum -infected dunnarts than in T. gondii -infected dunnarts, as shown by the severity of clinical and histopathological features of disease and higher tissue parasite burdens in the tissues evaluated. Transcriptome sequencing (RNA-seq) of spleens from infected dunnarts and mitogen-stimulated dunnart splenocytes was used to define the cytokine repertoires. Changes in mRNA expression during the time course of infection were measured using quantitative reverse transcription-PCR (qRT-PCR) for key Th1 (gamma interferon [IFN-γ] and tumor necrosis factor alpha [TNF-α]), Th2 (interleukin 4 [IL-4] and I...

Dong, H, Sun, L-D, Feng, W, Gu, Y, Li, F & Yan, C-H 2017, 'Versatile Spectral and Lifetime Multiplexing Nanoplatform with Excitation Orthogonalized Upconversion Luminescence', ACS Nano, vol. 11, no. 3, pp. 3289-3297.
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Donnelly, S, Huston, WM, Johnson, M, Tiberti, N, Saunders, B, O’Brien, B, Burke, C, Labbate, M & Combes, V 2017, 'Targeting the master regulator mTOR: a new approach to prevent the neurological of consequences of parasitic infections?', Parasites & Vectors, vol. 10, no. 1, pp. 1-6.
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© 2017 The Author(s). A systematic analysis of 240 causes of death in 2013 revealed that parasitic diseases were responsible for more than one million deaths. The vast majority of these fatalities resulted from protozoan infections presenting with neurological sequelae. In the absence of a vaccine, development of effective therapies is essential to improving global public health. In 2015, an intriguing strategy to prevent cerebral malaria was proposed by Gordon et al. 2015 mBio, 6:e00625. Their study suggested that inhibition of the mammalian target of rapamycin prevented experimental cerebral malaria by blocking the damage to the blood brain barrier and stopping the accumulation of parasitized red blood cells and T cells in the brain. Here, we hypothesize that the same therapeutic strategy could be adopted for other protozoan infections with a brain tropism, to prevent cerebral parasitosis by limiting pathogen replication and preventing immune mediated destruction of brain tissue.

Dorantes-Aranda, JJ, Campbell, K, Bradbury, A, Elliott, CT, Harwood, DT, Murray, SA, Ugalde, SC, Wilson, K, Burgoyne, M & Hallegraeff, GM 2017, 'Comparative performance of four immunological test kits for the detection of Paralytic Shellfish Toxins in Tasmanian shellfish', Toxicon, vol. 125, pp. 110-119.
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© 2016 Elsevier Ltd Blooms of the toxic dinoflagellate Alexandrium tamarense (Group 1) seriously impacted the Tasmanian shellfish industry during 2012 and 2015, necessitating product recalls and intensive paralytic shellfish toxin (PST) product testing. The performance of four commercial PST test kits, Abraxis™, Europroxima™, Scotia™ and Neogen™, was compared with the official AOAC LC-FLD method for contaminated mussels and oysters. Abraxis and Europroxima kits underestimated PST in 35–100% of samples when using standard protocols but quantification improved when concentrated extracts were further diluted (underestimation ≤18%). The Scotia kit (cut off 0.2–0.7 mg STX-diHCl eq/kg) delivered 0% false negatives, but 27% false positives. Neogen produced 5% false negatives and 13% false positives when the cut off was altered to 0.5–0.6 mg STX-diHCl eq/kg, the introduction of a conversion step eliminated false negatives. Based on their sensitivity, ease of use and performance, the Neogen kit proved the most suitable kit for use with Tasmanian mussels and oysters. Once formally validated for regulatory purposes, the Neogen kit could provide shellfish growers with a rapid tool for harvesting decisions at the farm gate. Effective rapid screening preventing compliant samples undergoing testing using the more expensive and time consuming LC-FLD method will result in significant savings in analytical costs.

Dowse, R, Palmer, CG, Hills, K, Torpy, F & Kefford, BJ 2017, 'The mayfly nymphAustrophlebioides pusillusHarker defies common osmoregulatory assumptions', Royal Society Open Science, vol. 4, no. 1, pp. 160520-160520.
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Osmoregulation is a key physiological function, critical for homeostasis. The basic physiological mechanisms of osmoregulation are thought to be well established. However, through a series of experiments exposing the freshwater mayfly nymphAustrophlebioides pusillus(Ephemeroptera) to increasing salinities, we present research that challenges the extent of current understanding of the relationship between osmoregulation and mortality.A. pusillushad modelled 96 h LC10, LC50and LC99of 2.4, 4.8 and 10 g l−1added synthetic marine salt (SMS), respectively. They were strong osmoregulators. At aquarium water osmolality of 256 ± 3.12 mmol kg−1(±s.e.; equivalent to 10 g l−1added SMS), the haemolymph osmolality ofA. pusilluswas a much higher 401 ± 4.18 mmol kg−1(±s.e.). The osmoregulatory capacity ofA. pusillusdid not break down, even at the salinity corresponding to their LC99, thus their mortality at this concentration is due to factors other than increased internal osmotic pressure. No freshwater invertebrate has been previously reported as suffering mortality from rises in salinity that are well below the iso-osmotic point. Recently, studies have reported reduced abundance/richness of Ephemeroptera with slightly elevated salinity. Given that salinization is an increasing global threat to freshwaters, there is an urgent need for studies into the osmophysiology of the Ephemeroptera to determine if their loss at locations with slightly elevated salinity is a direct result of external salinity or other, possibly physiological, causes.

Dua, K, Hansbro, NG & Hansbro, PM 2017, 'Steroid resistance and concomitant respiratory infections: A challenging battle in pulmonary clinic.', EXCLI J, vol. 16, pp. 981-985.
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Dua, K, Hansbro, NG, Foster, PS & Hansbro, PM 2017, 'MicroRNAs as therapeutics for future drug delivery systems in treatment of lung diseases', Drug Delivery and Translational Research, vol. 7, no. 1, pp. 168-178.
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© 2016, Controlled Release Society. The rapid advancement in the area of microRNAs (miRNAs) from discovery to their translation into therapeutic moieties reflects their significance as important regulators in the management of disease pathology. The miRNAs can potentially be a new class of drugs in the near future for the treatment of various lung diseases, but it lacks the current knowledge how these identified therapeutic moieties can be designed into an effective, patient complaint and targeted drug delivery system. miRNAs have characteristic features like small size and low molecular weight which makes them easily translated into an effective drug delivery system. In this review, we have summarised the concept of miRNAs and different approaches which can be employed to deliver miRNAs effectively and safely to the target cells including the challenges associated with their development in particular emphasis on pulmonary diseases. Such approaches will be of interest for both the biological and formulation scientists to understand and explore the new vistas in the area of miRNA delivery for pulmonary inflammatory diseases.

Dua, K, Shukla, SD & Hansbro, PM 2017, 'Aspiration techniques for bronchoalveolar lavage in translational respiratory research: Paving the way to develop novel therapeutic moieties', Journal of Biological Methods, vol. 4, no. 3, pp. e73-e73.
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Bronchoalveolar lavage (BAL) is a simple, yet informative tool in understanding the immunopathology of various lung diseases via quantifying various inflammatory cells, cytokines and growth factors. At present, this traditional method is often blended with several robust and sophisticated molecular and biological techniques sustaining the significance and longevity of this technique. Crucially, the existence of slightly distinct approaches and variables employed at different laboratories around the globe in performing BAL aspiration indeed demands an utmost need to optimize and develop an effective, cost-effective and a reproducible technique. This mini review will be of importance to the biological translational scientist, particularly respiratory researchers in understanding the fundamentals and approaches to apply and consider with BAL aspiration techniques. This will ensure generating a meaningful and clinically relevant data which in turn accelerate the development of new and effective therapeutic moieties for major respiratory conditions.

Dua, K, Shukla, SD, de Jesus Andreoli Pinto, T & Hansbro, PM 2017, 'Nanotechnology: Advancing the translational respiratory research', Interventional Medicine and Applied Science, vol. 9, no. 1, pp. 39-41.
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Considering the various limitations associated with the conventional dosage forms, nanotechnology is gaining increased attention in drug delivery particularly in respiratory medicine and research because of its advantages like targeting effects, improved pharmacotherapy, and patient compliance. This paper provides a quick snapshot about the recent trends and applications of nanotechnology to various translational and formulation scientists working on various respiratory diseases, which can help paving a new path in developing effective drug delivery system.

Dua, K, Shukla, SD, Tekade, RK & Hansbro, PM 2017, 'Whether a novel drug delivery system can overcome the problem of biofilms in respiratory diseases?', Drug Delivery and Translational Research, vol. 7, no. 1, pp. 179-187.
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© 2016, Controlled Release Society. Biofilm comprises a community of microorganisms which form on medical devices and can lead to various threatening infections. It is a major concern in various respiratory diseases like cystic fibrosis, chronic obstructive pulmonary disease, etc. The treatment strategies for such infections are difficult due to the resistance of the microflora existing in the biofilms against various antimicrobial agents, thus posing threats to the patient population. The present era witnesses the beginning of research to understand the biofilm physiology and the associated microfloral diversity by applying -omics approaches. There is very limited information about how the deposition of biofilm on the respiratory devices and lung itself affects the drug delivered, the delivery system, and other implications. The present mini review summarizes the basic introduction to the biofilms and its avoidance using various drug delivery systems with special emphasis on the respiratory diseases. Understanding the approaches, principles, and modes of drug delivery involved in preventing biofilm deposition will be of interest to both biological and formulation scientists, thereby opening avenues to explore the new vistas in biofilm research for identifying better treatments for pulmonary infectious diseases.

Dyari, HRE, Rawling, T, Chen, Y, Sudarmana, W, Bourget, K, Dwyer, JM, Allison, SE & Murray, M 2017, 'A novel synthetic analogue of ω‐3 17,18‐epoxyeicosatetraenoic acid activates TNF receptor‐1/ASK1/JNK signaling to promote apoptosis in human breast cancer cells', The FASEB Journal, vol. 31, no. 12, pp. 5246-5257.
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© FASEB A saturated analog of the cytochrome P450–mediated v-3-17,18-epoxide of v-3-eicosapentaenoic acid (C20E) activated apoptosis in human triple-negative MDA-MB-231 breast cancer cells. This study evaluated the apoptotic mechanism of C20E. Increased cytosolic cytochrome c expression and altered expression of pro- and antiapoptotic B-cell lymphoma-2 proteins indicated activation of the mitochondrial pathway. Caspase-3 activation by C20E was prevented by pharmacological inhibition and silencing of the JNK and p38 MAP kinases (MAPK), upstream MAPK kinases MKK4 and MKK7, and the upstream MAPK kinase kinase apoptosis signal-regulating kinase 1 (ASK1). Silencing of the death receptor TNF receptor 1 (TNFR1), but not Fas, DR4, or DR5, and the adapters TRADD and TNF receptor–associated factor 2, but not Fas-associated death domain, prevented C20E-mediated apoptosis. B-cell lymphoma-2 homology 3–interacting domain death agonist (Bid) cleavage by JNK/p38 MAPK linked the extrinsic and mitochondrial pathways of apoptosis. In further studies, an antibody against the extracellular domain of TNFR1 prevented apoptosis by TNF-a but not C20E. These findings suggest that C20E acts intracellularly at TNFR1 to activate ASK1-MKK4/7-JNK/p38 MAPK signaling and to promote Bid-dependent mitochondrial disruption and apoptosis. In in vivo studies, tumors isolated from C20E-treated nu/nu mice carrying MDA-MB-231 xenografts showed increased TUNEL staining and decreased Ki67 staining, reflecting increased apoptosis and decreased proliferation, respectively. v-3-Epoxy fatty acids like C20E could be incorporated into treatments for triple-negative breast cancers.

Eapen, MS, Hansbro, PM, McAlinden, K, Kim, RY, Ward, C, Hackett, T-L, Walters, EH & Sohal, SS 2017, 'Abnormal M1/M2 macrophage phenotype profiles in the small airway wall and lumen in smokers and chronic obstructive pulmonary disease (COPD)', Scientific Reports, vol. 7, no. 1, pp. 13392-13392.
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AbstractWe explore potential dysregulation of macrophage phenotypes in COPD pathogenesis through integrated study of human small airway tissue, bronchoalveolar lavage (BAL) and an experimental murine model of COPD. We evaluated human airway tissue and BAL from healthy controls, normal lung function smokers (NLFS), and COPD subjects. Both small airways and BAL cells were immunohistochemically stained with anti-CD68 for total macrophages and with anti-CD163 for M2, and anti-iNOS for M1 macrophages. Multiplex ELISA measured BAL cytokines. Comparable cigarette smoke-induced experimental COPD mouse model was assessed for relevant mRNA profiles. We found an increase in pro-inflammatory M1s in the small airways of NLFS and COPD compared to controls with a reciprocal decrease in M2 macrophages, which remained unchanged among pathological groups. However, luminal macrophages showed a dominant M2 phenotype in both NLFS and COPD subjects. BAL cytokine skewed towards an M2 profile with increase in CCL22, IL-4, IL-13, and IL-10 in both NLFS and COPDs. The mouse-model of COPD showed similar increase in mRNA for M2 markers. Our finding suggests abnormal macrophage switching in both mucosal and luminal areas of COPD patients, that strongly associated with cytokine balance. There may be potential for beneficial therapeutic cytokine manipulation of macrophage phenotypes in COPD.

Ebenezer, JA, Christensen, JM, Oliver, BG, Oliver, RA, Tijn, G, Ho, J, Habib, AR, Rimmer, J, Sacks, R & Harvey, RJ 2017, 'Periostin as a marker of mucosal remodelling in chronic rhinosinusitis', Rhinology journal, vol. 55, no. 3, pp. 234-241.
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© 2017, International Rhinologic Society. All rights reserved. Background: Although extracellular matrix (ECM) proteins are associated with irreversible lower airway changes, the relationship with upper airway remodelling which occurs during chronic rhinosinusitis (CRS) is poorly understood. This study assessed the expression of ECM proteins periostin, fibulin-1, fibronectin and collagenIV in nasal mucosa of patients with and without histologic features of remodelling. Methods: A cross-sectional study of sinonasal mucosal biopsies taken from patients, undergoing surgery for CRS was performed, where patients were grouped according to remodelling, defined by basement membrane thickening (BMT>7.5µm) and subepithelial fibrosis. An overall view and three random fields of immunostained tissue sections that included epithelium, basement membrane and submucosa, were imaged using Zeiss Zen software. The area and intensity of positive staining were scored by two blinded observers, using a 12-point ordinal scale of weak to strong. Results: 65 patients (47.6 ± 13.4years, 44.6% female) were assessed. Patients were grouped as controls 26.2%, BMT/no fibrosis 38.5% or BMT and fibrosis 33.8%. Stronger grade of periostin expression was associated with remodelling changes and tissue eosinophilia>10/HPF. Fibulin-1, fibronectin and collagenIV did not differ. Conclusion: Periostin expression was associated with the presence of BMT, fibrosis and tissue eosinophilia; and may identify patients undergoing remodelling changes.

Elsdon, DS, Spanswick, S, Zaslawski, C & Meier, PC 2017, 'Protocol: Testing the Relevance of Acupuncture Theory in the Treatment of Myofascial Pain in the Upper Trapezius Muscle', Journal of Acupuncture and Meridian Studies, vol. 10, no. 1, pp. 67-74.
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© 2017 Medical Association of Pharmacopuncture Institute A protocol for a prospective single-blind parallel four-arm randomized placebo-controlled trial with repeated measures was designed to test the effects of various acupuncture methods compared with sham. Eighty self-selected participants with myofascial pain in the upper trapezius muscle were randomized into four groups. Group 1 received acupuncture to a myofascial trigger point (MTrP) in the upper trapezius. Group 2 received acupuncture to the MTrP in addition to relevant distal points. Group 3 received acupuncture to the relevant distal points only. Group 4 received a sham treatment to both the MTrP and distal points using a deactivated acupuncture laser device. Treatment was applied four times within 2 weeks with outcomes measured throughout the trial and at 2 weeks and 4 weeks posttreatment. Outcome measurements were a 100-mm visual analog pain scale, SF-36, pressure pain threshold, Neck Disability Index, the Upper Extremity Functional Index, lateral flexion in the neck, McGill Pain Questionnaire, Massachusetts General Hospital Acupuncture Sensation Scale, Working Alliance Inventory (short form), and the Credibility Expectance Questionnaire. Two-way analysis of variance (ANOVA) with repeated measures were used to assess the differences between groups.

Faiz, A, Donovan, C, Nieuwenhuis, MA, van den Berge, M, Postma, DS, Yao, S, Park, CY, Hirsch, R, Fredberg, JJ, Tjin, G, Halayko, AJ, Rempel, KL, Ward, JPT, Lee, T, Bossé, Y, Nickle, DC, Obeidat, M, Vonk, JM, Black, JL, Oliver, BG, Krishnan, R, McParland, B, Bourke, JE & Burgess, JK 2017, 'Latrophilin receptors: novel bronchodilator targets in asthma', Thorax, vol. 72, no. 1, pp. 74-82.
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© 2017 Published by the BMJ Publishing Group Limited. Background Asthma affects 300 million people worldwide. In asthma, the major cause of morbidity and mortality is acute airway narrowing, due to airway smooth muscle (ASM) hypercontraction, associated with airway remodelling. However, little is known about the transcriptional differences between healthy and asthmatic ASM cells. Objectives To investigate the transcriptional differences between asthmatic and healthy airway smooth muscle cells (ASMC) in culture and investigate the identified targets using in vitro and ex vivo techniques. Methods Human asthmatic and healthy ASMC grown in culture were run on Affymetrix-Hugene-1.0-ST microarrays. Identified candidates were confirmed by PCR, and immunohistochemistry. Functional analysis was conducted using in vitro ASMC proliferation, attachment and contraction assays and ex vivo contraction of mouse airways. Results We suggest a novel role for latrophilin (LPHN) receptors, finding increased expression on ASMC from asthmatics, compared with non-asthmatics in vivo and in vitro, suggesting a role in mediating airway function. A single nucleotide polymorphism in LPHN1 was associated with asthma and with increased LPHN1 expression in lung tissue. When activated, LPHNs regulated ASMC adhesion and proliferation in vitro, and promoted contraction of mouse airways and ASMC. Conclusions Given the need for novel inhibitors of airway remodelling and bronchodilators in asthma, the LPHN family may represent promising novel targets for future dual therapeutic intervention.

Farooq, MU, Butt, S, Gao, K, Pang, XL, Sun, X, Asfandiyar, Mohmed, F, Ahmad, A, Mahmood, A & Mahmood, N 2017, 'Improved thermoelectric performance of BiCuSeO by Ag substitution at Cu site', Journal of Alloys and Compounds, vol. 691, pp. 572-577.
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Farrell, H, Murray, S, Zammit, A & Edwards, A 2017, 'Management of Ciguatoxin Risk in Eastern Australia', Toxins, vol. 9, no. 11, pp. 367-367.
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Between 2014 and 2016, five cases of ciguatera fish poisoning (CFP), involving twenty four individuals, were linked to Spanish Mackerel (Scomberomorus commerson) caught in the coastal waters of the state of New South Wales (NSW) on the east coast of Australia. Previously, documented cases of CFP in NSW were few, and primarily linked to fish imported from other regions. Since 2015, thirteen individuals were affected across four additional CFP cases in NSW, linked to fish imported from tropical locations. The apparent increase in CFP in NSW from locally sourced catch, combined with the risk of CFP from imported fish, has highlighted several considerations that should be incorporated into risk management strategies to minimize CFP exposure for seafood consumers.

Feng, S, Tan, CH, Constancias, F, Kohli, GS, Cohen, Y & Rice, SA 2017, 'Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules', FEMS Microbiology Ecology, vol. 93, no. 4.
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© FEMS 2017. All rights reserved. We recently isolated and characterised a predatory Bdellovibrio bacteriovorus strain from activated sludge (Ulu Pandan Water Reclamation Plant, Singapore), and this strain, B. bacteriovorus UP, was able to prey upon a broad spectrum of bacterial isolates from the activated sludge when grown as planktonic cells or as biofilms. Here, we have tested the effect of Bdellovibrio predation on floccular and granular sludge to determine if the spatial organisation, loosely or tightly aggregated communities, was protective from predation. The effect of predation was assessed using a combination of biomass quantification, cellular activity measurement and microscopic image analysis to determine community viability. Additionally, changes in the microbial communities due to predation by B. bacteriovorus UP were analysed through total RNA sequencing. Predation led to a significant reduction in microbial activity and total biomass for both floccular and granular sludge communities. Predation was also associated with significant changes in the microbial community composition in both communities, with > 90% of the community members reduced in relative abundance after 24 h. Of those community members, the dominant organisms, such as Proteobacteria and Bacteroidetes, were the most affected phylotypes. This suggests that predatory bacteria, which display indiscriminant feeding, could significantly shift the species composition and thus, may disturb the operational performance of wastewater treatment systems.

Ferrage, L, Bertrand, G, Lenormand, P, Grossin, D & Ben-Nissan, B 2017, 'A review of the additive manufacturing (3DP) of bioceramics: alumina, zirconia (PSZ) and hydroxyapatite', Journal of the Australian Ceramic Society, vol. 53, no. 1, pp. 11-20.
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© 2016 Australian Ceramic Society. The additive manufacturing of bioceramic parts has been investigated since the 1980s. This paper offers an overview of the present achievements in the production of alumina, zirconia and hydroxyapatite parts by means of selective laser sintering/melting of a powder bed or stereolithography. A focus is placed on these specific materials because of their widespread use in the biomedical field. It demonstrates that even though the manufacturing of parts with these processes is possible from pure bioceramics, the use of a binder (or another chemical adjuvant) is required in order to achieve good mechanical properties. Still, improvements in the raw material preparation and in the comprehension of the physical phenomena occurring during the processing remain necessary to be able to prevent the formation of cracks or to be able to control the porosity of the parts.

Finkelstein, DI, Billings, JL, Adlard, PA, Ayton, S, Sedjahtera, A, Masters, CL, Wilkins, S, Shackleford, DM, Charman, SA, Bal, W, Zawisza, IA, Kurowska, E, Gundlach, AL, Ma, S, Bush, AI, Hare, DJ, Doble, PA, Crawford, S, Gautier, ECL, Parsons, J, Huggins, P, Barnham, KJ & Cherny, RA 2017, 'The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson’s disease', Acta Neuropathologica Communications, vol. 5, no. 1, pp. 53-53.
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AbstractElevated iron in the SNpc may play a key role in Parkinson’s disease (PD) neurodegeneration since drug candidates with high iron affinity rescue PD animal models, and one candidate, deferirpone, has shown efficacy recently in a phase two clinical trial. However, strong iron chelators may perturb essential iron metabolism, and it is not yet known whether the damage associated with iron is mediated by a tightly bound (eg ferritin) or lower-affinity, labile, iron pool. Here we report the preclinical characterization of PBT434, a novel quinazolinone compound bearing a moderate affinity metal-binding motif, which is in development for Parkinsonian conditions. In vitro, PBT434 was far less potent than deferiprone or deferoxamine at lowering cellular iron levels, yet was found to inhibit iron-mediated redox activity and iron-mediated aggregation of α-synuclein, a protein that aggregates in the neuropathology. In vivo, PBT434 did not deplete tissue iron stores in normal rodents, yet prevented loss of substantia nigra pars compacta neurons (SNpc), lowered nigral α-synuclein accumulation, and rescued motor performance in mice exposed to the Parkinsonian toxins 6-OHDA and MPTP, and in a transgenic animal model (hA53T α-synuclein) of PD. These improvements were associated with reduced markers of oxidative damage, and increased levels of ferroportin (an iron exporter) and DJ-1. We conclude that compounds designed to target a pool of pathological iron that is not held in high-affinity complexes in the tissue can maintain the survival of SNpc neurons and could be disease-modifying in PD.

Fontana, C, Pelger, M & Platen, E 2017, 'On the existence of sure profits via flash strategies', J. Appl. Probab., vol. 56, no. 2, pp. 384-397.
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We introduce and study the notion of sure profit via flash strategy,consisting of a high-frequency limit of buy-and-hold trading strategies. In afully general setting, without imposing any semimartingale restriction, weprove that there are no sure profits via flash strategies if and only if assetprices do not exhibit predictable jumps. This result relies on the generaltheory of processes and provides the most general formulation of the well-knownfact that, in an arbitrage-free financial market, asset prices (includingdividends) should not exhibit jumps of a predictable direction or magnitude atpredictable times. We furthermore show that any price process is alwaysright-continuous in the absence of sure profits. Our results are robust undersmall transaction costs and imply that, under minimal assumptions, pricechanges occurring at scheduled dates should only be due to unanticipatedinformation releases.

Foster, PS, Maltby, S, Rosenberg, HF, Tay, HL, Hogan, SP, Collison, AM, Yang, M, Kaiko, GE, Hansbro, PM, Kumar, RK & Mattes, J 2017, 'Modeling T_H2 responses and airway inflammation to understand fundamental mechanisms regulating the pathogenesis of asthma', Immunological Reviews, vol. 278, no. 1, pp. 20-40.
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SummaryIn this review, we highlight experiments conducted in our laboratories that have elucidated functional roles for CD4+ T‐helper type‐2 lymphocytes (TH2 cells), their associated cytokines, and eosinophils in the regulation of hallmark features of allergic asthma. Notably, we consider the complexity of type‐2 responses and studies that have explored integrated signaling among classical TH2 cytokines (IL‐4, IL‐5, and IL‐13), which together with CCL11 (eotaxin‐1) regulate critical aspects of eosinophil recruitment, allergic inflammation, and airway hyper‐responsiveness (AHR). Among our most important findings, we have provided evidence that the initiation of TH2 responses is regulated by airway epithelial cell‐derived factors, including TRAIL and MID1, which promote TH2 cell development via STAT6‐dependent pathways. Further, we highlight studies demonstrating that microRNAs are key regulators of allergic inflammation and potential targets for anti‐inflammatory ther...

Fourment, M, Darling, AE & Holmes, EC 2017, 'The impact of migratory flyways on the spread of avian influenza virus in North America', BMC Evolutionary Biology, vol. 17, no. 1.
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Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby fostering opportunities for viruses to spread over long distances. However, the role played by such avian flyways in shaping the genetic structure of AIV populations has proven controversial. To assess the relative contribution of bird migration along flyways to the genetic structure of AIV we performed a large-scale phylogeographic study of viruses sampled in the USA and Canada, involving the analysis of 3805 to 4505 sequences from 36 to 38 geographic localities depending on the gene data set. To assist this we developed a maximum likelihood-based genetic algorithm to explore a wide range of complex spatial models, thereby depicting a more complete picture of the migration network than previous studies. Based on phylogenies estimated from nucleotide data sets, our results show that AIV migration rates within flyways are significantly higher than those between flyways, indicating that the migratory patterns of birds play a key role in pathogen dispersal. These findings provide valuable insights into the evolution, maintenance and transmission of AIVs, in turn allowing the development of improved programs for surveillance and risk assessment.

Fronzi, M & Nolan, M 2017, 'First-principles analysis of the stability of water on oxidised and reduced CuO(111) surfaces', RSC Advances, vol. 7, no. 89, pp. 56721-56731.
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A first-principles density functional theory investigation, with the inclusion of the Hubbard + U correction (PBE + U) on Cu-3d states, on the interaction of water with a CuO(111) surface.

Fronzi, M & Nolan, M 2017, 'Surface Modification of Perfect and Hydroxylated TiO₂ Rutile (110) and Anatase (101) with Chromium Oxide Nanoclusters', ACS Omega, vol. 2, no. 10, pp. 6795-6808.
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© 2017 American Chemical Society. We use first-principles density functional theory calculations to analyze the effect of chromia nanocluster modification on TiO 2 rutile (110) and anatase (101) surfaces, in which both dry/perfect and wet/hydroxylated TiO 2 surfaces are considered. We show that the adsorption of chromia nanoclusters on both surfaces is favorable and results in a reduction of the energy gap due to a valence band upshift. A simple model of the photoexcited state confirms this red shift and shows that photoexcited electrons and holes will localize on the chromia nanocluster. The oxidation states of the cations show that Ti 3+ , Cr 4+ , and Cr 2+ (with no Cr6+) can be present. To probe potential reactivity, the energy of oxygen vacancy formation is shown to be significantly reduced compared to that of pure TiO 2 and chromia. Finally, we show that inclusion of water on the TiO 2 surface, to begin inclusion of environment effects, has no notable effect on the energy gap or oxygen vacancy formation. These results help us to understand earlier experimental work on chromia-modified anatase TiO 2 and demonstrate that chromia-modified TiO 2 presents an interesting composite system for photocatalysis.

Fu, L, Morsch, M, Shi, B, Wang, G, Lee, A, Radford, R, Lu, Y, Jin, D & Chung, R 2017, 'A versatile upconversion surface evaluation platform for bio–nano surface selection for the nervous system', Nanoscale, vol. 9, no. 36, pp. 13683-13692.
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There is considerable interest in developing diagnostic nanotools for early detection and delivery of various therapeutic agents for treatment of neurodegenerative diseases.

Fuller, B, Garland, J, Anne, S, Beh, R, McNevin, D & R. Tse 2017, 'Increased epicardial fat thickness in sudden death from stable coronary artery atherosclerosis', Pathology, vol. 49, pp. S102-S102.
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Fuller, B, Garland, J, Anne, S, Beh, R, McNevin, D & Tse, R 2017, 'Increased Epicardial Fat Thickness in Sudden Death From Stable Coronary Artery Atherosclerosis', American Journal of Forensic Medicine & Pathology, vol. 38, no. 2, pp. 162-166.
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Background Sudden death from stable coronary artery atherosclerosis (SCAA) is well recognized. However, individuals can have ischemic heart disease or coronary artery atherosclerosis but die of noncardiac causes. Recently, it has been recognized that increased epicardial fat is detrimental to normal heart function. We hypothesize that individuals who die of SCAA have increased epicardial fat. Aim The aim of this study was to investigate whether there is an increase in epicardial fat in individuals who suddenly died of SCAA. Methods This was a 1-year retrospective study comparing the average epicardial fat thickness using postmortem computed tomography scan between individuals who suddenly died of SCAA (SCAA group) with individuals who primarily died of natural noncardiac causes but had established ischemic heart disease or significant coronary artery atherosclerosis (NCC group). Results Average epicardial fat thickness was significantly higher in the SCAA group (8 ± 2 mm) than in the NCC group (6 ± 2 mm, P = 0.008). Conclusions Individuals who die of SCAA appear to have higher epicardial fat thickness. The increase in epicardial fat may have an additional detrimental effect to the heart predisposing sudden death in individuals with coronary artery atherosclerosis.

Gali, MA, Gentle, AR, Arnold, MD & Smith, GB 2017, 'Extending the applicability of the four-flux radiative transfer method', Applied Optics, vol. 56, no. 31, pp. 8699-8699.
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© 2017 Optical Society of America. A generalized four-flux method capable of modeling and tuning the spectral reflectance of a diverse range of complex composite coatings is presented. An example application is exploring and maximizing the visible and near-infrared (IR) spectral reflectance available from the diverse structures arising from combinations of the many practical paint ingredients that are available or can be made when applied to different substrates. This requires consideration of scatterers that can differ in composition, particle size, size distribution, and fill factor, and are held in place by a variety of organic binders, which typically partially absorb in the near IR. This extended model is further enhanced by an explicit matrix algorithm that allows analysis of diverse multilayer stacks. This is applied to a multilayer and is designed to model useful changes that result from varying the pigment fill factor as a function of depth within a layer. What we believe is a novel feature is the way the scattering affects matrix absorptance. The model includes contributions to total absorptance from the scattering pigments and from the paint binder that can arise in different bands or simultaneously at the same wavelengths. Model accuracy is demonstrated by example results when compared to experimental data on dried single layer paint profiles using imaged cross sections. The model input covering the actual pigment and binder properties used are material, shape, size, and size distributions, mass added, and the measured optical constants from 400 nm to 2,500 nm of the undoped binder resin layer. One interesting result is the comparison of a two-layered stack, with bigger particles in the first layer and smaller ones in the second, to one with the opposite depth profile.

Gao, J, Djaidi, D, Marjo, CE, Bhadbhade, MM, Ung, AT & Bishop, R 2017, 'Weak Intermolecular Forces, but High Melting Points', Australian Journal of Chemistry, vol. 70, no. 5, pp. 538-538.
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The poorly soluble racemic compound 6,6a,13,13a-tetrahydropentaleno[1,2-b:4,5-b′]diquinoline (4) has an exceptionally high melting point range of 352–354°C despite its low molar mass (308.38) and a structure containing only 40 atoms (38 of which are C and H). Analysis of the X-ray crystal structure and Hirshfeld surface of 4, along with comparison with its isostructural homologue 2, reveals how this occurs in the absence of Pauling-type hydrogen bonding. Excellent complementarity between homochiral molecules of 4 allows formation of enantiomerically pure layers using C–H⋯π, aromatic π⋯π, and C–H⋯N interactions. The alternating layers of opposite handedness are then crosslinked by means of aza-1,3-peri hydrogen interactions. This bifurcated C–H⋯N⋯H–C motif acts as a molecular clip creating a highly rigid network structure. The role of weaker intermolecular forces in influencing the solubility and bioavailability of potential drug molecules is discussed in the context of the popular Lipinski ‘rule of 5’ guidelines.

Gao, X & Carroll, RJ 2017, 'Data integration with high dimensionality', Biometrika, vol. 104, no. 2, pp. 251-272.
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Summary We consider situations where the data consist of a number of responses for each individual, which may include a mix of discrete and continuous variables. The data also include a class of predictors, where the same predictor may have different physical measurements across different experiments depending on how the predictor is measured. The goal is to select which predictors affect any of the responses, where the number of such informative predictors tends to infinity as the sample size increases. There are marginal likelihoods for each experiment; we specify a pseudolikelihood combining the marginal likelihoods, and propose a pseudolikelihood information criterion. Under regularity conditions, we establish selection consistency for this criterion with unbounded true model size. The proposed method includes a Bayesian information criterion with appropriate penalty term as a special case. Simulations indicate that data integration can dramatically improve upon using only one data source.

Garby, TJ, Matys, ED, Ongley, SE, Salih, A, Larkum, AWD, Walter, MR, Summons, RE & Neilan, BA 2017, 'Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress', Applied and Environmental Microbiology, vol. 83, no. 13, pp. 1-15.
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ABSTRACT To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S -adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting Δ hpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the Δ hpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and Δ hpnP mutant strains were similar to those of vegetative cell-dominated cultures. However, the Δ hpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the Δ hpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions. IMPORTANCE As the first group of organisms to develop oxygenic photosynthesis,

Gardiner, M, Vicaretti, M, Sparks, J, Bansal, S, Bush, S, Liu, M, Darling, A, Harry, E & Burke, CM 2017, 'A longitudinal study of the diabetic skin and wound microbiome', PeerJ, vol. 5, no. 7, pp. e3543-e3543.
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Background Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes. Methods Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. Samples were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region. Results The diabetic skin microbiome was significantly less diverse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus, while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa. Discussion The major difference observ...

Gardner, SG, Raina, J-B, Nitschke, MR, Nielsen, DA, Stat, M, Motti, CA, Ralph, PJ & Petrou, K 2017, 'A multi-trait systems approach reveals a response cascade to bleaching in corals', BMC Biology, vol. 15, no. 1, p. 117.
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BACKGROUND: Climate change causes the breakdown of the symbiotic relationships between reef-building corals and their photosynthetic symbionts (genus Symbiodinium), with thermal anomalies in 2015-2016 triggering the most widespread mass coral bleaching on record and unprecedented mortality on the Great Barrier Reef. Targeted studies using specific coral stress indicators have highlighted the complexity of the physiological processes occurring during thermal stress, but have been unable to provide a clear mechanistic understanding of coral bleaching.RESULTS: Here, we present an extensive multi-trait-based study in which we compare the thermal stress responses of two phylogenetically distinct and widely distributed coral species, Acropora millepora and Stylophora pistillata, integrating 14 individual stress indicators over time across a simulated thermal anomaly. We found that key stress responses were conserved across both taxa, with the loss of symbionts and the activation of antioxidant mechanisms occurring well before collapse of the physiological parameters, including gross oxygen production and chlorophyll a. Our study also revealed species-specific traits, including differences in the timing of antioxidant regulation, as well as drastic differences in the production of the sulfur compound dimethylsulfoniopropionate during bleaching. Indeed, the concentration of this antioxidant increased two-fold in A. millepora after the corals started to bleach, while it decreased 70% in S. pistillata.CONCLUSIONS: We identify a well-defined cascading response to thermal stress, demarking clear pathophysiological reactions conserved across the two species, which might be central to fully understanding the mechanisms triggering thermally induced coral bleaching. These results highlight that bleaching is a conserved mechanism, but specific adaptations linked to the coral's antioxidant capacity drive differences in the sensitivity and thus tolerance of each coral spe...

Gardner, SG, Raina, J-B, Ralph, PJ & Petrou, K 2017, 'Reactive oxygen species (ROS) and dimethylated sulphur compounds in coral explants under acute thermal stress', Journal of Experimental Biology, vol. 220, no. 10, pp. 1787-1791.
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Coral bleaching is intensifying with global climate change. While the causes for these catastrophic events are well understood, the cellular mechanism that triggers bleaching is not well established. Our understanding of coral bleaching processes is hindered by the lack of robust methods for studying interactions between host and symbiont at the single-cell level. Here we exposed coral explants to acute thermal stress and measured oxidative stress, more specifically, reactive oxygen species (ROS), in individual symbiont cells. Furthermore, we measured concentrations of dimethylsulphoniopropionate (DMSP) and dimethylsulphoxide (DMSO) to elucidate the role of these compounds in coral antioxidant function. This work demonstrates the application of coral explants for investigating coral physiology and biochemistry under thermal stress and delivers a new approach to study host-symbiont interactions at the microscale, allowing us to directly link intracellular ROS with DMSP and DMSO dynamics.

Gates, AR, Benfield, MC, Booth, DJ, Fowler, AM, Skropeta, D & Jones, DOB 2017, 'Deep-sea observations at hydrocarbon drilling locations: Contributions from the SERPENT Project after 120 field visits', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 137, pp. 463-479.
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© 2016 The SERPENT Project has been running for over ten years. In this time scientists from universities and research institutions have made more than 120 visits to oil rigs, drill ships and survey vessels operated by 16 oil companies, in order to work with the industry's Remotely Operated Vehicles (ROV). Visits have taken place in Europe, North and South America, Africa and Australasia at water depths from 100 m to nearly 3000 m. The project has directly produced >40 peer reviewed publications and data from the project's >2600 entry online image and video archive have been used in many others. The aim of this paper is to highlight examples of how valuable data can be obtained through collaboration with hydrocarbon exploration and production companies to use existing industry infrastructure to increase scientific discovery in unexplored areas and augment environmental monitoring of industrial activity. The large number of industry ROVs operating globally increases chance encounters with large, enigmatic marine organisms. SERPENT video observations include the deepest known records of species previously considered epipelagic such as scalloped hammerhead (Sphyrna lewini) and southern sunfish (Mola ramsayi) and the first in situ observations of pelagic species such as oarfish (Regalecus glesne). Such observations enable improvements to distribution records and description of behaviour of poorly understood species. Specimen collection has been used for taxonomic descriptions, functional studies and natural products chemistry research. Anthropogenic effects been assessed at the local scale using in situ observations and sample collection at the time of drilling operations and subsequent visits have enabled study of recovery from drilling. Future challenges to be addressed using the SERPENT approach include ensuring unique faunal observations by industry ROV operators are reported, further study of recovery from deep-water drilling activity and to carry out ...

Genoud, S, Roberts, BR, Gunn, AP, Halliday, GM, Lewis, SJG, Ball, HJ, Hare, DJ & Double, KL 2017, 'Subcellular compartmentalisation of copper, iron, manganese, and zinc in the Parkinson's disease brain', Metallomics, vol. 9, no. 10, pp. 1447-1455.
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Altered iron and copper levels in the Parkinson's disease substantia nigra are confined to the cytosolic compartment of the cell.

Gerace, D, Martiniello-Wilks, R, Nassif, NT, Lal, S, Steptoe, R & Simpson, AM 2017, 'CRISPR-targeted genome editing of mesenchymal stem cell-derived therapies for type 1 diabetes: a path to clinical success?', Stem Cell Research & Therapy, vol. 8, no. 1.
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© 2017 The Author(s). Due to their ease of isolation, differentiation capabilities, and immunomodulatory properties, the therapeutic potential of mesenchymal stem cells (MSCs) has been assessed in numerous pre-clinical and clinical settings. Currently, whole pancreas or islet transplantation is the only cure for people with type 1 diabetes (T1D) and, due to the autoimmune nature of the disease, MSCs have been utilised either natively or transdifferentiated into insulin-producing cells (IPCs) as an alternative treatment. However, the initial success in pre-clinical animal models has not translated into successful clinical outcomes. Thus, this review will summarise the current state of MSC-derived therapies for the treatment of T1D in both the pre-clinical and clinical setting, in particular their use as an immunomodulatory therapy and targets for the generation of IPCs via gene modification. In this review, we highlight the limitations of current clinical trials of MSCs for the treatment of T1D, and suggest the novel clustered regularly interspaced short palindromic repeat (CRISPR) gene-editing technology and improved clinical trial design as strategies to translate pre-clinical success to the clinical setting.

Ghadiri, M, Young, PM, Jarolimek, W, Grau, GER, Oliver, BGG & Traini, D 2017, 'The effect of non-specific tight junction modulators on the transepithelial transport of poorly permeable drugs across airway epithelial cells', Journal of Drug Targeting, vol. 25, no. 4, pp. 342-349.
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© 2016 Informa UK Limited, trading as Taylor & Francis Group. The epithelial barrier in the respiratory system is a major obstacle for drug delivery to the systemic circulation in the lung. Epithelial barrier hinders the transport of large macromolecules or polar drugs. Essential components of this epithelial fence are physical intercellular structures termed tight junctions. Therefore, modulating tight junctions can enhance paracellular transport across epithelial barrier. In this study, the effect of some of non-specific tight junction modulators (TJMs); (Sodium (Na) decanoate, oleic acid and ethyleneglycol-bis-(β-aminoethyl ether)-N, N′-tetraacetic acid (EGTA)) with established effect on intestinal tight junctions was evaluated for its effects on bronchial epithelial cells (Calu-3 cells). It was demonstrated that the effect of TJMs especially Na decanoate resulted in a reversible opening of tight junctions evidenced by the decrease in the transepithelial resistance. It was also demonstrated that this reduction of TEER upon exposing the epithelial cells to the TJMs resulted in a significant increase in Flu-Na (paracellular marker) and PXS25 (anti-fibrotic compound) transepithelial transport through this barrier. In conclusion, among the investigated non-specific TJMs, Na decanoate fulfilled the requirements of an effective, non-toxic and reversible tight junction modulator for Calu-3 lung epithelial cells.

Gilbert, RC, Trafalis, TB, Richman, MB & Leslie, LM 2017, 'A data-driven kernel method assimilation technique for geophysical modelling', Optimization Methods and Software, vol. 32, no. 2, pp. 237-249.
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Girkin, JL, Hatchwell, LM, Collison, AM, Starkey, MR, Hansbro, PM, Yagita, H, Foster, PS & Mattes, J 2017, 'TRAIL signaling is proinflammatory and proviral in a murine model of rhinovirus 1B infection', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 312, no. 1, pp. L89-L99.
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the aim of this study is to elucidate the role of TRAIL during rhinovirus (RV) infection in vivo. Naïve wild-type and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-deficient ( Tnfsf10 −/−) BALB/c mice were infected intranasally with RV1B. In separate experiments, Tnfsf10 −/− mice were sensitized and challenged via the airway route with house dust mite (HDM) to induce allergic airways disease and then challenged with RVIB or UV-RVIB. Airway hyperreactivity (AHR) was invasively assessed as total airways resistance in response to increasing methacholine challenge and inflammation was assessed in bronchoalveolar lavage fluid at multiple time points postinfection. Chemokines were quantified by ELISA of whole lung lysates and viral load was determined by quantitative RT-PCR and tissue culture infective dose (TCID50). Human airway epithelial cells (BEAS2B) were infected with RV1B and stimulated with recombinant TRAIL or neutralizing anti-TRAIL antibodies and viral titer assessed by TCID50. HDM-challenged Tnfsf10 −/− mice were protected against RV-induced AHR and had suppressed cellular infiltration in the airways upon RV infection. Chemokine C-X-C-motif ligand 2 (CXCL2) production was suppressed in naïve Tnfsf10 −/− mice infected with RV1B, with less RV1B detected 24 h postinfection. This was associated with reduced apoptotic cell death and a reduction of interferon (IFN)-λ2/3 but not IFN-α or IFN-β. TRAIL stimulation increased, whereas anti-TRAIL antibodies reduced viral replication in RV1B-infected BEAS2B cells in vitro. In conclusion, TRAIL promotes RV-induced AHR, inflammation and RV1B replication, implicating this molecule and its downstream signaling pathways as a possible target for the amelioration of RV1B-induced allergic and nonallergic lung inflammation and AHR.

Glastras, SJ, Chen, H, Tsang, M, Teh, R, McGrath, RT, Zaky, A, Chen, J, Wong, MG, Pollock, CA & Saad, S 2017, 'The renal consequences of maternal obesity in offspring are overwhelmed by postnatal high fat diet', PLOS ONE, vol. 12, no. 2, pp. e0172644-e0172644.
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AIMS/HYPOTHESIS: Developmental programming induced by maternal obesity influences the development of chronic disease in offspring. In the present study, we aimed to determine whether maternal obesity exaggerates obesity-related kidney disease. METHODS: Female C57BL/6 mice were fed high-fat diet (HFD) for six weeks prior to mating, during gestation and lactation. Male offspring were weaned to normal chow or HFD. At postnatal Week 8, HFD-fed offspring were administered one dose streptozotocin (STZ, 100 mg/kg i.p.) or vehicle control. Metabolic parameters and renal functional and structural changes were observed at postnatal Week 32. RESULTS: HFD-fed offspring had increased adiposity, glucose intolerance and hyperlipidaemia, associated with increased albuminuria and serum creatinine levels. Their kidneys displayed structural changes with increased levels of fibrotic, inflammatory and oxidative stress markers. STZ administration did not potentiate the renal effects of HFD. Though maternal obesity had a sustained effect on serum creatinine and oxidative stress markers in lean offspring, the renal consequences of maternal obesity were overwhelmed by the powerful effect of diet-induced obesity. CONCLUSION: Maternal obesity portends significant risks for metabolic and renal health in adult offspring. However, diet-induced obesity is an overwhelming and potent stimulus for the development of CKD that is not potentiated by maternal obesity.

Gleason, FH, Gadd, GM, Pitt, JI & Larkum, AWD 2017, 'The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts', Mycology, vol. 8, no. 3, pp. 205-215.
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© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Endolithic true fungi and fungus-like microorganisms penetrate calcareous substrates formed by living organisms, cause significant bioerosion and are involved in diseases of many host animals in marine ecosystems. A theoretical interactive model for the ecology of reef-building corals is proposed in this review. This model includes five principle partners that exist in a dynamic equilibrium: polyps of a colonial coelenterate, endosymbiotic zooxanthellae, endolithic algae (that penetrate coral skeletons), endolithic fungi (that attack the endolithic algae, the zooxanthellae and the polyps) and prokaryotic and eukaryotic microorganisms (which live in the coral mucus). Endolithic fungi and fungus-like boring microorganisms are important components of the marine calcium carbonate cycle because they actively contribute to the biodegradation of shells of animals composed of calcium carbonate and calcareous geological substrates.

Gleason, FH, Gadd, GM, Pitt, JI & Larkum, AWD 2017, 'The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs', Mycology, vol. 8, no. 3, pp. 216-227.
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© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Anamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.

Gloag, ES, Elbadawi, C, Zachreson, CJ, Aharonovich, I, Toth, M, Charles, IG, Turnbull, L & Whitchurch, CB 2017, 'Micro-Patterned Surfaces That Exploit Stigmergy to Inhibit Biofilm Expansion', Frontiers in Microbiology, vol. 7, no. JAN, pp. 1-10.
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© 2017 Gloag, Elbadawi, Zachreson, Aharonovich, Toth, Charles, Turnbull and Whitchurch. Twitching motility is a mode of surface translocation that is mediated by the extension and retraction of type IV pili and which, depending on the conditions, enables migration of individual cells or can manifest as a complex multicellular collective behavior that leads to biofilm expansion. When twitching motility occurs at the interface of an abiotic surface and solidified nutrient media, it can lead to the emergence of extensive self-organized patterns of interconnected trails that form as a consequence of the actively migrating bacteria forging a furrow network in the substratum beneath the expanding biofilm. These furrows appear to direct bacterial movements much in the same way that roads and footpaths coordinate motor vehicle and human pedestrian traffic. Self-organizing systems such as these can be accounted for by the concept of stigmergy which describes self-organization that emerges through indirect communication via persistent signals within the environment. Many bacterial communities are able to actively migrate across solid and semi-solid surfaces through complex multicellular collective behaviors such as twitching motility and flagella-mediated swarming motility. Here, we have examined the potential of exploiting the stigmergic behavior of furrow-mediated trail following as a means of controlling bacterial biofilm expansion along abiotic surfaces. We found that incorporation of a series of parallel micro-fabricated furrows significantly impeded active biofilm expansion by Pseudomonas aeruginosa and Proteus vulgaris. We observed that in both cases bacterial movements tended to be directed along the furrows. We also observed that narrow furrows were most effective at disrupting biofilm expansion as they impeded the ability of cells to self-organize into multicellular assemblies required for escape from the furrows and migration into new territory. Our re...

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2017, 'On the application of reverse vaccinology to parasitic diseases: a perspective on feature selection and ranking of vaccine candidates', International Journal for Parasitology, vol. 47, no. 12, pp. 779-790.
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Reverse vaccinology has the potential to rapidly advance vaccine development against parasites, but it is unclear which features studied in silico will advance vaccine development. Here we consider Neospora caninum which is a globally distributed protozoan parasite causing significant economic and reproductive loss to cattle industries worldwide. The aim of this study was to use a reverse vaccinology approach to compile a worthy vaccine candidate list for N. caninum, including proteins containing pathogen-associated molecular patterns to act as vaccine carriers. The in silico approach essentially involved collecting a wide range of gene and protein features from public databases or computationally predicting those for every known Neospora protein. This data collection was then analysed using an automated high-throughput process to identify candidates. The final vaccine list compiled was judged to be the optimum within the constraints of available data, current knowledge, and existing bioinformatics programs. We consider and provide some suggestions and experience on how ranking of vaccine candidate lists can be performed. This study is therefore important in that it provides a valuable resource for establishing new directions in vaccine research against neosporosis and other parasitic diseases of economic and medical importance.

Gorle, AK, Bottomley, AL, Harry, EJ, Collins, JG, Keene, FR & Woodward, CE 2017, 'DNA condensation in live E. coli provides evidence for transertion', Molecular BioSystems, vol. 13, no. 4, pp. 677-680.
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Fluorescence microscopy has been used to examine the condensation of DNA in live bacteria by a tetranuclear polypyridylruthenium(ii) complex.

Gorrie, C, Nguyen, T, Mao, Y & Sutherland, T 2017, 'Neural progenitor cells but not astrocytes respond distally to thoracic spinal cord injury in rat models', Neural Regeneration Research, vol. 12, no. 11, pp. 1885-1885.
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Traumatic spinal cord injury (SCI) is a detrimental condition that causes loss of sensory and motor function in an individual. Many complex secondary injury cascades occur after SCI and they offer great potential for therapeutic targeting. In this study, we investigated the response of endogenous neural progenitor cells, astrocytes, and microglia to a localized thoracic SCI throughout the neuroaxis. Twenty-five adult female Sprague-Dawley rats underwent mild-contusion thoracic SCI (n = 9), sham surgery (n = 8), or no surgery (n = 8). Spinal cord and brain tissues were fixed and cut at six regions of the neuroaxis. Immunohistochemistry showed increased reactivity of neural progenitor cell marker nestin in the central canal at all levels of the spinal cord. Increased reactivity of astrocyte-specific marker glial fibrillary acidic protein was found only at the lesion epicenter. The number of activated microglia was significantly increased at the lesion site, and activated microglia extended to the lumbar enlargement. Phagocytic microglia and macrophages were significantly increased only at the lesion site. There were no changes in nestin, glial fibrillary acidic protein, microglia and macrophage response in the third ventricle of rats subjected to mild-contusion thoracic SCI compared to the sham surgery or no surgery. These findings indicate that neural progenitor cells, astrocytes and microglia respond differently to a localized SCI, presumably due to differences in inflammatory signaling. These different cellular responses may have implications in the way that neural progenitor cells can be manipulated for neuroregeneration after SCI. This needs to be further investigated.

Goyen, S, Pernice, M, Szabó, M, Warner, ME, Ralph, PJ & Suggett, DJ 2017, 'A molecular physiology basis for functional diversity of hydrogen peroxide production amongst Symbiodinium spp. (Dinophyceae)', Marine Biology, vol. 164, no. 3.
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© 2017, Springer-Verlag Berlin Heidelberg. Hydrogen peroxide (H2O2) production has been demonstrated to play a pivotal role in the photosynthetic stability of higher plants, corals and algae, and considered a primary reactive oxygen species (ROS) associated with the thermal susceptibility of Symbiodinium spp. Here, we simultaneously subjected a large number of Symbiodinium isolates (n = 16) covering broad phylogenetic diversity (clades A, B, D, F) to heat stress and characterized their photosynthetic response via fast repetition rate fluorometry (FRRf) and parallel measurements of H2O2 emissions. Based on their physiological response, isolates clustered into three novel functional groups: (1) thermally tolerant (unchanged photochemical efficiency (Fv/Fm), electron turnover (τQA) or H2O2 emission), or (2) thermally susceptible via decreased Fv/Fm, unchanged τQA, but increased H2O2, indicating energetically uncoupled PSII (thylakoid membrane instability), versus (3) thermally responsive via decreased Fv/Fm, increased τQA and H2O2, indicative of energetically coupled (but downregulated) PSII. There was no correlation between the algal phylogenetic groups and the distribution of isolates amongst these novel functional groups. Two model Symbiodinium isolates for functional groups (1) and (2) (ITS2 type A1, Symbiodinium microadriaticum, and type D1–5, Symbiodinium spp., respectively) were selected to further examine how their different thermal responses corresponded with the expression levels of two genes coding for different metalloforms of superoxide dismutase (MnSOD and NiSOD) that potentially regulate production of H2O2. S. microadriaticum demonstrated the greatest upregulation of MnSOD gene confirming recent suggestions of a role for this metalloform in the antioxidant network associated with thermal stress protection. Assigning Symbiodinium isolates into such functional groups based on coupled molecular-physiological assessment is an important step need...

Gramaglia, I, Velez, J, Combes, V, Grau, GER, Wree, M & van der Heyde, HC 2017, 'Platelets activate a pathogenic response to blood-stage Plasmodium infection but not a protective immune response', Blood, vol. 129, no. 12, pp. 1669-1679.
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Key PointsPlatelets are not killer cells of blood-stage Plasmodium parasites. Platelets are not required to activate the protective immune response to blood-stage Plasmodium infection in mice.

Green, DW, Ben-Nissan, B, Yoon, KS, Milthorpe, B & Jung, H-S 2017, 'Natural and Synthetic Coral Biomineralization for Human Bone Revitalization', Trends in Biotechnology, vol. 35, no. 1, pp. 43-54.
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Coral skeletons can regenerate replacement human bone in nonload-bearing excavated skeletal locations. A combination of multiscale, interconnected pores and channels and highly bioactive surface chemistry has established corals as an important alternative to using healthy host bone replacements. Here, we highlight how coral skeletal systems are being remolded into new calcified structures or synthetic corals by biomimetic processes, as places for the organized permeation of bone tissue cells and blood vessels. Progressive technologies in coral aquaculture and self-organization inorganic chemistry are helping to modify natural corals and create synthetic coral architectures able to accelerate bone regeneration with proper host integration at more skeletal locations, adapted to recent surgical techniques and used to treat intrinsic skeletal deformities and metabolic conditions.

Greene, GW, Thapa, R, Holt, SA, Wang, X, Garvey, CJ & Tabor, RF 2017, 'Structure and Property Changes in Self-Assembled Lubricin Layers Induced by Calcium Ion Interactions', Langmuir, vol. 33, no. 10, pp. 2559-2570.
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Gribben, PE, Nielsen, S, Seymour, JR, Bradley, DJ, West, MN & Thomas, T 2017, 'Microbial communities in marine sediments modify success of an invasive macrophyte', Scientific Reports, vol. 7, no. 1, pp. 1-8.
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AbstractInvasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrass Zostera capricorni and the invasive alga Caulerpa taxifolia and that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities in Z. capricorni sediments provide biotic resistance by reducing C. taxifolia fragment growth 119% compared to when they are inactive, and intact microbial communities in C. taxifolia sediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.

Griebel, A, Bennett, LT & Arndt, SK 2017, 'Evergreen and ever growing – Stem and canopy growth dynamics of a temperate eucalypt forest', Forest Ecology and Management, vol. 389, pp. 417-426.
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Irregular growth rings and long-lived leaves present challenges to quantify stem growth and canopy dynamics of evergreen eucalypt trees, which has impeded understanding of seasonal and inter-year biomass allocation in temperate eucalypt forests. To address this knowledge gap, we examined the sub-annual dynamics of stem and canopy growth by tree canopy class of three co-occurring species over 35months in a temperate eucalypt forest of southeastern Australia. We used dendrometers to monitor basal area increments and daily terrestrial lidar scans to monitor integrated and height-specific canopy dynamics. Associations with concomitant weather data and stand-level carbon fluxes were used to enhance understanding of biomass allocation patterns.Comparisons of growth patterns indicated seasonal asynchronicity of stem and crown growth: the canopy expanded mainly in summer and early autumn, and the stems grew mainly in spring and autumn, but also to a lesser degree in winter. Eucalypts in the dominant crown classes grew all year, with growth allocated to crown expansion and thickening in the summer months, or to stem growth in all other months. Canopy volume was stable during the first part of the study period and subsequently increased by 20%. However, stratum-specific dynamics indicated a distinct seasonality of canopy turnover, characterised by volume gains at the top of the canopy and concurrent volume losses in the middle stratum during summer. Growth patterns, as either canopy expansion or stem increment, were not clearly associated with ecosystem-scale carbon dynamics. In addition, relationships of growth with climatic variables appeared to be associative rather than causative, indicating that allocation dynamics to root growth and nonstructural carbohydrate pools will be essential in explaining ecosystem carbon dynamics in temperate eucalypt forests.

Griebel, A, Watson, D & Pendall, E 2017, 'Mistletoe, friend and foe: synthesizing ecosystem implications of mistletoe infection', Environmental Research Letters, vol. 12, no. 11, pp. 115012-115012.
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Biotic disturbances are affecting a wide range of tree species in all climates, and their occurrence is contributing to increasing rates of tree mortality globally. Mistletoe is a widespread group of parasitic plants that establishes long-lasting relationships with a diverse range of host tree species. With climate change, ecophysiological stress is increasing, potentially making trees more susceptible to mistletoe infection, which in turn leads to higher forest mortality rates. The perception of mistletoe presence in individual trees and forest stands is divided within the scientific community, leading to an ongoing debate regarding its impacts. Forest managers concerned about stand health and carbon sequestration may view mistletoe as a foe that leads to reduced productivity. In contrast, ecologists may see mistletoe as a friend, in light of the wildlife habitat, biodiversity and nutrient cycling it promotes. However, individual studies typically focus on isolated effects of mistletoe presence within their respective research area and lack a balanced, interdisciplinary perspective of mistletoe disturbance. With this conceptual paper we aim to bring together the positive and negative impacts of mistletoe presence on tree physiology, soil nutrient cycling as well as stand health and stand dynamics. We focus on the role of mistletoe-induced tree mortality in ecosystem succession and biodiversity. In addition, we present potential modifications of mistletoe presence on the energy budget and on forest vulnerability to climate change, which could feed back into stand dynamics and disturbance patterns. Lastly, we will identify the most pressing remaining knowledge gaps and highlight priorities for future research on this widespread agent of biotic disturbance.

Grosso, G, Moon, H, Lienhard, B, Ali, S, Efetov, DK, Furchi, MM, Jarillo-Herrero, P, Ford, MJ, Aharonovich, I & Englund, D 2017, 'Tunable and high-purity room temperature single-photon emission from atomic defects in hexagonal boron nitride', Nature Communications, vol. 8, no. 1.
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Two-dimensional van der Waals materials have emerged as promising platforms for solid-state quantum information processing devices with unusual potential for heterogeneous assembly. Recently, bright and photostable single photon emitters were reported from atomic defects in layered hexagonal boron nitride (hBN), but controlling inhomogeneous spectral distribution and reducing multi-photon emission presented open challenges. Here, we demonstrate that strain control allows spectral tunability of hBN single photon emitters over 6 meV, and material processing sharply improves the single photon purity. We observe high single photon count rates exceeding 7 × 106 counts per second at saturation, after correcting for uncorrelated photon background. Furthermore, these emitters are stable to material transfer to other substrates. High-purity and photostable single photon emission at room temperature, together with spectral tunability and transferability, opens the door to scalable integration of high-quality quantum emitters in photonic quantum technologies.

GRZYWACZ, A, WALLMAN, JF & PIWCZYŃSKI, M 2017, 'To be or not to be a valid genus: the systematic position of Ophyra R.‐D. revised (Diptera: Muscidae)', Systematic Entomology, vol. 42, no. 4, pp. 714-723.
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AbstractOphyra Robineau‐Desvoidy is one of the better‐studied genera of the family Muscidae (Diptera). The larvae of species of this genus feed on highly decomposed organic matter of various origins, and may reveal predatory behaviour as they mature. These feeding habits, combined with the widespread distribution and close association with human dwellings of some species, give the genus commercial and medico‐legal importance. However, the systematic position of Ophyra has been a matter of debate for many years. Ophyra has been considered by muscid workers to be either a valid genus or a junior synonym of Hydrotaea Robineau‐Desvoidy. A lack of agreement about the systematic position of Ophyra has led to serious errors, particularly in the applied literature. Recent molecular and morphological studies provided contradictory information on the validity of the genus and its subfamilial classification. We revise the systematic position of Ophyra herein by means of molecular phylogenetic reconstruction. Our results are incongruent with opinions on the systematic position of Ophyra based on previously published molecular phylogenies, although they correspond with the concept of the genus based on adult morphology. All analyses of the concatenated dataset revealed Ophyra as monophyletic and placed within a paraphyletic Azeliini. Depending on the phylogenetic approach, Ophyra was placed within either a monophyletic, paraphyletic or polyphyletic Hydrotaea, yet always closely related to a certain group of species. We conclude that Ophyra, as currently defined, should not be considered a valid name, yet a detailed reconstruction of the genus...

Gunawan, C, Marquis, CP, Amal, R, Sotiriou, GA, Rice, SA & Harry, EJ 2017, 'Widespread and Indiscriminate Nanosilver Use: Genuine Potential for Microbial Resistance', ACS Nano, vol. 11, no. 4, pp. 3438-3445.
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© 2017 American Chemical Society. In this era of increasing antibiotic resistance, the use of alternative antimicrobials such as silver has become more widespread. Superior antimicrobial activity has been provided through fabrication of silver nanoparticles or nanosilver (NAg), which imparts cytotoxic actions distinct from those of bulk silver. In the wake of the recent discoveries of bacterial resistance to NAg and its rising incorporation in medical and consumer goods such as wound dressings and dietary supplements, we argue that there is an urgent need to monitor the prevalence and spread of NAg microbial resistance. In this Perspective, we describe how the use of NAg in commercially available products facilitates prolonged microorganism exposure to bioavailable silver, which underpins the development of resistance. Furthermore, we advocate for a judicial approach toward NAg use in order to preserve its efficacy and to avoid environmental disruption.

Guo, X, Sun, B, Su, D, Liu, X, Liu, H, Wang, Y & Wang, G 2017, 'Recent developments of aprotic lithium-oxygen batteries: functional materials determine the electrochemical performance', Science Bulletin, vol. 62, no. 6, pp. 442-452.
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© 2017 Lithium oxygen battery has the highest theoretical capacity among the rechargeable batteries and it can reform energy storage technology if it comes to commercialization. However, many critical challenges, mainly embody as low charge/discharge round-trip efficiency and poor cycling stability, impede the development of Li-O2 batteries. The electrolyte decomposition, lithium metal anode corrosion and sluggish oxygen reaction kinetics at cathode are all responsible for poor electrochemical performances. Particularly, the catalytic cathode of Li-O2 batteries, playing a crucial role to reduce the oxygen during discharging and to decompose discharge products during charging, is regarded as a breakthrough point that has been comprehensive investigated. In this review, the progress and issues of electrolyte, anode and cathode, especially the catalysts used at cathode, are systematically summarized and discussed. Then the perspectives toward the developments of a long life Li-O2 battery are also presented at last.

Guo, X, Xie, X, Choi, S, Zhao, Y, Liu, H, Wang, C, Chang, S & Wang, G 2017, 'Sb₂O₃/MXene(Ti₃C₂T_x) hybrid anode materials with enhanced performance for sodium-ion batteries', Journal of Materials Chemistry A, vol. 5, no. 24, pp. 12445-12452.
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Sb₂O₃/MXene(Ti₃C₂T_x) composites with Sb₂O₃nanoparticles confined in the 3D network of Ti₃C₂T_xflakes were fabricated as anodes for Na-ion batteries.

Gupta, A, Curran, JM, Coulson, S & Triggs, CM 2017, 'Comparison of intra-day and inter-day variation in LIBS spectra', Forensic Chemistry, vol. 3, pp. 36-40.
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© 2017 Elsevier B.V. Laser Induced Breakdown Spectroscopy (LIBS) is an analytical chemistry technique that has the potential to identify and measure the elements in a substance of interest. LIBS is applicable for any phase (solid, liquid or gas). LIBS has gained importance in the fields of material identification, biomedical science, forensics, military, art and archaeology in the recent years. In spite of its many advantages over other instruments, it has a few drawbacks such as poor precision and repeatability. That is, different spectra may be observed for the same sample over successive runs. This indicates poor precision of the instrument. This paper presents an experiment designed to investigate the claim that there is higher variation in the experiments conducted on different days as compared to the experiments conducted on the same day. This study examines the variability in the spectra between the runs on the same day, and the variability between runs on different days using samples from a standard reference glass, and discusses the conclusions that can be drawn from the results.

Gururaj, S, Palmer, EE, Sheehan, GD, Kandula, T, Macintosh, R, Ying, K, Morris, P, Tao, J, Dias, K-R, Zhu, Y, Dinger, ME, Cowley, MJ, Kirk, EP, Roscioli, T, Sachdev, R, Duffey, ME, Bye, A & Bhattacharjee, A 2017, 'A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy', Cell Reports, vol. 21, no. 4, pp. 926-933.
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© 2017 The Author(s) Early infantile epileptic encephalopathies (EOEE) are a debilitating spectrum of disorders associated with cognitive impairments. We present a clinical report of a KCNT2 mutation in an EOEE patient. The de novo heterozygous variant Phe240Leu SLICK was identified by exome sequencing and confirmed by Sanger sequencing. Phe240Leu rSlick and hSLICK channels were electrophysiologically, heterologously characterized to reveal three significant alterations to channel function. First, [Cl−]i sensitivity was reversed in Phe240Leu channels. Second, predominantly K+-selective WT channels were made to favor Na+ over K+ by Phe240Leu. Third, and consequent to altered ion selectivity, Phe240Leu channels had larger inward conductance. Further, rSlick channels induced membrane hyperexcitability when expressed in primary neurons, resembling the cellular seizure phenotype. Taken together, our results confirm that Phe240Leu is a “change-of-function” KCNT2 mutation, demonstrating unusual altered selectivity in KNa channels. These findings establish pathogenicity of the Phe240Leu KCNT2 mutation in the reported EOEE patient. Gururaj et al. report a KCNT2 mutation in a patient with epileptic encephalopathy and employ electrophysiological analyses to establish channel properties that could underlie epileptogenesis: namely, inhibition by high [Cl−]i and loss of exclusive selectivity to K+. Furthermore, primary neurons expressing Ph240Leu display a hyperexcitable phenotype.

Haddadi, N, Lin, Y, Simpson, A, Nassif, N & McGowan, E 2017, '“Dicing and Splicing” Sphingosine Kinase and Relevance to Cancer', International Journal of Molecular Sciences, vol. 18, no. 9, pp. 1891-1891.
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Sphingosine kinase (SphK) is a lipid enzyme that maintains cellular lipid homeostasis. Two SphK isozymes, SphK1 and SphK2, are expressed from different chromosomes and several variant isoforms are expressed from each of the isozymes, allowing for the multi-faceted biological diversity of SphK activity. Historically, SphK1 is mainly associated with oncogenicity, however in reality, both SphK1 and SphK2 isozymes possess oncogenic properties and are recognized therapeutic targets. The absence of mutations of SphK in various cancer types has led to the theory that cancer cells develop a dependency on SphK signaling (hyper-SphK signaling) or “non-oncogenic addiction”. Here we discuss additional theories of SphK cellular mislocation and aberrant “dicing and splicing” as contributors to cancer cell biology and as key determinants of the success or failure of SphK/S1P (sphingosine 1 phosphate) based therapeutics.

Hamidian, M & Hall, RM 2017, 'Acinetobacter baumannii ATCC 19606 Carries GI sul2 in a Genomic Island Located in the Chromosome', Antimicrobial Agents and Chemotherapy, vol. 61, no. 1.
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Hamidian, M & Hall, RM 2017, 'Origin of the AbGRI1 antibiotic resistance island found in the comM gene of Acinetobacter baumannii GC2 isolates', Journal of Antimicrobial Chemotherapy, vol. 72, no. 10, pp. 2944-2947.
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Hamidian, M, Nigro, SJ & Hall, RM 2017, 'Problems with the Oxford Multilocus Sequence Typing Scheme for Acinetobacter baumannii: Do Sequence Type 92 (ST92) and ST109 Exist?', Journal of Clinical Microbiology, vol. 55, no. 7, pp. 2287-2289.
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Hamidian, M, Nigro, SJ, Hartstein, RM & Hall, RM 2017, 'RCH51, a multiply antibiotic-resistant Acinetobacter baumannii ST103IP isolate, carries resistance genes in three plasmids, including a novel potentially conjugative plasmid carrying oxa235 in transposon Tn6252', Journal of Antimicrobial Chemotherapy, vol. 72, no. 7, pp. 1907-1910.
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To determine the identity and context of genes conferring antibiotic resistance in a sporadic multiply antibiotic-resistant Acinetobacter baumannii recovered at Royal Children's Hospital, Brisbane.The antibiotic resistance phenotype for 23 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of RCH51 was determined using the Illumina HiSeq platform. Antibiotic resistance determinants were identified using ResFinder. Plasmids were recovered by transformation.Isolate RCH51 belongs to the uncommon STs ST103 IP (7-3-2-1-7-1-4) and ST514 OX (1-52-29-28-18-114-7). It was found to be resistant to sulfamethoxazole, tetracycline, gentamicin, tobramycin and kanamycin and also exhibited reduced susceptibility to imipenem (MIC 2 mg/L) and meropenem (MIC 6 mg/L). RCH51 carries the oxa235 , sul2 , floR , aadB and tet39 resistance genes, all located on plasmids. The largest of the three plasmids, pRCH51-3, is 52 789 bp and carries oxa235 in the ISAba1-bounded transposon Tn 6252 , as well as sul2 and floR . pRCH51-3 represents a new A. baumannii plasmid family that is potentially conjugative as it contains several genes predicted to encode transfer functions. However, conjugation of pRCH51-3 was not detected. The aadB and tet39 resistance genes were each found in small plasmids identical to the known plasmids pRAY*-v1 and pRCH52-1, respectively.The resistance gene complement of RCH51 was found in three plasmids. pRCH51-3, which carries the oxa235 , sul2 and floR resistance genes, represents a new, potentially conjugative A. baumannii plasmid type.

Hamidian, M, Venepally, P, Hall, RM & Adams, MD 2017, 'Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1', Genome Announcements, vol. 5, no. 35, pp. 1-2.
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ABSTRACT Extensively antibiotic-resistant Acinetobacter baumannii isolate AB0057 recovered in the United States in 2004 was one of the first global clone 1 isolates to be completely sequenced. Here, the complete 4.05-Mb genome sequence (chromosome and one plasmid) has been revised using Illumina HiSeq data and targeted sequencing of PCR products.

Hansbro, PM, Haw, TJ, Starkey, MR & Miyake, K 2017, 'Toll-like receptors in COPD', European Respiratory Journal, vol. 49, no. 5, pp. 1700739-1700739.
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Hansbro, PM, Kim, RY, Starkey, MR, Donovan, C, Dua, K, Mayall, JR, Liu, G, Hansbro, NG, Simpson, JL, Wood, LG, Hirota, JA, Knight, DA, Foster, PS & Horvat, JC 2017, 'Mechanisms and treatments for severe, steroid‐resistant allergic airway disease and asthma', Immunological Reviews, vol. 278, no. 1, pp. 41-62.
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SummarySevere, steroid‐resistant asthma is clinically and economically important since affected individuals do not respond to mainstay corticosteroid treatments for asthma. Patients with this disease experience more frequent exacerbations of asthma, are more likely to be hospitalized, and have a poorer quality of life. Effective therapies are urgently required, however, their development has been hampered by a lack of understanding of the pathological processes that underpin disease. A major obstacle to understanding the processes that drive severe, steroid‐resistant asthma is that the several endotypes of the disease have been described that are characterized by different inflammatory and immunological phenotypes. This heterogeneity makes pinpointing processes that drive disease difficult in humans. Clinical studies strongly associate specific respiratory infections with severe, steroid‐resistant asthma. In this review, we discuss key findings from our studies where we describe the development of representative experimental models to improve our understanding of the links between infection and severe, steroid‐resistant forms of this disease. We also discuss their use in elucidating the mechanisms, and their potential for developing effective therapeutic strategies, for severe, steroid‐resistant asthma. Finally, we highlight how the immune mechanisms and therapeutic targets we have identified may be applicable to obesity‐or pollution‐associated asthma.

Hare, DJ 2017, 'Commentary: Comments regarding Becker et al. (Analytica Chimica Acta, 835, 2014, 1–18)', Analytica Chimica Acta, vol. 972, pp. 12-15.
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Hare, DJ 2017, 'Hepcidin: a real-time biomarker of iron need', Metallomics, vol. 9, no. 6, pp. 606-618.
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There are numerous blood-based biomarkers for assessing iron stores, but all come with certain limitations. Hepcidin is a hormone primarily produced in the liver that has been proposed as the 'master regulator' of dietary uptake and iron metabolism, and has enormous potential to provide a 'real time' indicator of body iron levels. In this Minireview, the biochemical function of hepcidin in regulating iron levels will be discussed, with a specific focus on how hepcidin can aid in the assessment of iron stores and clinical diagnosis of iron deficiency, iron deficiency anaemia and other iron-related disorders. The role hepcidin itself plays in diseases of iron metabolism will be examined, and current efforts to translate hepcidin assays into the clinic will be critically appraised. Potential limitations of hepcidin as a marker of iron need will also be addressed, as well as the development of new therapies that directly target the hormone that sits atop the hierarchy of systemic iron metabolism.

Hare, DJ, Cardoso, BR, Raven, EP, Double, KL, Finkelstein, DI, Szymlek-Gay, EA & Biggs, B-A 2017, 'Excessive early-life dietary exposure: a potential source of elevated brain iron and a risk factor for Parkinson’s disease', npj Parkinson's Disease, vol. 3, no. 1, pp. 1-5.
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AbstractIron accumulates gradually in the ageing brain. In Parkinson’s disease, iron deposition within the substantia nigra is further increased, contributing to a heightened pro-oxidant environment in dopaminergic neurons. We hypothesise that individuals in high-income countries, where cereals and infant formulae have historically been fortified with iron, experience increased early-life iron exposure that predisposes them to age-related iron accumulation in the brain. Combined with genetic factors that limit iron regulatory capacity and/or dopamine metabolism, this may increase the risk of Parkinson’s diseases. We propose to (a) validate a retrospective biomarker of iron exposure in children; (b) translate this biomarker to adults; (c) integrate it with in vivo brain iron in Parkinson’s disease; and (d) longitudinally examine the relationships between early-life iron exposure and metabolism, brain iron deposition and Parkinson’s disease risk. This approach will provide empirical evidence to support therapeutically addressing brain iron deposition in Parkinson’s diseases and produce a potential biomarker of Parkinson’s disease risk in preclinical individuals.

Hare, DJ, Kysenius, K, Paul, B, Knauer, B, Hutchinson, RW, O'Connor, C, Fryer, F, Hennessey, TP, Bush, AI, Crouch, PJ & Doble, PA 2017, 'Imaging Metals in Brain Tissue by Laser Ablation - Inductively Coupled Plasma - Mass Spectrometry (LA-ICP-MS)', Journal of Visualized Experiments, vol. 2017, no. 119, pp. 1-8.
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© 2017 Journal of Visualized Experiments. Metals are found ubiquitously throughout an organism, with their biological role dictated by both their chemical reactivity and abundance within a specific anatomical region. Within the brain, metals have a highly compartmentalized distribution, depending on the primary function they play within the central nervous system. Imaging the spatial distribution of metals has provided unique insight into the biochemical architecture of the brain, allowing direct correlation between neuroanatomical regions and their known function with regard to metal-dependent processes. In addition, several age-related neurological disorders feature disrupted metal homeostasis, which is often confined to small regions of the brain that are otherwise difficult to analyze. Here, we describe a comprehensive method for quantitatively imaging metals in the mouse brain, using laser ablation - inductively coupled plasma - mass spectrometry (LA-ICP-MS) and specially designed image processing software. Focusing on iron, copper and zinc, which are three of the most abundant and disease-relevant metals within the brain, we describe the essential steps in sample preparation, analysis, quantitative measurements and image processing to produce maps of metal distribution within the low micrometer resolution range. This technique, applicable to any cut tissue section, is capable of demonstrating the highly variable distribution of metals within an organ or system, and can be used to identify changes in metal homeostasis and absolute levels within fine anatomical structures.

Hare, DJ, New, EJ & McColl, G 2017, 'Imaging metals in biology: pictures of metals in health and disease', Metallomics, vol. 9, no. 4, pp. 343-345.
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Hare, NJ, Lee, LY, Loke, I, Britton, WJ, Saunders, BM & Thaysen-Andersen, M 2017, 'Mycobacterium tuberculosis Infection Manipulates the Glycosylation Machinery and the N-Glycoproteome of Human Macrophages and Their Microparticles', Journal of Proteome Research, vol. 16, no. 1, pp. 247-263.
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© 2016 American Chemical Society. Tuberculosis (TB) remains a prevalent and lethal infectious disease. The glycobiology associated with Mycobacterium tuberculosis infection of frontline alveolar macrophages is still unresolved. Herein, we investigated the regulation of protein N-glycosylation in human macrophages and their secreted microparticles (MPs) used for intercellular communication upon M. tb infection. LC-MS/MS-based proteomics and glycomics were performed to monitor the regulation of glycosylation enzymes and receptors and the N-glycome in in vitro-differentiated macrophages and in isolated MPs upon M. tb infection. Infection promoted a dramatic regulation of the macrophage proteome. Most notably, significant infection-dependent down-regulation (4-26 fold) of 11 lysosomal exoglycosidases, e.g., β-galactosidase, β-hexosaminidases and α-/β-mannosidases, was observed. Relative weak infection-driven transcriptional regulation of these exoglycosidases and a stronger augmentation of the extracellular hexosaminidase activity demonstrated that the lysosome-centric changes may originate predominantly from infection-induced secretion of the lysosomal content. The macrophages showed heterogeneous N-glycan profiles and displayed significant up-regulation of complex-type glycosylation and concomitant down-regulation of paucimannosylation upon infection. Complementary intact N-glycopeptide analysis supported a subcellular-specific manipulation of the glycosylation machinery and altered glycosylation patterns of lysosomal N-glycoproteins within infected macrophages. Interestingly, the corresponding macrophage-derived MPs displayed unique N-glycome and proteome signatures supporting a preferential packaging from plasma membranes. The MPs were devoid of infection-dependent N-glycosylation signatures, but interestingly displayed increased levels of the glyco-initiating oligosaccharyltransferase complex and associated α-glucosidases that correlated with increased...

Harmer, CJ, Hamidian, M & Hall, RM 2017, 'pIP40a, a type 1 IncC plasmid from 1969 carries the integrative element GI sul2 and a novel class II mercury resistance transposon', Plasmid, vol. 92, pp. 17-25.
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The 167.5kb sequence of the conjugative IncC plasmid pIP40a, isolated from a Pseudomonas aeruginosa in 1969, was analysed. pIP40a confers resistance to kanamycin, neomycin, ampicillin, sulphonamides and mercuric ions, and several insertions in a type 1 IncC backbone were found, including copies of IS3, Tn1000 and a novel mercury resistance transposon, Tn6182. The antibiotic resistance genes were in two locations. Tn6023, containing the aphA1 kanamycin and neomycin resistance gene, is in a partial copy of Tn1/Tn2/Tn3 (blaTEM, ampicillin resistance) in the kfrA gene, and the sul2 sulphonamide resistance gene is in the integrative element GIsul2 in the position of ARI-B islands. The 11.5kb class II transposon Tn6182 is only distantly related to other class II transposons, with at most 33% identity between the TnpA of Tn6182 and TnpA of other group members. In addition, the inverted repeats are 37bp rather than 38bp, and the likely resolution enzyme is a tyrosine recombinase (TnpI). Re-annotation of GIsul2 revealed genes predicted to confer resistance to arsenate and arsenite, but resistance was not detected. The location of GIsul2 confirms it as the progenitor of the ARI-B configurations seen in many IncC plasmids isolated more recently. However, GIsul2 has integrated at the same site in type 1 and type 2 IncC plasmids, indicating that it targets this site. Analysis of the distribution of GIsul2 revealed that it in addition to its chromosomal integration site at the 3'-end of the guaA gene, it has also integrated into other plasmids, increasing its mobility.

Hatoum, D, Haddadi, N, Lin, Y, Nassif, NT & McGowan, EM 2017, 'Mammalian sphingosine kinase (SphK) isoenzymes and isoform expression: challenges for SphK as an oncotarget', Oncotarget, vol. 8, no. 22, pp. 36898-36929.
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The various sphingosine kinase (SphK) isoenzymes (isozymes) and isoforms, key players in normal cellular physiology, are strongly implicated in cancer and other diseases. Mutations in SphKs, that may justify abnormal physiological function, have not been recorded. Nonetheless, there is a large and growing body of evidence demonstrating the contribution of gain or loss of function and the imbalance in the SphK/S1P rheostat to a plethora of pathological conditions including cancer, diabetes and inflammatory diseases. SphK is expressed as two isozymes SphK1 and SphK2, transcribed from genes located on different chromosomes and both isozymes catalyze the phosphorylation of sphingosine to S1P. Expression of each SphK isozyme produces alternately spliced isoforms. In recent years the importance of the contribution of SpK1 expression to treatment resistance in cancer has been highlighted and, additionally, differences in treatment outcome appear to also be dependent upon SphK isoform expression. This review focuses on an exciting emerging area of research involving SphKs functions, expression and subcellular localization, highlighting the complexity of targeting SphK in cancer and also comorbid diseases. This review also covers the SphK isoenzymes and isoforms from a historical perspective, from their first discovery in murine species and then in humans, their role(s) in normal cellular function and in disease processes, to advancement of SphK as an oncotarget.

Hatoum, D, Yagoub, D, Ahadi, A, Nassif, NT & McGowan, EM 2017, 'Annexin/S100A Protein Family Regulation through p14ARF-p53 Activation: A Role in Cell Survival and Predicting Treatment Outcomes in Breast Cancer', PLOS ONE, vol. 12, no. 1, pp. e0169925-e0169925.
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© 2017 Hatoum et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The annexin family and S100A associated proteins are important regulators of diverse calcium- dependent cellular processes including cell division, growth regulation and apoptosis. Dysfunction of individual annexin and S100A proteins is associated with cancer progression, metastasis and cancer drug resistance. This manuscript describes the novel finding of differential regulation of the annexin and S100A family of proteins by activation of p53 in breast cancer cells. Additionally, the observed differential regulation is found to be beneficial to the survival of breast cancer cells and to influence treatment efficacy. We have used unbiased, quantitative proteomics to determine the proteomic changes occurring post p14ARF-p53 activation in estrogen receptor (ER) breast cancer cells. In this report we identified differential regulation of the annexin/S100A family, through unique peptide recognition at the N-terminal regions, demonstrating p14ARF-p53 is a central orchestrator of the annexin/S100A family of calcium regulators in favor of pro-survival functions in the breast cancer cell. This regulation was found to be cell-type specific. Retrospective human breast cancer studies have demonstrated that tumors with functional wild type p53 (p53wt) respond poorly to some chemotherapy agents compared to tumors with a non-functional p53. Given that modulation of calcium signaling has been demonstrated to change sensitivity of chemotherapeutic agents to apoptotic signals, in principle, we explored the paradigm of how p53 modulation of calcium regulators in ER+ breast cancer patients impacts and influences therapeutic outcomes.

Heather, E, Bortz, A, Shimmon, R & McDonagh, AM 2017, 'Organic impurity profiling of methylone and intermediate compounds synthesized from catechol', Drug Testing and Analysis, vol. 9, no. 3, pp. 436-445.
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This work examined the synthesis and organic impurity profile of methylone prepared from catechol. The primary aim of this work was to determine whether the synthetic pathway used to prepare 3,4‐methylenedioxypropiophenone could be ascertained through analysis of the synthesized methylone. The secondary aim was the structural elucidation and origin determination of the organic impurities detected in methylone and the intermediate compounds. The organic impurities present in the reaction products were identified using GC–MS and NMR spectroscopy. Six organic impurities were detected in 1,3‐benzodioxole and identified as the 1,3‐benzodioxole dimer, 1,3‐benzodioxole trimer, [1,3] dioxolo[4,5‐b]oxanthrene, 4,4′‐, 4,5′‐, and 5,5′‐methylenebis‐1,3‐benzodioxole. Six organic impurities were detected in 3,4‐methylenedioxypropiophenone and identified as (2‐hydroxyphenyl) propanoate, [2‐(chloromethoxy) phenyl] propanoate, (2‐propanoyloxyphenyl)propanoate, 5‐[1‐(1,3‐benzodioxol‐5‐yl)prop‐1‐enyl]‐1,3‐benzodioxole, (5E)‐ and (5Z)‐7‐(1,3‐benzodioxol‐5‐yl)‐5‐ethylidene‐6‐methyl‐cyclopenta[f][1,3]benzodioxole). Exploratory synthetic experiments were also conducted to unambiguously identify the organic impurities detected in 3,4‐methylenedioxypropiophenone. Two organic impurities were detected in 5‐bromo‐3,4‐methylenedioxypropiophenone and identified as [2‐(chloromethoxy)phenyl] propanoate and 3,4‐methylenedioxypropiophenone. Five organic impurities were detected in methylone and identified as 3,4‐methylenedioxypropiophenone, 1‐(1,3‐benzodioxol‐5‐yl)‐N‐methyl‐propan‐1‐imine, 1‐(1,3‐benzodioxol‐5‐yl)‐2‐methylimino‐propan‐1‐one, 1‐(1,3‐benzodioxol‐5‐yl)‐N1,N2‐dimethyl‐propane‐1,2‐diimine and butylated hydroxytoluene. The origin of these organic impurities was also ascertained, pro...

Hing, ML, Klanten, OS, Dowton, M & Wong, MYL 2017, 'The Right Tools for the Job: Cooperative Breeding Theory and an Evaluation of the Methodological Approaches to Understanding the Evolution and Maintenance of Sociality', Frontiers in Ecology and Evolution, vol. 5, no. AUG.
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© 2017 Hing, Klanten, Dowton and Wong. Why do we observe so many examples in nature in which individuals routinely delay or completely forgo their own reproductive opportunities in order to join and remain within a group? Cooperative breeding theory provides a rich framework with which to study the factors that may influence the costs and benefits of remaining philopatric as a non-breeder. This is often viewed as an initial step in the development of costly helping behavior provided by non-breeding subordinates. Despite many excellent empirical studies testing key concepts of the theory, there is still debate regarding the relative importance of various evolutionary forces, suggesting that there may not be a general explanation but rather a dynamic and taxonomically varied combination of factors influencing the evolution and maintenance of sociality. Here, we explore two potential improvements in the study of sociality that could aid in the progress of this field. The first addresses the fact that empirical studies of social evolution are typically conducted using either comparative, observational or manipulative methodologies. Instead, we suggest a holistic approach, whereby observational and experimental studies are designed with the explicit view of advancing comparative analyses of sociality for the taxon, and in tandem, where comparative work informs targeted research effort on specific (usually understudied) species within the lineage. A second improvement relates to the broadening of tests of cooperative breeding theory to include taxa where subordinates do not necessarily provide active cooperation within the group. The original bias toward "helpful subordinates" arose from a focus on terrestrial taxa. However, recent consideration of other taxa, especially marine taxa, is slowly revealing that the theory can and should encompass a continuum of cooperative social systems, including those where subordinates do not actively help. This review summarizes the ...

Hofstetter, C, Maitre, M, Beavis, A, Roux, CP, Weyermann, C & Gassner, A-L 2017, 'A study of transfer and prevalence of organic gunshot residues', Forensic Science International, vol. 277, pp. 241-251.
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The main goal of the present study was to determine the amounts and distribution of organic gunshot residues (OGSR) on the shooter's upper body and clothing after discharging a pistol. A preliminary study was also performed to evaluate the prevalence of OGSR in the general population as well as in a police laboratory environment. In the transfer study, results indicated that OGSR are not only transferred to the hand of the shooter, but also to other parts of the upper body. Thus, wrists and forearms also represent interesting targets as they are washed less frequently than hands. Samples from the face and hair of the shooters resulted in no OGSR detection just after firing. It was also observed that the concentrations recovered from clothing are generally higher compared to the same skin area. Prevalence in both general (n=27) and police populations (n=25) was low. No OGSR was detected in the samples from the general population and only two samples from the police population were found positive.

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 2017, '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. 26, no. 14, pp. 2616-2626.
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Amyotrophic lateral sclerosis (ALS) is a rapidly progressive, fatal neurodegenerative disease characterised by the death of upper and lower motor neurons. Approximately 10% of cases have a known family history of ALS and disease-linked mutations in multiple genes have been identified. ALS-linked mutations in CCNF were recently reported, however the pathogenic mechanisms associated with these mutations are yet to be established. To investigate possible disease mechanisms, we developed in vitro and in vivo models based on an ALS-linked missense mutation in CCNF. Proteomic analysis of the in vitro models identified the disruption of several cellular pathways in the mutant model, including caspase-3 mediated cell death. Transient overexpression of human CCNF in zebrafish embryos supported this finding, with fish expressing the mutant protein found to have increased levels of cleaved (activated) caspase-3 and increased cell death in the spinal cord. The mutant CCNF fish also developed a motor neuron axonopathy consisting of shortened primary motor axons and increased frequency of aberrant axonal branching. Importantly, we demonstrated a significant correlation between the severity of the CCNF-induced axonopathy and a reduced motor response to a light stimulus (photomotor response). This is the first report of an ALS-linked CCNF mutation in vivo and taken together with the in vitro model identifies the disruption of cell death pathways as a significant consequence of this mutation. Additionally, this study presents a valuable new tool for use in ongoing studies investigating the pathobiology of ALS-linked CCNF mutations.

Ho-Le, TP, Center, JR, Eisman, JA, Nguyen, HT & Nguyen, TV 2017, 'Prediction of Bone Mineral Density and Fragility Fracture by Genetic Profiling', Journal of Bone and Mineral Research, vol. 32, no. 2, pp. 285-293.
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ABSTRACT   Although the susceptibility to fracture is partly determined by genetic factors, the contribution of newly discovered genetic variants to fracture prediction is still unclear. This study sought to define the predictive value of a genetic profiling for fracture prediction. Sixty-two bone mineral density (BMD)-associated single-nucleotide polymorphisms (SNPs) were genotyped in 557 men and 902 women who had participated in the Dubbo Osteoporosis Epidemiology Study. The incidence of fragility fracture was ascertained from X-ray reports between 1990 and 2015. Femoral neck BMD was measured by dual-energy X-ray absorptiometry. A weighted polygenic risk score (genetic risk score [GRS]) was created as a function of the number of risk alleles and their BMD-associated regression coefficients for each SNP. The association between GRS and fracture risk was assessed by the Cox proportional hazards model. Individuals with greater GRS had lower femoral neck BMD (p &lt; 0.01), but the variation in GRS accounted for less than 2% of total variance in BMD. Each unit increase in GRS was associated with a hazard ratio of 1.20 (95% CI, 1.04 to 1.38) for fracture, and this association was independent of age, prior fracture, fall, and in a subset of 33 SNPs, independent of femoral neck BMD. The significant association between GRS and fracture was observed for the vertebral and wrist fractures, but not for hip fracture. The area under the receiver-operating characteristic (ROC) curve (AUC) for the model with GRS and clinical risk factors was 0.71 (95% CI, 0.68 to 0.74). With GRS, the correct reclassification of fracture versus nonfracture ranged from 12% for hip fracture to 23% for wrist fracture. A genetic profiling of BMD- associated genetic variants could improve the accuracy of fracture prediction over and above that of clinical risk factors ...

Hong, C, Ning, Y, Wang, S, Wu, H, Carroll, RJ & Chen, Y 2017, 'PLEMT: A Novel Pseudolikelihood-Based EM Test for Homogeneity in Generalized Exponential Tilt Mixture Models', Journal of the American Statistical Association, vol. 112, no. 520, pp. 1393-1404.
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Motivated by analyses of DNA methylation data, we propose a semiparametric mixture model, namely the generalized exponential tilt mixture model, to account for heterogeneity between differentially methylated and non-differentially methylated subjects in the cancer group, and capture the differences in higher order moments (e.g. mean and variance) between subjects in cancer and normal groups. A pairwise pseudolikelihood is constructed to eliminate the unknown nuisance function. To circumvent boundary and non-identifiability problems as in parametric mixture models, we modify the pseudolikelihood by adding a penalty function. In addition, the test with simple asymptotic distribution has computational advantages compared with permutation-based test for high-dimensional genetic or epigenetic data. We propose a pseudolikelihood based expectation-maximization test, and show the proposed test follows a simple chi-squared limiting distribution. Simulation studies show that the proposed test controls Type I errors well and has better power compared to several current tests. In particular, the proposed test outperforms the commonly used tests under all simulation settings considered, especially when there are variance differences between two groups. The proposed test is applied to a real data set to identify differentially methylated sites between ovarian cancer subjects and normal subjects.

Horvat, JC, Ali, MK, Johnstone, D, Kim, RY, Mayall, JR, Karim, R, Pinkerton, JW, Heidari, M, Martin, KL, Donovam, C, Liu, G, Milward, EA & Hansbro, PM 2017, 'Role for dysregulated iron in the pathogenesis of murine models of lung disease', The Journal of Immunology, vol. 198, no. 1_Supplement, pp. 53.8-53.8.
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Abstract Altered iron levels and/or dysregulated iron homeostasis have been associated with a number of lung diseases, however, the mechanisms that underpin these associations, and whether iron plays a role in the pathogenesis of disease, are yet to be fully elucidated. In this study, systemic and pulmonary iron and lung structure and function were assessed in transferrin receptor (TFR)2 mutant and wild-type (WT) BALB/c mice fed a high-iron diet (containing 2% carbonyl iron) compared to normal diet controls, respectively. The effects of increased iron loading on murine models of ovalbumin- and house dust mite-induced allergic airways disease (AAD) were also assessed. Excess iron accumulation was observed in the lungs in both the genetic and diet-induced models of iron overloading. Increased iron levels in the lung were associated with emphysema-like alveolar enlargement, small airways collagen deposition, alterations in baseline lung function and increased airways hyper-responsiveness (AHR). Increased iron loading also resulted in altered type 1, 2 and 17 cytokine production, increased eosinophilic inflammation and severe, steroid-resistant AHR in AAD. Interestingly, AAD also results in altered systemic and pulmonary iron levels and iron regulatory molecule expression. These data show that increased iron levels in the lung results in emphysema and airways fibrosis that corresponds with reduced lung function. We also show that lung disease may be closely associated with changes in iron homeostasis. These models will be used to characterize the interplay between iron and immunity in the pathogenesis of lung disease and determine the therapeutic effectiveness of correcting dysregulated iron homeostasis for the treatment of lung disease.

Horvat, JC, Mayall, JR, Mangan, NE, Brown, AC, Chevalier, A, Starkey, MR, Kim, RY, Hertzog, PJ & Hansbro, PM 2017, 'IFN-ɛ regulated innate immune responses in the female reproductive tract during Chlamydia infection', The Journal of Immunology, vol. 198, no. 1_Supplement, pp. 149.21-149.21.
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Abstract The immune processes involved in the clearance and immunopathology of Chlamydia infection in the female reproductive tract (FRT) are not well understood. In previous ground-breaking studies we showed that IFN-ɛ, a novel type I IFN that is exclusively and constitutively expressed in the FRT, plays an important role in protecting against Chlamydia infections. Here, we examined the effects of IFN-ɛ on innate immune processes in the FRT in order to elucidate the mechanisms by which IFN-ɛ protects against Chlamydia infections. Female WT and IFN-ɛ−/− C57BL/6 mice were pre-treated with progesterone and infected intra-vaginally with Chlamydia muridarum or sham-infected. Uterine horns were harvested and the effects of IFN-ɛ deficiency on immune factor expression and cellular infiltration were assessed using microarray/bioinformatics analyses, real-time qPCR and flow cytometry. IFN-ɛ uniquely regulated the expression of 744 genes at baseline and 802 genes during Chlamydia infection, and universally regulated the transcription of 61 genes, regardless of infection status. Of note, pathways associated with protective innate responses, such as IFN regulatory factor activation and pattern recognition receptor signalling were down-regulated in Chlamydia-infected IFN-ɛ−/− mice compared to WT controls. These changes correlate with a decrease in the expression of many important IFN-γ signalling molecules and number of IFN-γ-producing NK cells in the FRT during infection. These findings suggest that IFN-ɛ may protect against Chlamydia FRT infections by potentiating innate immune processes important for the clearance of infection, particularly pathways associated with IFN-γ signalling and the activation of NK cell responses.

Hossain, KR, Holt, SA, Le Brun, AP, Al Khamici, H & Valenzuela, SM 2017, 'X-ray and Neutron Reflectivity Study Shows That CLIC1 Undergoes Cholesterol-Dependent Structural Reorganization in Lipid Monolayers', Langmuir, vol. 33, no. 43, pp. 12497-12509.
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© 2017 American Chemical Society. CLIC1 belongs to the ubiquitous family of chloride intracellular ion channel proteins that are evolutionarily conserved across species. The CLICs are unusual in that they exist mainly as soluble proteins but possess the intriguing property of spontaneous conversion from the soluble to an integral membrane-bound form. This conversion is regulated by the membrane lipid composition, especially by cholesterol, together with external factors such as oxidation and pH. However, the precise physiological mechanism regulating CLIC1 membrane insertion is currently unknown. In this study, X-ray and neutron reflectivity experiments were performed to study the interaction of CLIC1 with different phospholipid monolayers prepared using POPC, POPE, or POPS with and without cholesterol in order to better understand the regulatory role of cholesterol in CLIC1 membrane insertion. Our findings demonstrate for the first time two different structural orientations of CLIC1 within phospholipid monolayers, dependent upon the absence or presence of cholesterol. In phospholipid monolayers devoid of cholesterol, CLIC1 was unable to insert into the lipid acyl chain region. However, in the presence of cholesterol, CLIC1 showed significant insertion within the phospholipid acyl chains occupying an area per protein molecule of 6-7 nm2 with a total CLIC1 thickness ranging from ∼50 to 56 Å across the entire monolayer. Our data strongly suggests that cholesterol not only facilitates the initial docking or binding of CLIC1 to the membrane but also promotes deeper penetration of CLIC1 into the hydrophobic tails of the lipid monolayer.

Hou, Z, Shankar, YV, Liu, Y, Ding, F, Subramanion, JL, Ravikumar, V, Zamudio-Vázquez, R, Keogh, D, Lim, H, Tay, MYF, Bhattacharjya, S, Rice, SA, Shi, J, Duan, H, Liu, X-W, Mu, Y, Tan, NS, Tam, KC, Pethe, K & Chan-Park, MB 2017, 'Nanoparticles of Short Cationic Peptidopolysaccharide Self-Assembled by Hydrogen Bonding with Antibacterial Effect against Multidrug-Resistant Bacteria', ACS Applied Materials & Interfaces, vol. 9, no. 44, pp. 38288-38303.
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© 2017 American Chemical Society. Cationic antimicrobial peptides (AMPs) and polymers are active against many multidrug-resistant (MDR) bacteria, but only a limited number of these compounds are in clinical use due to their unselective toxicity. The typical strategy for achieving selective antibacterial efficacy with low mammalian cell toxicity is through balancing the ratio of cationicity to hydrophobicity. Herein, we report a cationic nanoparticle self-assembled from chitosan-graft-oligolysine (CSM5-K5) chains with ultralow molecular weight (1450 Da) that selectively kills bacteria. Further, hydrogen bonding rather than the typical hydrophobic interaction causes the polymer chains to be aggregated together in water into small nanoparticles (with about 37 nm hydrodynamic radius) to concentrate the cationic charge of the lysine. When complexed with bacterial membrane, these cationic nanoparticles synergistically cluster anionic membrane lipids and produce a greater membrane perturbation and antibacterial effect than would be achievable by the same quantity of charge if dispersed in individual copolymer molecules in solution. The small zeta potential (+15 mV) and lack of hydrophobicity of the nanoparticles impedes the insertion of the copolymer into the cell bilayer to improve biocompatibility. In vivo study (using a murine excisional wound model) shows that CSM5-K5 suppresses the growth of methicillin-resistant Staphylococcus aureus (MRSA) bacteria by 4.0 orders of magnitude, an efficacy comparable to that of the last resort MRSA antibiotic vancomycin; it is also noninflammatory with little/no activation of neutrophils (CD11b and Ly6G immune cells). This study demonstrates a promising new class of cationic polymers - short cationic peptidopolysaccharides - that effectively attack MDR bacteria due to the synergistic clustering of, rather than insertion into, bacterial anionic lipids by the concentrated polymers in the resulting hydrogen-bonding-stabilize...

Howlin, RP, Cathie, K, Hall-Stoodley, L, Cornelius, V, Duignan, C, Allan, RN, Fernandez, BO, Barraud, N, Bruce, KD, Jefferies, J, Kelso, M, Kjelleberg, S, Rice, SA, Rogers, GB, Pink, S, Smith, C, Sukhtankar, PS, Salib, R, Legg, J, Carroll, M, Daniels, T, Feelisch, M, Stoodley, P, Clarke, SC, Connett, G, Faust, SN & Webb, JS 2017, 'Low-Dose Nitric Oxide as Targeted Anti-biofilm Adjunctive Therapy to Treat Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis', Molecular Therapy, vol. 25, no. 9, pp. 2104-2116.
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Despite aggressive antibiotic therapy, bronchopulmonary colonization by Pseudomonas aeruginosa causes persistent morbidity and mortality in cystic fibrosis (CF). Chronic P. aeruginosa infection in the CF lung is associated with structured, antibiotic-tolerant bacterial aggregates known as biofilms. We have demonstrated the effects of non-bactericidal, low-dose nitric oxide (NO), a signaling molecule that induces biofilm dispersal, as a novel adjunctive therapy for P. aeruginosa biofilm infection in CF in an ex vivo model and a proof-of-concept double-blind clinical trial. Submicromolar NO concentrations alone caused disruption of biofilms within ex vivo CF sputum and a statistically significant decrease in ex vivo biofilm tolerance to tobramycin and tobramycin combined with ceftazidime. In the 12-patient randomized clinical trial, 10 ppm NO inhalation caused significant reduction in P. aeruginosa biofilm aggregates compared with placebo across 7 days of treatment. Our results suggest a benefit of using low-dose NO as adjunctive therapy to enhance the efficacy of antibiotics used to treat acute P. aeruginosa exacerbations in CF. Strategies to induce the disruption of biofilms have the potential to overcome biofilm-associated antibiotic tolerance in CF and other biofilm-related diseases.

Hsu, AC-Y, Dua, K, Starkey, MR, Haw, T-J, Nair, PM, Nichol, K, Zammit, N, Grey, ST, Baines, KJ, Foster, PS, Hansbro, PM & Wark, PA 2017, 'MicroRNA-125a and -b inhibit A20 and MAVS to promote inflammation and impair antiviral response in COPD', JCI Insight, vol. 2, no. 7, pp. e90443-e90443.
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Influenza A virus (IAV) infections lead to severe inflammation in the airways. Patients with chronic obstructive pulmonary disease (COPD) characteristically have exaggerated airway inflammation and are more susceptible to infections with severe symptoms and increased mortality. The mechanisms that control inflammation during IAV infection and the mechanisms of immune dysregulation in COPD are unclear. We found that IAV infections lead to increased inflammatory and antiviral responses in primary bronchial epithelial cells (pBECs) from healthy nonsmoking and smoking subjects. In pBECs from COPD patients, infections resulted in exaggerated inflammatory but deficient antiviral responses. A20 is an important negative regulator of NF-κB-mediated inflammatory but not antiviral responses, and A20 expression was reduced in COPD. IAV infection increased the expression of miR-125a or -b, which directly reduced the expression of A20 and mitochondrial antiviral signaling (MAVS), and caused exaggerated inflammation and impaired antiviral responses. These events were replicated in vivo in a mouse model of experimental COPD. Thus, miR-125a or -b and A20 may be targeted therapeutically to inhibit excessive inflammatory responses and enhance antiviral immunity in IAV infections and in COPD.

Hu, S, Gao, H, Qi, Y, Tao, Y, Li, Y, Reimers, JR, Bokdam, M, Franchini, C, Di Sante, D, Stroppa, A & Ren, W 2017, 'Dipole Order in Halide Perovskites: Polarization and Rashba Band Splittings', The Journal of Physical Chemistry C, vol. 121, no. 41, pp. 23045-23054.
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© 2017 American Chemical Society. ABX3 (A = organic cation; B = Sn, Pb; and X = halogen) organohalide perovskites have recently attracted much attention for their photovoltaic applications. Such hybrid compounds are derived from the replacement of the inorganic monovalent metal element by an organic cation, for example, methylammonium ion (MA = CH3NH3+) and formamidinium ion (FA= +HC(NH2)2). In particular, since the organic cations are polar, it is interesting to investigate their possible long-range ordering and the corresponding Rashba spin-split bands. In this work, by using density functional theory calculations, we estimate the ferroelectric polarization corresponding to a complete ordering of dipole moments for the optimized structures of 12 perovskite halides, with A = MA, FA; B = Pb, Sn; X = Cl, Br, I. The adiabatic path and functional mode analysis have been discussed for all cases. The calculated values of the polarization may be as high as a conventional inorganic ferroelectric compound, such as BaTiO3. The concomitant inversion symmetry breaking, coupled to the sizable spin-orbit coupling of Pb and Sn, results in a fairly large Rashba spin-splitting effect for both valence and conduction bands. We highlight a rather anisotropic dispersion of spin-orbit split bands which gives rise to different Rashba parameters in different directions perpendicular to the polar axis in k-space. Furthermore, we found a weak and positive correlation between the magnitude of polarization and relevant spin-split band parameters. Since the mechanism for enhanced carrier lifetime in 3D Rashba materials is connected to the reduced recombination rate due to the spin-forbidden transition, our study could aid in the understanding of the fundamental physics of organometal halide perovskites and the optimization and design of materials for better performance.

Huff, RD, Hsu, AC-Y, Nichol, KS, Jones, B, Knight, DA, Wark, PAB, Hansbro, PM & Hirota, JA 2017, 'Regulation of xanthine dehydrogensase gene expression and uric acid production in human airway epithelial cells', PLOS ONE, vol. 12, no. 9, pp. e0184260-e0184260.
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© 2017 Huff 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 airway epithelium is a physical and immunological barrier that protects the pulmonary system from inhaled environmental insults. Uric acid has been detected in the respiratory tract and can function as an antioxidant or damage associated molecular pattern. We have demonstrated that human airway epithelial cells are a source of uric acid. Our hypothesis is that uric acid production by airway epithelial cells is induced by environmental stimuli associated with chronic respiratory diseases. We therefore examined how airway epithelial cells regulate uric acid production. Materials and methods: Allergen and cigarette smoke mouse models were performed using house dust mite (HDM) and cigarette smoke exposure, respectively, with outcome measurements of lung uric acid levels. Primary human airway epithelial cells isolated from clinically diagnosed patients with asthma and chronic obstructive pulmonary disease (COPD) were grown in submerged cultures and compared to age-matched healthy controls for uric acid release. HBEC-6KT cells, a human airway epithelial cell line, were grown under submerged monolayer conditions for mechanistic and gene expression studies. Results: HDM, but not cigarette smoke exposure, stimulated uric acid production in vivo and in vitro. Primary human airway epithelial cells from asthma, but not COPD patients, displayed elevated levels of extracellular uric acid in culture. In HBEC-6KT, production of uric acid was sensitive to the xanthine dehydrogenase (XDH) inhibitor, allopurinol, and the ATP Binding Cassette C4 (ABCC4) inhibitor, MK-571. Lastly, the pro-inflammatory cytokine combination of TNF-α and IFN-γ elevated extracellular uric acid levels and XDH gene expression in...

Huynh, TT, Jamil, I, Pianegonda, NA, Blanksby, SJ, Barker, PJ, Manefield, M & Rice, SA 2017, 'Investigation of the microbial communities colonizing prepainted steel used for roofing and walling', MicrobiologyOpen, vol. 6, no. 2, pp. 1-11.
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AbstractMicrobial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next‐generation sequencing and microbial community finger printing (T‐RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52‐week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation‐based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T‐RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling.

Iqbal, MA, Nizio, KD, Ueland, M & Forbes, SL 2017, 'Forensic decomposition odour profiling: A review of experimental designs and analytical techniques', TrAC Trends in Analytical Chemistry, vol. 91, pp. 112-124.
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© 2017 Elsevier B.V. The complex process of cadaveric decomposition releases diverse volatile organic compounds (VOCs) as by-products. These VOCs are significant in forensic science as the odour they comprise can be tracked by trained canines when searching for human remains in cases of missing persons, homicide, or mass disaster. Although this is an emerging area of research, numerous studies have been conducted to form a greater understanding of decomposition odour and its range of applications. While some of these studies are conducted in laboratories, most are conducted at specialised field sites (e.g., forensic, archaeological, taphonomic, search and rescue training facilities). This paper reviews these studies to provide a critical overview of the experimental approaches and analytical techniques used in decomposition odour analysis. Discussion covers the outcomes of these studies, their contribution to the field, and future directions, particularly the advances in analytical instrumentation currently being employed to provide a comprehensive decomposition odour profile.

Irga, PJ, Abdo, P, Zavattaro, M & Torpy, FR 2017, 'An assessment of the potential fungal bioaerosol production from an active living wall', Building and Environment, vol. 111, pp. 140-146.
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© 2016 Active living walls, or indoor air biofilters, have been proposed as a sustainable and aesthetic means of improving indoor air quality. However these systems have yet to be adequately assessed for their potential contribution to airborne fungal proliferation in indoor spaces. The current work represents a simulation study to determine, under realistic office conditions, whether a typical active living wall makes a quantifiable contribution to the airborne aeromycota. We found that the living wall studied made no significant contribution to the density or diversity of airborne culturable fungi in a test room. Few organisms of concern to public health were identified. We conclude that active biofilters are unlikely to make hazardous contributions to indoor fungi; however, further work that documents the bioaerosol generation rate with variations in temperature, airflow, plant varieties, planting densities, maintenance schedule, age of plants, plant growth substrates and substrate moisture content need further elucidation.

Irga, PJ, Braun, JT, Douglas, ANJ, Pettit, T, Fujiwara, S, Burchett, MD & Torpy, FR 2017, 'The distribution of green walls and green roofs throughout Australia: Do policy instruments influence the frequency of projects?', Urban Forestry & Urban Greening, vol. 24, pp. 164-174.
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© 2017 Elsevier GmbH Green roofs and green walls are gaining popularity as a means of mitigating a range of environmental impacts associated with urbanisation. Although this technology has been widely implemented in some parts of the world, uptake within Australia has been slow. This might be attributed to a range of factors, including a lack of awareness; a scarcity of urban green infrastructure policies; a lack of examples to give urban designers confidence in the technology; and perhaps also a limited number of professionals capable of installing green infrastructure systems. This paper researches the distribution of green wall and green roof projects in urban Australia, and the possible influence of local government policies and guidelines that have been designed to promote the increase of green infrastructure in Australia's cities. Differences were observed among project distributions and frequency, both within and between cities. In addition, councils that offered policy instruments and guidance tended to have more green wall and green roof projects than those which have no such policies in place. Compared to successful examples seen internationally, further policy implementation in Australia could increase the frequency of green infrastructure projects, indicating that governmental influence may play a substantial role in encouraging green infrastructure installation.

Irga, PJ, Paull, NJ, Abdo, P & Torpy, FR 2017, 'An assessment of the atmospheric particle removal efficiency of an in-room botanical biofilter system', Building and Environment, vol. 115, pp. 281-290.
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© 2017 Elsevier Ltd In addition to the growing requirement to reduce building energy needs, demand has arisen to find sustainable methods of improving indoor air quality. Recent advances in green wall technology have led to the development of activated systems, termed botanical biofilters, that move air through the plant growth substrate to increase the rate at which the interior atmospheric environment is exposed to the components of the plant-substrate system that are active in air pollutant removal. Development of this technology is moving towards green wall integration within building air conditioning and ventilation systems. The work presented here describes an evaluation of several parameters essential for determining the functionality of a modular botanical biofilter, as well as experiments to systematically determine the filtration performance of the device, specifically the single-pass particulate rem filtration efficiency was evaluated and defined. The maximum filtration efficiency for total suspended particulate matter peaked at an air flow rate of 11.25 L s−1 through the 0.25 m2 filter, with any increases in air flow rate met with a reduction in efficiency. The system recorded removal efficiencies were 53.35 ± 9.73% for total suspend particles, 53.51 ± 15.99% for PM10, and 48.21 ± 14.71% for PM2.5. Comparisons were made against the single pass efficiency of the system without the botanical component, as well as a common in-duct pleated panel air filter, indicating that further development is required to enhance the filtration capacity of the system if it is match current air filtration standards.

Jaiswal, R, Johnson, MS, Pokharel, D, Krishnan, SR & Bebawy, M 2017, 'Microparticles shed from multidrug resistant breast cancer cells provide a parallel survival pathway through immune evasion', BMC Cancer, vol. 17, no. 1, pp. 1-12.
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© 2017 The Author(s). Background: Breast cancer is the most frequently diagnosed cancer in women. Resident macrophages at distant sites provide a highly responsive and immunologically dynamic innate immune response against foreign infiltrates. Despite extensive characterization of the role of macrophages and other immune cells in malignant tissues, there is very little known about the mechanisms which facilitate metastatic breast cancer spread to distant sites of immunological integrity. The mechanisms by which a key healthy defense mechanism fails to protect distant sites from infiltration by metastatic cells in cancer patients remain undefined. Breast tumors, typical of many tumor types, shed membrane vesicles called microparticles (MPs), ranging in size from 0.1-1μm in diameter. MPs serve as vectors in the intercellular transfer of functional proteins and nucleic acids and in drug sequestration. In addition, MPs are also emerging to be important players in the evasion of cancer cell immune surveillance. Methods: A comparative analysis of effects of MPs isolated from human breast cancer cells and non-malignant human brain endothelial cells were examined on THP-1 derived macrophages in vitro. MP-mediated effects on cell phenotype and functionality was assessed by cytokine analysis, cell chemotaxis and phagocytosis, immunolabelling, flow cytometry and confocal imaging. Student's t-test or a one-way analysis of variance (ANOVA) was used for comparison and statistical analysis. Results: In this paper we report on the discovery of a new cellular basis for immune evasion, which is mediated by breast cancer derived MPs. MPs shed from multidrug resistant (MDR) cells were shown to selectively polarize macrophage cells to a functionally incapacitated state and facilitate their engulfment by foreign cells. Conclusions: We propose this mechanism may serve to physically disrupt the inherent immune response prior to cancer cell colonization whilst releasing mediato...

James, SA, Churches, QI, de Jonge, MD, Birchall, IE, Streltsov, V, McColl, G, Adlard, PA & Hare, DJ 2017, 'Iron, Copper, and Zinc Concentration in Aβ Plaques in the APP/PS1 Mouse Model of Alzheimer’s Disease Correlates with Metal Levels in the Surrounding Neuropil', ACS Chemical Neuroscience, vol. 8, no. 3, pp. 629-637.
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The metal ions of iron, copper, and zinc have long been associated with the aggregation of β-amyloid (Aβ) plaques in Alzheimer's disease; an interaction that has been suggested to promote increased oxidative stress and neuronal dysfunction. We examined plaque metal load in the hippocampus of APP/PS1 mice using X-ray fluorescence microscopy to assess how the anatomical location of Aβ plaques was influenced by the metal content of surrounding tissue. Immunohistochemical staining of Aβ plaques colocalized with areas of increased X-ray scattering power in unstained tissue sections, allowing direct X-ray based-assessment of plaque metal levels in sections subjected to minimal chemical fixation. We identified and mapped 48 individual plaques in four subregions of the hippocampus from four biological replicates. Iron, Cu, and Zn areal concentrations (ng cm(-2)) were increased in plaques compared to the surrounding neuropil. However, this elevation in metal load reflected the local metal makeup of the surrounding neuropil, where different brain regions are enriched for different metal ions. After correcting for tissue density, only Zn levels remained elevated in plaques. This study suggests that the in vivo binding of Zn to plaques is not simply due to increased protein deposition.

Jha, SR, Hannu, MK, Newton, PJ, Wilhelm, K, Hayward, CS, Jabbour, A, Kotlyar, E, Keogh, A, Dhital, K, Granger, E, Connellan, M, Jansz, P, Spratt, PM, Montgomery, E, Smith, A, Harkess, M, Tunicliff, P, Davidson, PM & Macdonald, PS 2017, 'Reversibility of Frailty After Bridge-to-Transplant Ventricular Assist Device Implantation or Heart Transplantation', Transplantation Direct, vol. 3, no. 7, pp. e167-e167.
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Background We recently reported that frailty is independently predictive of increased mortality in patients with advanced heart failure referred for heart transplantation (HTx). The aim of this study was to assess the impact of frailty on short-term outcomes after bridge-to-transplant ventricular assist device (BTT-VAD) implantation and/or HTx and to determine if frailty is reversible after these procedures. Methods Between August 2013 and August 2016, 100 of 126 consecutive patients underwent frailty assessment using Fried’s Frailty Phenotype before surgical intervention: 40 (21 nonfrail, 19 frail) BTT-VAD and 77 (60 nonfrail, 17 frail) HTx—including 17 of the 40 BTT-VAD supported patients. Postprocedural survival, intubation time, intensive care unit, and hospital length of stay were compared between frail and nonfrail groups. Twenty-six frail patients were reassessed at 2 months or longer postintervention. Results Frail patients had lower survival (63 ± 10% vs 94 ± 3% at 1 year, P = 0.012) and experienced significantly longer intensive care unit (11 vs 5 days, P = 0.002) and hospital (49 vs 25 days, P = 0.003) length of stay after surgical intervention compared with nonfrail patients. Twelve of 13 frail patients improved their frailty score after VAD (4.0 ± 0.8 to 1.4 ± 1.1, P < 0.001) and 12 of 13 frail patients improved their frailty score after HTx (3.2 ± 0.4 to 0.9 ± 0.9, P < 0.001). Handgrip strength and depression improved postintervention. Only a slight improve...

Jha, SR, Mcdonagh, J, Ferguson, C, Macdonald, PS & Newton, PJ 2017, 'Commentary response: Frailty, not just about old people: Reply to Smith GD & Kydd A (2017) Getting care of older people right: the need for appropriate frailty assessment?', Journal of Clinical Nursing, vol. 26, no. 23-24, pp. e4-e5.
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Jian, X, Liu, S, Gao, Y, Zhang, W, He, W, Mahmood, A, Subramaniyam, CM, Wang, X, Mahmood, N & Dou, SX 2017, 'Facile Synthesis of Three-Dimensional Sandwiched MnO₂@GCs@MnO₂ Hybrid Nanostructured Electrode for Electrochemical Capacitors', ACS Applied Materials & Interfaces, vol. 9, no. 22, pp. 18872-18882.
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Jiang, Z, Kumar, M, Padula, MP, Pernice, M, Kahlke, T, Kim, M & Ralph, PJ 2017, 'Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis', Frontiers in Plant Science, vol. 8, pp. 1-14.
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© 2017 Jiang, Kumar, Padula, Pernice, Kahlke, Kim and Ralph. The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2%PVPPand protease inhibitors. Further, the extracted proteins were solubilized in 0.5%of zwitterionic detergent (C7BzO) instead of 4%CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoe...

Jiang, Z, Liu, S, Zhang, J, Zhao, C, Wu, Y, Yu, S, Zhang, X, Huang, C, Huang, X & Kumar, M 2017, 'Newly discovered seagrass beds and their potential for blue carbon in the coastal seas of Hainan Island, South China Sea', Marine Pollution Bulletin, vol. 125, no. 1-2, pp. 513-521.
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© 2017 Elsevier Ltd Eight new seagrass beds were discovered along the coastline of Hainan Island in South China Sea with an area of 203.64 ha. The leaf N content of all seagrasses was above the median value, indicative of N limitation, with their C:N ratio recorded significantly lower than the limiting criteria. This suggested that N is not limiting but in replete status. Further, the lower C content observed in the seagrass leaves was accompanied by higher nutrient concentration. The mean seagrass biomass C was 0.23 ± 0.16 Mg C ha− 1, while the average sediment organic carbon (SOC) stock was 7.02 ± 3.57 Mg C ha− 1. The entire SOC stock of the newly discovered seagrass beds was 1306.45 Mg C, and the overall SOC stock of seagrass bed at Hainan Island was 40858.5 Mg C. These seagrass beds are under constant threats from sea reclamation, nutrient input, aquaculture activities for oyster and snail farming, and fishing activities.

Jogdeo, P, Chai, R, Shuyang, S, Saballus, M, Constancias, F, Wijesinghe, SL, Thierry, D, Blackwood, DJ, McDougald, D, Rice, SA & Marsili, E 2017, 'Onset of Microbial Influenced Corrosion (MIC) in Stainless Steel Exposed to Mixed Species Biofilms from Equatorial Seawater', Journal of The Electrochemical Society, vol. 164, no. 9, pp. C532-C538.
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© The Author(s) 2017. The understanding of microbial influenced corrosion (MIC) in aerobic mixed biofilms benefits from advanced microscopy and microbial ecology characterization of biofilms. Here, the onset of MIC in stainless steel coupons was studied in both natural and artificial seawater. Rapid selection of biofilm-forming microorganisms from natural seawater was observed for field experiments. Potential ennoblement was observed only in natural seawater. A seawater derived mixed microbial consortium enriched in artificial seawater was used to characterize the effect of several parameters on MIC. The concentration of organic carbon was the major determinant of MIC, while shaking speed and polishing played minor roles. The biofilm was preferentially formed at the grain boundaries. These results outline the need for MIC onset characterization with mixed microbial consortia to predict long-term corrosion behavior of stainless steel in seawater.

John, P, Bhatti, A, Ain, NU, Iqbal, T, Sadaf, T & Malik, JM 2017, 'Estudo caso‐controle do polimorfismo do gene receptor da vitamina D em pacientes paquistaneses com artrite reumatoide', Revista Brasileira de Reumatologia, vol. 57, no. 6, pp. 633-636.
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John, P, Bhatti, A, ul Ain, N, Iqbal, T, Sadaf, T & Malik, JM 2017, 'Case-control study of vitamin D receptor gene polymorphism in Pakistani rheumatoid arthritis patients', Revista Brasileira de Reumatologia (English Edition), vol. 57, no. 6, pp. 633-636.
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Jones, A, Pravadali-Cekic, S, Dennis, GR, Bashir, R, Mahon, PJ & Shalliker, RA 2017, 'Ferric reducing antioxidant potential (FRAP) of antioxidants using reaction flow chromatography', Analytica Chimica Acta, vol. 967, pp. 93-101.
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High performance liquid chromatography coupled with post column derivatisation (HPLC-PCD) may be used to profile the antioxidant content of a sample. There are, however, drawbacks in the use of HPLC-PCD setups; namely the high volume reaction coils that are typically used lowering the observed separation efficiency. Reaction flow chromatography has the ability to overcome these inefficiencies by using a more efficient mixing technique inside the outlet fitting itself, post column reaction loops can be removed with resulting improvement in signal to noise response, plus the separation efficiency is maintained. We assessed two methods of HPLC-PCD antioxidant analysis based on the ferric reducing antioxidant power (FRAP) assay in both conventional and reaction flow HPLC-PCD modes. It was found that the reaction flow technique demonstrated significant advantages over the conventional technique in terms of signal to noise, linear range, precision and observed separation efficiency.

Jones, B, Donovan, C, Liu, G, Gomez, HM, Chimankar, V, Harrison, CL, Wiegman, CH, Adcock, IM, Knight, DA, Hirota, JA & Hansbro, PM 2017, 'Animal models of COPD: What do they tell us?', Respirology, vol. 22, no. 1, pp. 21-32.
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ABSTRACTCOPD is a major cause of global mortality and morbidity but current treatments are poorly effective. This is because the underlying mechanisms that drive the development and progression of COPD are incompletely understood. Animal models of disease provide a valuable, ethically and economically viable experimental platform to examine these mechanisms and identify biomarkers that may be therapeutic targets that would facilitate the development of improved standard of care. Here, we review the different established animal models of COPD and the various aspects of disease pathophysiology that have been successfully recapitulated in these models including chronic lung inflammation, airway remodelling, emphysema and impaired lung function. Furthermore, some of the mechanistic features, and thus biomarkers and therapeutic targets of COPD identified in animal models are outlined. Some of the existing therapies that suppress some disease symptoms that were identified in animal models and are progressing towards therapeutic development have been outlined. Further studies of representative animal models of human COPD have the strong potential to identify new and effective therapeutic approaches for COPD.

Jones, LA, Kimball, JS, Reichle, R, Madani, N, Glassy, J, Ardizzone, JV, Colliander, A, Cleverly, J, Desai, AR, Eamus, D, Euskirchen, ES, Hutley, LB, Macfarlane, C & Scott, RL 2017, 'The SMAP Level 4 Carbon Product for Monitoring Ecosystem Land-Atmosphere CO2 Exchange.', IEEE Trans. Geosci. Remote. Sens., vol. 55, no. 11, pp. 6517-6532.
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The National Aeronautics and Space Administration's Soil Moisture Active Passive (SMAP) mission Level 4 Carbon (L4C) product provides model estimates of the Net Ecosystem CO2 exchange (NEE) incorporating SMAP soil moisture information. The L4C product includes NEE, computed as total ecosystem respiration less gross photosynthesis, at a daily time step posted to a 9-km global grid by plant functional type. Component carbon fluxes, surface soil organic carbon stocks, underlying environmental constraints, and detailed uncertainty metrics are also included. The L4C model is driven by the SMAP Level 4 Soil Moisture data assimilation product, with additional inputs from the Goddard Earth Observing System, Version 5 weather analysis, and Moderate Resolution Imaging Spectroradiometer satellite vegetation data. The L4C data record extends from March 31, 2015 to present with ongoing production and 8-12 day latency. Comparisons against concurrent global CO2 eddy flux tower measurements, satellite solar-induced canopy florescence, and other independent observation benchmarks show favorable L4C performance and accuracy, capturing the dynamic biosphere response to recent weather anomalies. Model experiments and L4C spatiotemporal variability were analyzed to understand the independent value of soil moisture and SMAP observations relative to other sources of input information. This analysis highlights the potential for microwave observations to inform models where soil moisture strongly controls land CO2 flux variability; however, skill improvement relative to flux towers is not yet discernable within the relatively short validation period. These results indicate that SMAP provides a unique and promising capability for monitoring the linked global terrestrial water and carbon cycles.

Jones, MWM, Hare, DJ, James, SA, de Jonge, MD & McColl, G 2017, 'Radiation Dose Limits for Bioanalytical X-ray Fluorescence Microscopy', Analytical Chemistry, vol. 89, no. 22, pp. 12168-12175.
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Analytical approaches that preserve the endogenous state of the examined system are essential for the in vivo study of bioinorganics. X-ray fluorescence microscopy of biological samples can map elements in vivo at subcellular resolutions in tissue samples and multicellular organisms. However, X-ray irradiation induces modifications that accumulate with dose. Consequently, the utility of X-ray fluorescence microscopy is intrinsically limited by the radiation damage it causes and the degree to which it alters the target features of interest. Identification of the dose threshold, below which the integrity of the specimen and its elemental distribution is preserved, is required to ensure valid interpretation of concentrations. Here we use the nematode, Caenorhabditis elegans, to explore these issues using three chemical-free specimen preparations: lyophilization, cryofixation, and live. We develop quantitative methods for investigating damage and present dose limits for each preparation pertaining to the micrometer-scale spatial distribution of specific analytes (potassium, calcium, manganese, iron, and zinc), and discuss dose-appropriate guidelines for X-ray fluorescence microscopy of microscale biological samples.

Jones, PM & George, AM 2017, 'How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer', Journal of Chemical Theory and Computation, vol. 13, no. 4, pp. 1712-1722.
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A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.

Kabakova, IV, Xiang, Y, Paterson, C & Török, P 2017, 'Fiber-integrated Brillouin microspectroscopy: Towards Brillouin endoscopy', Journal of Innovative Optical Health Sciences, vol. 10, no. 06, pp. 1742002-1742002.
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Brillouin imaging (BI) for micromechanical characterization of tissues and biomaterials is a fast-developing field of research with a strong potential for medical diagnosis of disease-modified tissues and cells. Although the principles of BI imply its compatibility with in vivo and in situ measurements, the integration of BI with a flexible catheter, capable of reaching the region of interest within the body, is yet to be reported. Here, for the first time, we experimentally investigate integration of the Brillouin spectroscope with standard optical fiber components to achieve a Brillouin endoscope. The performance of single-fiber and dual-fiber endoscopes are demonstrated and analyzed. We show that a major challenge in construction of Brillouin endoscopes is the strong backward Brillouin scattering in the optical fiber and we present a dual-fiber geometry as a possible solution. Measurements of Brillouin spectra in test liquids (water, ethanol and glycerol) are demonstrated using the dual-fiber endoscope and its performance is analyzed numerically with the help of a beam propagation model.

Kamal, MA, Shakil, S, Nawaz, MS, Yu, Q-S, Tweedie, D, Tan, Y, Qu, X & Greig, NH 2017, 'Inhibition of Butyrylcholinesterase with Fluorobenzylcymserine, An Experimental Alzheimer's Drug Candidate: Validation of Enzoinformatics Results by Classical and Innovative Enzyme Kinetic Analyses', CNS & Neurological Disorders - Drug Targets, vol. 16, no. 7, pp. 820-827.
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© 2017 Bentham Science Publishers. Background: Selective butyrylcholinesterase (BuChE)-inhibition, increases acetylcholine (ACh) levels. In rodents, this inhibition is known to boost cognition. Also, this occurs without the typical unwanted adverse effects of acetylcholinesterase-inhibitors or AChE-Is. The novel compound, fluorobenzylcymserine (FBC), is derived from our effort to design a selective BuChE-inhibitor. Also, we wanted to check whether butyrylcholinesterase-inhibitors (BuChE-Is) possessed an edge over AChE-Is in Alzheimer’s disease (AD) in terms of efficacy and/or tolerance. Method: FBC was synthesized as reported earlier while enzymatic activity of BuChE was calculated by Ellman-technique. Molecular docking was performed using Autodock4.2. We applied classical as well as innovative analyses of enzyme-kinetics for exploring “FBC:human BuChE-interaction”. The mode of inhibition and kinetic parameters were also determined. Results: Docking results displayed two strong interacting sites for FBC. One of these binding sites was previously identified as a deep narrow groove having polar aromatic residues while a second site was identified during this study which displayed better interaction and was lined with aliphatic and sulphur containing residues. At low concentrations of BuChE, the IC50 was found to be very low i.e. 4.79 and 6.10 nM for 12 and 36 μg, respectively, whereas it increased exponentially by increasing the units of BuChE. Conclusion: These analyses indicate that FBC is an interesting AD drug candidate that could provide a potent and partial mixed type of inhibition of human BuChE.

Karacan, I, Macha, IJ, Choi, G, Cazalbou, S & Ben-Nissan, B 2017, 'Antibiotic Containing Poly Lactic Acid/Hydroxyapatite Biocomposite Coatings for Dental Implant Applications', Key Engineering Materials, vol. 758, pp. 120-125.
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The biodegradable and biocompatible antibiotic containing thin film composites are very appropriate biomaterials as coating materials for dental implants because of their adjustable drug loading and release rates for the prevention of implant related infections. Coralline hydroxyapatite (HAp) was loaded with gentamicin antibiotics and combined with a biodegradable polylactic acid (PLA) to form thin film composites. PLA-HAp, PLA-Gentamicin (GM) and PLA-HAp-GM composites were produced, and their dissolution studies were carried out in phosphate buffered saline under SINK conditions. It was observed that the coatings could be efficiently applied to titanium dental implants and the drug release rates can be efficiently controlled.

Karampatzakis, A, Song, CZ, Allsopp, LP, Filloux, A, Rice, SA, Cohen, Y, Wohland, T & Török, P 2017, 'Probing the internal micromechanical properties of Pseudomonas aeruginosa biofilms by Brillouin imaging', npj Biofilms and Microbiomes, vol. 3, no. 1, pp. 20-20.
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AbstractBiofilms are organised aggregates of bacteria that adhere to each other or surfaces. The matrix of extracellular polymeric substances that holds the cells together provides the mechanical stability of the biofilm. In this study, we have applied Brillouin microscopy, a technique that is capable of measuring mechanical properties of specimens on a micrometre scale based on the shift in frequency of light incident upon a sample due to thermal fluctuations, to investigate the micromechanical properties of an active, live Pseudomonas aeruginosa biofilm. Using this non-contact and label-free technique, we have extracted information about the internal stiffness of biofilms under continuous flow. No correlation with colony size was found when comparing the averages of Brillouin shifts of two-dimensional cross-sections of randomly selected colonies. However, when focusing on single colonies, we observed two distinct spatial patterns: in smaller colonies, stiffness increased towards their interior, indicating a more compact structure of the centre of the colony, whereas, larger (over 45 μm) colonies were found to have less stiff interiors.

Kaufer, A, Ellis, J, Stark, D & Barratt, J 2017, 'The evolution of trypanosomatid taxonomy', Parasites & Vectors, vol. 10, no. 1, pp. 1-17.
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© 2017 The Author(s). Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifte...

Kaur, A, Shimoni, O & Wallach, M 2017, 'Celiac disease: from etiological factors to evolving diagnostic approaches', Journal of Gastroenterology, vol. 52, no. 9, pp. 1001-1012.
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© 2017, Japanese Society of Gastroenterology. Celiac disease has advanced from a medical rarity to a highly prevalent disorder. Patients with the disease show varying degrees of chronic inflammation within the small intestine due to an aberrant immune response to the digestion of gliadin found in wheat. As a result, cytokines and antibodies are produced in celiac patients that can be used as specific biomarkers for developing diagnostic tests. This review paper describes celiac disease in terms of its etiological cause, pathological effects, current diagnostic tests based on mucosal biopsy, and the genetic basis for the disease. In addition, it discusses the use of gliadin-induced cytokines, antibodies and autoantibodies as a diagnostic tool for celiac disease. Despite good initial results in terms of sensitivity and specificity, when these immunological tests were used on a large scale, even in combination with genetic testing, the results showed lower predictive value. This review addresses that issue and ends with an outlook on future work required to develop diagnostic tests with greater accuracy in predicting celiac disease in the general public, thus avoiding the need for endoscopy and mucosal biopsy.

KEADLE, SK, SAMPSON, JN, LI, H, LYDEN, K, MATTHEWS, CE & CARROLL, RJ 2017, 'An Evaluation of Accelerometer-derived Metrics to Assess Daily Behavioral Patterns', Medicine & Science in Sports & Exercise, vol. 49, no. 1, pp. 54-63.
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© 2016 by the American College of Sports Medicine. Introduction The way physical activity (PA) and sedentary behavior (SB) are accumulated throughout the day (i.e., patterns) may be important for health, but identifying measurable and meaningful metrics of behavioral patterns is challenging. This study evaluated accelerometer-derived metrics to determine whether they predicted PA and SB patterns and were reliably measured. Methods We defined and measured 55 metrics that describe daily PA and SB using data collected by using the activPAL monitor in four studies. The first two studies were randomized crossover designs that included recreationally active participants. Study 1 experimentally manipulated time spent in moderate-to-vigorous-intensity PA and sedentary time, and study 2 held time in exercise constant and manipulated SB. Study 3 included inactive participants who increased exercise, decreased sedentary time, or both. The study conditions induced distinct behavioral patterns; thus, we tested whether the new metrics could improve the prediction of an individual's study condition after adjusting for the overall volume of PA or SB using conditional logistic regression. In study 4, we measured the 3-month reliability for the pattern metrics by calculating intraclass correlation coefficients in a community-dwelling sample who wore the activPAL monitor twice for 7 d. Results In each of the experimental studies, we identified new metrics that could improve the accuracy for predicting condition beyond SB and moderate-to-vigorous-intensity PA volume. In study 1, 23 metrics were predictive of a highly active condition, and in study 2, 24 metrics were predictive of a highly sedentary condition. In study 4, the median intraclass correlation coefficients (25-75th percentiles) of the metrics were 0.59 (0.46-0.65). Conclusions Several new metrics were predictive of patterns of SB, exercise, and nonexercise behavior and are moderately reliable for a 3-month perio...

Kedzierski, L, Tate, MD, Hsu, AC, Kolesnik, TB, Linossi, EM, Dagley, L, Dong, Z, Freeman, S, Infusini, G, Starkey, MR, Bird, NL, Chatfield, SM, Babon, JJ, Huntington, N, Belz, G, Webb, A, Wark, PAB, Nicola, NA, Xu, J, Kedzierska, K, Hansbro, PM & Nicholson, SE 2017, 'Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling', eLife, vol. 6.
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Influenza virus infections have a significant impact on global human health. Individuals with suppressed immunity, or suffering from chronic inflammatory conditions such as COPD, are particularly susceptible to influenza. Here we show that suppressor of cytokine signaling (SOCS) five has a pivotal role in restricting influenza A virus in the airway epithelium, through the regulation of epidermal growth factor receptor (EGFR). Socs5-deficient mice exhibit heightened disease severity, with increased viral titres and weight loss. Socs5 levels were differentially regulated in response to distinct influenza viruses (H1N1, H3N2, H5N1 and H11N9) and were reduced in primary epithelial cells from COPD patients, again correlating with increased susceptibility to influenza. Importantly, restoration of SOCS5 levels restricted influenza virus infection, suggesting that manipulating SOCS5 expression and/or SOCS5 targets might be a novel therapeutic approach to influenza.

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA & Ralph, PJ 2017, 'Sediment and carbon deposition vary among vegetation assemblages in a coastal salt marsh', Biogeosciences, vol. 14, no. 16, pp. 3763-3779.
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Abstract. Coastal salt marshes are dynamic, intertidal ecosystems that are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of salt marshes and their capacity to store C under rising sea levels, however, is partially reliant upon sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dynamics within a single marsh that contains three salt marsh vegetation types common throughout southeastern (SE) Australia.We found that surface accretion varies among vegetation assemblages, with medium-term (19 months) bulk accretion rates in the upper marsh rush (Juncus) assemblage (1.74 ± 0.13 mm yr−1) consistently in excess of estimated local sea-level rise (1.15 mm yr−1). Accretion rates were lower and less consistent in both the succulent (Sarcocornia, 0.78 ± 0.18 mm yr−1) and grass (Sporobolus, 0.88 ± 0.22 mm yr−1) assemblages located lower in the tidal frame. Short-term (6 days) experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 1.14 ± 0.41 mg C cm−2 d−1 (neap tidal period) to 2.37 ± 0.44 mg C cm−2 d−1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sarcocornia (0.10 ± 0.02 to 0.62 ± 0.08 mg C cm−2 d−1) and Sporobolus (0.17 ± 0.04 to 0.40 ± 0.07 mg C cm−2 d−1) assemblages.Elemental (C : N), isotopic (δ13C), mid-infrared (MIR) and 13C nuclear magnetic resonance (NMR) analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and Sporobolus assemblages, compared to high retention and preservation of organic inputs in the Juncus...

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA, Heijnis, H, Zawadzki, A, Gadd, P, Jacobsen, G & Ralph, PJ 2017, 'Geochemical analyses reveal the importance of environmental history for blue carbon sequestration', Journal of Geophysical Research: Biogeosciences, vol. 122, no. 7, pp. 1789-1805.
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©2017. American Geophysical Union. All Rights Reserved. Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands are known to respond to changes imposed by geomorphic evolution, climatic, sea level, and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores—two collected from marine-influenced saltmarshes (Wapengo marine site (WAP-M) and Port Stephens marine site (POR-M)) and two from fluvial influenced saltmarshes (Wapengo fluvial site (WAP-F) and Port Stephens fluvial site (POR-F))—highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13C nuclear magnetic resonance analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C; however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales.

Kerr, MC, Gomez, GA, Ferguson, C, Tanzer, MC, Murphy, JM, Yap, AS, Parton, RG, Huston, WM & Teasdale, RD 2017, 'Laser-mediated rupture of chlamydial inclusions triggers pathogen egress and host cell necrosis', Nature Communications, vol. 8, no. 1, pp. 1-12.
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AbstractRemarkably little is known about how intracellular pathogens exit the host cell in order to infect new hosts. Pathogenic chlamydiae egress by first rupturing their replicative niche (the inclusion) before rapidly lysing the host cell. Here we apply a laser ablation strategy to specifically disrupt the chlamydial inclusion, thereby uncoupling inclusion rupture from the subsequent cell lysis and allowing us to dissect the molecular events involved in each step. Pharmacological inhibition of host cell calpains inhibits inclusion rupture, but not subsequent cell lysis. Further, we demonstrate that inclusion rupture triggers a rapid necrotic cell death pathway independent of BAK, BAX, RIP1 and caspases. Both processes work sequentially to efficiently liberate the pathogen from the host cytoplasm, promoting secondary infection. These results reconcile the pathogen's known capacity to promote host cell survival and induce cell death.

Kheirallah, AK, de Moor, CH, Faiz, A, Sayers, I & Hall, IP 2017, 'Lung function associated gene Integrator Complex subunit 12 regulates protein synthesis pathways', BMC Genomics, vol. 18, no. 1, pp. 248-20.
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BACKGROUND: Genetic studies of human lung function and Chronic Obstructive Pulmonary Disease have identified a highly significant and reproducible signal on 4q24. It remains unclear which of the two candidate genes within this locus may regulate lung function: GSTCD, a gene with unknown function, and/or INTS12, a member of the Integrator Complex which is currently thought to mediate 3'end processing of small nuclear RNAs.RESULTS: We found that, in lung tissue, 4q24 polymorphisms associated with lung function correlate with INTS12 but not neighbouring GSTCD expression. In contrast to the previous reports in other species, we only observed a minor alteration of snRNA processing following INTS12 depletion. RNAseq analysis of knockdown cells instead revealed dysregulation of a core subset of genes relevant to airway biology and a robust downregulation of protein synthesis pathways. Consistent with this, protein translation was decreased in INTS12 knockdown cells. In addition, ChIPseq experiments demonstrated INTS12 binding throughout the genome, which was enriched in transcriptionally active regions. Finally, we defined the INTS12 regulome which includes genes belonging to the protein synthesis pathways.CONCLUSION: INTS12 has functions beyond the canonical snRNA processing. We show that it regulates translation by regulating the expression of genes belonging to protein synthesis pathways. This study provides a detailed analysis of INTS12 activities on a genome-wide scale and contributes to the biology behind the genetic association for lung function at 4q24.

Kianinia, M, Bradac, C, Wang, F, Sontheimer, B, Tran, TT, Nguyen, M, Kim, S, Xu, Z-Q, Jin, D, Schell, AW, Lobo, CJ, Aharonovich, I & Toth, M 2017, 'Super-resolution imaging of quantum emitters in layered materials', Nature Communications, vol. 9, no. 1, pp. 874-874.
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Layered van der Waals materials are emerging as compelling two-dimensional(2D) platforms for studies of nanophotonics, polaritonics, valleytronics andspintronics, and have the potential to transform applications in sensing,imaging and quantum information processing. Amongst these, hexagonal boronnitride (hBN) is unique in that it hosts ultra-bright, room temperature singlephoton emitters (SPEs). However, an outstanding challenge is to locate SPEs inhBN with high precision, a task which requires breaking the optical diffractionlimit. Here, we report the imaging of SPEs in layered hBN with a spatialresolution of 63 nm using ground state depletion (GSD) nanoscopy. Furthermore,we show that SPEs in hBN possess nonlinear photophysical properties which canbe used to realize a new variant of GSD that employs a coincident pair ofdoughnut-shaped lasers to reduce the laser power that is needed to achieve agiven resolution target. Our findings expand the current understanding of thephotophysics of quantum emitters in layered hBN and demonstrate the potentialfor advanced nanophotonic and bio-imaging applications which requirelocalization of individual emitters with super-resolution accuracy.

Kim, RY, Horvat, JC, Pinkerton, JW, Starkey, MR, Essilfie, AT, Mayall, JR, Nair, PM, Hansbro, NG, Jones, B, Haw, TJ, Sunkara, KP, Nguyen, TH, Jarnicki, AG, Keely, S, Mattes, J, Adcock, IM, Foster, PS & Hansbro, PM 2017, 'MicroRNA-21 drives severe, steroid-insensitive experimental asthma by amplifying phosphoinositide 3-kinase–mediated suppression of histone deacetylase 2', Journal of Allergy and Clinical Immunology, vol. 139, no. 2, pp. 519-532.
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© 2016 American Academy of Allergy, Asthma & Immunology Background Severe steroid-insensitive asthma is a substantial clinical problem. Effective treatments are urgently required, however, their development is hampered by a lack of understanding of the mechanisms of disease pathogenesis. Steroid-insensitive asthma is associated with respiratory tract infections and noneosinophilic endotypes, including neutrophilic forms of disease. However, steroid-insensitive patients with eosinophil-enriched inflammation have also been described. The mechanisms that underpin infection-induced, severe steroid-insensitive asthma can be elucidated by using mouse models of disease. Objective We sought to develop representative mouse models of severe, steroid-insensitive asthma and to use them to identify pathogenic mechanisms and investigate new treatment approaches. Methods Novel mouse models of Chlamydia, Haemophilus influenzae, influenza, and respiratory syncytial virus respiratory tract infections and ovalbumin-induced, severe, steroid-insensitive allergic airway disease (SSIAAD) in BALB/c mice were developed and interrogated. Results Infection induced increases in the levels of microRNA (miRNA)-21 (miR-21) expression in the lung during SSIAAD, whereas expression of the miR-21 target phosphatase and tensin homolog was reduced. This was associated with an increase in levels of phosphorylated Akt, an indicator of phosphoinositide 3-kinase (PI3K) activity, and decreased nuclear histone deacetylase (HDAC)2 levels. Treatment with an miR-21–specific antagomir (Ant-21) increased phosphatase and tensin homolog levels. Treatment with Ant-21, or the pan-PI3K inhibitor LY294002, reduced PI3K activity and restored HDAC2 levels. This led to suppression of airway hyperresponsiveness and restored steroid sensitivity to allergic airway disease. These observations were replicated with SSIAAD associated with 4 different pathogens. Conclusion We identify a previously unrecognized role f...

Kim, RY, Pinkerton, JW, Essilfie, AT, Robertson, AAB, Baines, KJ, Brown, AC, Mayall, JR, Ali, MK, Starkey, MR, Hansbro, NG, Hirota, JA, Wood, LG, Simpson, JL, Knight, DA, Wark, PA, Gibson, PG, O’Neill, LAJ, Cooper, MA, Horvat, JC & Hansbro, PM 2017, 'Role for NLRP3 Inflammasome–mediated, IL-1β–Dependent Responses in Severe, Steroid-Resistant Asthma', American Journal of Respiratory and Critical Care Medicine, vol. 196, no. 3, pp. 283-297.
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© 2017 by the American Thoracic Society. Rationale: Severe, steroid-resistant asthma is the major unmet need in asthma therapy. Disease heterogeneity and poor understanding of pathogenic mechanisms hampers the identification of therapeutic targets. Excessive nucleotide-binding oligomerization domain-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome and concomitant IL-1β responses occur in chronic obstructive pulmonary disease, respiratory infections, and neutrophilic asthma. However, the direct contributions to pathogenesis, mechanisms involved, and potential for therapeutic targeting remain poorly understood, and are unknown in severe, steroid-resistant asthma. Objectives: To investigate the roles and therapeutic targeting of the NLRP3 inflammasome and IL-1β in severe, steroid-resistant asthma. Methods: We developed mouse models of Chlamydia and Haemophilus respiratory infection-mediated, ovalbumin-induced severe, steroid-resistant allergic airway disease. These models share the hallmark features of human disease, including elevated airway neutrophils, and NLRP3 inflammasome and IL-1β responses. The roles and potential for targeting of NLRP3 inflammasome, caspase-1, and IL-1β responses in experimental severe, steroid-resistant asthma were examined using a highly selective NLRP3 inhibitor, MCC950; the specific caspase-1 inhibitor Ac-YVAD-cho; and neutralizing anti-IL-1β antibody. Roles for IL-1β-induced neutrophilic inflammation were examined using IL-1β and anti-Ly6G. Measurements and Main Results: Chlamydia and Haemophilus infections increase NLRP3, caspase-1, IL-1β responses that drive steroid-resistant neutrophilic inflammation and airway hyperresponsiveness. Neutrophilic airway inflammation, disease severity, and steroid resistance in human asthma correlate with NLRP3 and IL-1β expression. Treatment with anti-IL-1β, Ac- YVAD-cho, and MCC950 suppressed IL-1β responses and the important steroid-resistant features of disease in mice...

Klein, SG, Pitt, KA, Nitschke, MR, Goyen, S, Welsh, DT, Suggett, DJ & Carroll, AR 2017, 'Symbiodinium mitigate the combined effects of hypoxia and acidification on a noncalcifying cnidarian', Global Change Biology, vol. 23, no. 9, pp. 3690-3703.
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AbstractAnthropogenic nutrient inputs enhance microbial respiration within many coastal ecosystems, driving concurrent hypoxia and acidification. During photosynthesis, Symbiodinium spp., the microalgal endosymbionts of cnidarians and other marine phyla, produce O2 and assimilate CO2 and thus potentially mitigate the exposure of the host to these stresses. However, such a role for Symbiodinium remains untested for noncalcifying cnidarians. We therefore contrasted the fitness of symbiotic and aposymbiotic polyps of a model host jellyfish (Cassiopea sp.) under reduced O2 (~2.09 mg/L) and pH (~ 7.63) scenarios in a full‐factorial experiment. Host fitness was characterized as asexual reproduction and their ability to regulate internal pH and Symbiodinium performance characterized by maximum photochemical efficiency, chla content and cell density. Acidification alone resulted in 58% more asexual reproduction of symbiotic polyps than aposymbiotic polyps (and enhanced Symbiodinium cell density) suggesting Cassiopea sp. fitness was enhanced by CO2‐stimulated Symbiodinium photosynthetic activity. Indeed, greater CO2 drawdown (elevated pH) was observed within host tissues of symbiotic polyps under acidification regardless of O2 co...

Knauer, B, Majka, P, Watkins, KJ, Taylor, AWR, Malamanova, D, Paul, B, Yu, H-H, Bush, AI, Hare, DJ & Reser, DH 2017, 'Whole-brain metallomic analysis of the common marmoset (Callithrix jacchus)', Metallomics, vol. 9, no. 4, pp. 411-423.
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Despite the importance of transition metals for normal brain function, relatively little is known about the distribution of these elemental species across the different tissue compartments of the primate brain. In this study, we employed laser ablation-inductively coupled plasma-mass spectrometry on PFA-fixed brain sections obtained from two adult common marmosets. Concurrent cytoarchitectonic, myeloarchitectonic, and chemoarchitectonic measurements allowed for identification of the major neocortical, archaecortical, and subcortical divisions of the brain, and precise localisation of iron, manganese, and zinc concentrations within each division. Major findings across tissue compartments included: (1) differentiation of white matter tracts from grey matter based on manganese and zinc distribution; (2) high iron concentrations in the basal ganglia, cortex, and substantia nigra; (3) co-localization of high concentrations of iron and manganese in the primary sensory areas of the cerebral cortex; and (4) high manganese in the hippocampus. The marmoset has become a model species of choice for connectomic, aging, and transgenic studies in primates, and the application of metallomics to these disciplines has the potential to yield high translational and basic science value.

Kohli, GS, Campbell, K, John, U, Smith, KF, Fraga, S, Rhodes, LL & Murray, SA 2017, 'Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin‐Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae)', Journal of Eukaryotic Microbiology, vol. 64, no. 5, pp. 691-706.
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AbstractGambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s‐malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I

Kohli, GS, Haslauer, K, Sarowar, C, Kretzschmar, AL, Boulter, M, Harwood, DT, Laczka, O & Murray, SA 2017, 'Qualitative and quantitative assessment of the presence of ciguatoxin, P-CTX-1B, in Spanish Mackerel (Scomberomorus commerson) from waters in New South Wales (Australia)', Toxicology Reports, vol. 4, pp. 328-334.
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© 2017 The Author(s) Ciguatera Fish Poisoning (CFP) is a tropical disease caused by the consumption of fish contaminated with ciguatoxins (CTXs). Currently, the only feasible prevention methods for CFP are to avoid the consumption of fish of certain species from some regions, avoid larger fish of certain species, or avoid all fish caught from specific regions. Here, we quantified levels of P-CTX-1B in Spanish Mackerel (Scomberomorus commerson), which is the main fish species that causes CFP in New South Wales and Queensland, Australia, using LC–MS detection against a toxin standard. We found detectable P-CTX-1B in both flesh and liver tissues in fish from New South Wales (n = 71, 1.4% prevalence rate, with a confidence interval of 1%–4%, and 7% prevalence, 1%–12%, in flesh and liver, respectively). In the small sample of fish from Queensland, there was a 46% prevalence (19–73%, n = 13). Toxin levels found were 0.13 μg kg−1 to <0.1 μg kg−1 in flesh, and 1.39 μg kg−1 to <0.4 μg kg−1 in liver, indicating that liver tissue had a significantly higher concentration (∼5 fold) of P-CTX-1B. No apparent relationship was observed between the length or weight of S. commerson and the detection of P-CTX-1B in this study. Footnote

Kondaveeti, S, Damato, TC, Carmona-Ribeiro, AM, Sierakowski, MR & Petri, DFS 2017, 'Sustainable hydroxypropyl methylcellulose/xyloglucan/gentamicin films with antimicrobial properties', Carbohydrate Polymers, vol. 165, pp. 285-293.
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Koottatep, T, Phong, VHN, Chapagain, SK, Panuvatvanich, A, Polprasert, C & Ahn, K-H 2017, 'Potential of Laterite Soil Coupling Fenton Reaction in Acetaminophen (ACT) Removal in Constructed Wetlands', Water, Air, & Soil Pollution, vol. 228, no. 8.
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Kordzakhia, N, Novikov, A & Ycart, B 2017, 'Approximations for weighted Kolmogorov–Smirnov distributions via boundary crossing probabilities', Statistics and Computing, vol. 27, no. 6, pp. 1513-1523.
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© 2016 The Author(s)A statistical application to Gene Set Enrichment Analysis implies calculating the distribution of the maximum of a certain Gaussian process, which is a modification of the standard Brownian bridge. Using the transformation into a boundary crossing problem for the Brownian motion and a piecewise linear boundary, it is proved that the desired distribution can be approximated by an n-dimensional Gaussian integral. Fast approximations are defined and validated by Monte Carlo simulation. The performance of the method for the genomics application is discussed.

Kota, A, Deshpande, DA, Haghi, M, Oliver, B & Sharma, P 2017, 'Autophagy and airway fibrosis: Is there a link?', F1000Research, vol. 6, no. 409, pp. 409-409.
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In the past decade, an emerging process named “autophagy” has generated intense interest in many chronic lung diseases. Tissue remodeling and fibrosis is a common feature of many airway diseases, and current therapies do not prevent or reverse these structural changes. Autophagy has evolved as a conserved process for bulk degradation and recycling of cytoplasmic components to maintain basal cellular homeostasis and healthy organelle populations in the cell. Furthermore, autophagy serves as a cell survival mechanism and can also be induced by chemical and physical stress to the cell. Accumulating evidence demonstrates that autophagy plays an essential role in vital cellular processes, including tissue remodeling. This review will discuss some of the recent advancements made in understanding the role of this fundamental process in airway fibrosis with emphasis on airway remodeling, and how autophagy can be exploited as a target for airway remodeling in asthma and chronic obstructive pulmonary disease.

Kretschmer, K, Sun, B, Zhang, J, Xie, X, Liu, H & Wang, G 2017, '3D Interconnected Carbon Fiber Network‐Enabled Ultralong Life Na₃V₂(PO₄)₃@Carbon Paper Cathode for Sodium‐Ion Batteries', Small, vol. 13, no. 9, pp. 1603318-1603318.
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Sodium‐ion batteries (NIBs) are an emerging technology, which can meet increasing demands for large‐scale energy storage. One of the most promising cathode material candidates for sodium‐ion batteries is Na3V2(PO4)3 due to its high capacity, thermal stability, and sodium (Na) Superionic Conductor 3D (NASICON)‐type framework. In this work, the authors have significantly improved electrochemical performance and cycling stability of Na3V2(PO4)3 by introducing a 3D interconnected conductive network in the form of carbon fiber derived from ordinary paper towel. The free‐standing Na3V2(PO4)3‐carbon paper (Na3V2(PO4)3@CP) hybrid electrodes do not require a metallic current collector, polymeric binder, or conducting additives to function as a cathode material in an NIB system. The Na3V2(PO4)3@CP cathode demonstrates extraordinary long term cycling stability for 30 000 deep charge–discharge cycles at a current density of 2.5 mA cm−2. Such outstanding cycling stability can meet the stringent requirements for renewable energy storage.

Kretzschmar, AL, Verma, A, Harwood, T, Hoppenrath, M & Murray, S 2017, 'Characterization of Gambierdiscus lapillus sp. nov. (Gonyaulacales, Dinophyceae): a new toxic dinoflagellate from the Great Barrier Reef (Australia)', Journal of Phycology, vol. 53, no. 2, pp. 283-297.
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Gambierdiscus is a genus of benthic dinoflagellates found worldwide. Some species produce neurotoxins (maitotoxins and ciguatoxins) that bioaccumulate and cause ciguatera fish poisoning (CFP), a potentially fatal food‐borne illness that is common worldwide in tropical regions. The investigation of toxigenic species of Gambierdiscus in CFP endemic regions in Australia is necessary as a first step to determine which species of Gambierdiscus are related to CFP cases occurring in this region. In this study, we characterized five strains of Gambierdiscus collected from Heron Island, Australia, a region in which ciguatera is endemic. Clonal cultures were assessed using (i) light microscopy; (ii) scanning electron microscopy; (iii) DNA sequencing based on the nuclear encoded ribosomal 18S and D8‐D10 28S regions; (iv) toxicity via mouse bioassay; and (v) toxin profile as determined by Liquid Chromatography‐Mass Spectrometry. Both the morphological and phylogenetic data indicated that these strains represent a new species of Gambierdiscus, G. lapillus sp. nov. (plate formula Po, 3′, 0a, 7″, 6c, 7‐8s, 5‴, 0p, 2″″ and distinctive by size and hatchet‐shaped 2′ plate). Culture extracts were found to be toxic using the mouse bioassay. Using chemical analysis, it was determined that they did not contain maitotoxin (MTX1) or known algal‐derived ciguatoxin analogs (CTX3B, 3C, CTX

Kumar, M, Padula, MP, Davey, P, Pernice, M, Jiang, Z, Sablok, G, Contreras-Porcia, L & Ralph, PJ 2017, 'Proteome Analysis Reveals Extensive Light Stress-Response Reprogramming in the Seagrass Zostera muelleri (Alismatales, Zosteraceae) Metabolism', Frontiers in Plant Science, vol. 7, pp. 1-19.
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© 2017, Kumar, Padula, Davey, Pernice, Jiang, Sablok, Contreras-Porcia and Ralph. Seagrasses are marine ecosystem engineers that are currently declining in abundance at an alarming rate due to both natural and anthropogenic disturbances in ecological niches. Despite reports on the morphological and physiological adaptations of seagrasses to extreme environments, little is known of the molecular mechanisms underlying photo-acclimation, and/or tolerance in these marine plants. This study applies the two-dimensional isoelectric focusing (2D-IEF) proteomics approach to identify photo-acclimation/tolerance proteins in the marine seagrass Zostera muelleri. For this, Z. muelleri was exposed for 10 days in laboratory mesocosms to saturating (control, 200 µmol photons m−2 s−1), super-saturating (SSL, 600 µmol photons m−2 s−1), and limited light (LL, 20 µmol photons m−2 s−1) irradiance conditions. Using LC-MS/MS analysis, 93 and 40 protein spots were differentially regulated under SSL and LL conditions, respectively, when compared to the control. In contrast to the LL condition, Z. muelleri robustly tolerated super-saturation light than control conditions, evidenced by their higher relative maximum electron transport rate and minimum saturating irradiance values. Proteomic analyses revealed up-regulation and/or appearances of proteins belonging to the Calvin-Benson and Krebs cycle, glycolysis, the glycine cleavage system of photorespiration, and the antioxidant system. These proteins, together with those from the inter-connected glutamate-proline-GABA pathway, shaped Z. muelleri photosynthesis andgrowth under SSL conditions. In contrast, the LL condition negatively impacted the metabolic activities of Z. muelleri by down-regulating key metabolic enzymes for photosynthesis and the metabolism of carbohydrates and amino acids, which is consistent with the observation with lower photosynthetic performance under LL condition. This study provides novel insights into th...

Kundukad, B, Schussman, M, Yang, K, Seviour, T, Yang, L, Rice, SA, Kjelleberg, S & Doyle, PS 2017, 'Mechanistic action of weak acid drugs on biofilms', Scientific Reports, vol. 7, no. 1, pp. 1-12.
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AbstractSelective permeability of a biofilm matrix to some drugs has resulted in the development of drug tolerant bacteria. Here we studied the efficacy of a weak organic acid drug, N-acetyl-L-cysteine (NAC), on the eradication of biofilms formed by the mucoid strain of Pseudomonas aeruginosa and investigated the commonality of this drug with that of acetic acid. We showed that NAC and acetic acid at pH < pKa can penetrate the matrix and eventually kill 100% of the bacteria embedded in the biofilm. Once the bacteria are killed, the microcolonies swell in size and passively shed bacteria, suggesting that the bacteria act as crosslinkers within the extracellular matrix. Despite shedding of the bacteria, the remnant matrix remains intact and behaves as a pH-responsive hydrogel. These studies not only have implications for drug design but also offer a route to generate robust soft matter materials.

Lambert, BS, Raina, J-B, Fernandez, VI, Rinke, C, Siboni, N, Rubino, F, Hugenholtz, P, Tyson, GW, Seymour, JR & Stocker, R 2017, 'A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities', Nature Microbiology, vol. 2, no. 10, pp. 1344-1349.
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© 2017 The Author(s). Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.

Langford, NK, Sagastizabal, R, Kounalakis, M, Dickel, C, Bruno, A, Luthi, F, Thoen, DJ, Endo, A & DiCarlo, L 2017, 'Experimentally simulating the dynamics of quantum light and matter at deep-strong coupling', Nature Communications, vol. 8, no. 1, pp. 1715-1715.
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AbstractThe quantum Rabi model describing the fundamental interaction between light and matter is a cornerstone of quantum physics. It predicts exotic phenomena like quantum phase transitions and ground-state entanglement in ultrastrong and deep-strong coupling regimes, where coupling strengths are comparable to or larger than subsystem energies. Demonstrating dynamics remains an outstanding challenge, the few experiments reaching these regimes being limited to spectroscopy. Here, we employ a circuit quantum electrodynamics chip with moderate coupling between a resonator and transmon qubit to realise accurate digital quantum simulation of deep-strong coupling dynamics. We advance the state of the art in solid-state digital quantum simulation by using up to 90 second-order Trotter steps and probing both subsystems in a combined Hilbert space dimension of ∼80, demonstrating characteristic Schrödinger-cat-like entanglement and large photon build-up. Our approach will enable exploration of extreme coupling regimes and quantum phase transitions, and demonstrates a clear first step towards larger complexities such as in the Dicke model.

Lapine, M 2017, 'New degrees of freedom in nonlinear metamaterials', physica status solidi (b), vol. 254, no. 4, pp. 1600462-1600462.
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© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim This is an overview of the recent achievements in exploiting novel degrees of freedom in metamaterial design, which enable sophisticated nonlinear coupling mechanisms and bring enhancement to nonlinear behavior. One of the novel paradigms makes use of mechanical feedback, achieved by embedding electromagnetic resonators within elastic medium or engineering explicit elastic links between them, such as rotational feedback. These designs provide broad-band self-adjustable resonances, self-oscillations, chaotic regimes, nonlinear chirality and, spontaneous chiral symmetry breaking. With this respect, a range of implementations has been analyzed, from flexible helices for microwaves to artificial electrostriction in optics. Another concept benefits from multi-frequency operation, where the properties in completely distinct frequency ranges become entangled through specific metamaterial design –for example, direct optical coupling can be introduced between microwave resonators, providing an independent interaction channel. It was also found that hyperbolic metamaterials can bring notable benefits to classical nonlinear processes by imposing unusual phase matching solutions, with a rich choice of matching combinations. Finally, the boundary structure of metamaterials add yet another possibility to control their properties. Overall, the recent progress in these topics suggests a very positive outlook into the future of nonlinear metamaterials.

Larkum, AWD, Davey, PA, Kuo, J, Ralph, PJ & Raven, JA 2017, 'Carbon-concentrating mechanisms in seagrasses', Journal of Experimental Botany, vol. 68, no. 14, pp. 3773-3784.
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Seagrasses are unique angiosperms that carry out growth and reproduction submerged in seawater. They occur in at least three families of the Alismatales. All have chloroplasts mainly in the cells of the epidermis. Living in seawater, the supply of inorganic carbon (Ci) to the chloroplasts is diffusion limited, especially under unstirred conditions. Therefore, the supply of CO2 and bicarbonate across the diffusive boundary layer on the outer side of the epidermis is often a limiting factor. Here we discuss the evidence for mechanisms that enhance the uptake of Ci into the epidermal cells. Since bicarbonate is plentiful in seawater, a bicarbonate pump might be expected; however, the evidence for such a pump is not strongly supported. There is evidence for a carbonic anhydrase outside the outer plasmalemma. This, together with evidence for an outward proton pump, suggests the possibility that local acidification leads to enhanced concentrations of CO2 adjacent to the outer tangential epidermal walls, which enhances the uptake of CO2, and this could be followed by a carbon-concentrating mechanism (CCM) in the cytoplasm and/or chloroplasts. The lines of evidence for such an epidermal CCM are discussed, including evidence for special 'transfer cells' in some but not all seagrass leaves in the tangential inner walls of the epidermal cells. It is concluded that seagrasses have a CCM but that the case for concentration of CO2 at the site of Rubisco carboxylation is not proven.

Larsson, ME, Ajani, PA, Rubio, AM, Guise, K, McPherson, RG, Brett, SJ, Davies, KP & Doblin, MA 2017, 'Long-term perspective on the relationship between phytoplankton and nutrient concentrations in a southeastern Australian estuary', Marine Pollution Bulletin, vol. 114, no. 1, pp. 227-238.
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© 2016 Elsevier Ltd Sixteen years (1997–2013) of physicochemical, nutrient and phytoplankton biomass (Chlorophyll-a (Chl-a)) data and a decade (2003-2013) of phytoplankton composition and abundance data were analyzed to assess how the algal community in a temperate southeastern Australian estuary has responded to decreased chronic point source nitrogen loading following effluent treatment upgrade works in 2003. Nitrogen concentrations were significantly lower (P < 0.05) following enhanced effluent treatment and Chl-a levels decreased (P < 0.05) during the warmer months. Temperature and nutrient concentrations significantly influenced temporal changes of Chl-a (explaining 55% of variability), while salinity, temperature, pH and nutrient concentrations influenced phytoplankton abundance and composition (25% explained). Harmful Algal Bloom (HAB) dynamics differed between sites likely influenced by physical attributes of the estuary. This study demonstrates that enhanced effluent treatment can significantly decrease chronic point source nitrogen loading and that Chl-a concentrations can be lowered during the warmer months when the risk of blooms and HABs is greatest.

Lee, D, Carroll, RJ & Sinha, S 2017, 'Frequentist standard errors of Bayes estimators', Computational Statistics, vol. 32, no. 3, pp. 867-888.
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© 2017, Springer-Verlag Berlin Heidelberg. Frequentist standard errors are a measure of uncertainty of an estimator, and the basis for statistical inferences. Frequestist standard errors can also be derived for Bayes estimators. However, except in special cases, the computation of the standard error of Bayesian estimators requires bootstrapping, which in combination with Markov chain Monte Carlo can be highly time consuming. We discuss an alternative approach for computing frequentist standard errors of Bayesian estimators, including importance sampling. Through several numerical examples we show that our approach can be much more computationally efficient than the standard bootstrap.

Lee, HW, Lee, MS, Kim, T-H, Alraek, T, Zaslawski, C, Kim, JW & Moon, DG 2017, 'Ginseng for erectile dysfunction', Cochrane Database of Systematic Reviews, no. 5.
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Lee, J, Wen, B, Carter, EA, Combes, V, Grau, GER & Lay, PA 2017, 'Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation', The FASEB Journal, vol. 31, no. 7, pp. 2817-2827.
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Microvesicles (MVs) are involved in cell-cell interactions, including disease pathogenesis. Nondestructive Fourier-transform infrared (FTIR) spectra from MVs were assessed as a technique to provide new biochemical insights into a LPS-induced monocyte model of septic shock. FTIR spectroscopy provided a quick method to investigate relative differences in biomolecular content of different MV populations that was complementary to traditional semiquantitative omics approaches, with which it is difficult to provide information on relative changes between classes (proteins, lipids, nucleic acids, carbohydrates) or protein conformations. Time-dependent changes were detected in biomolecular contents of MVs and in the monocytes from which they were released. Differences in phosphatidylcholine and phosphatidylserine contents were observed in MVs released under stimulation, and higher relative concentrations of RNA and α-helical structured proteins were present in stimulated MVs compared with MVs from resting cells. FTIR spectra of stimulated monocytes displayed changes that were consistent with those observed in the corresponding MVs they released. LPS-stimulated monocytes had reduced concentrations of nucleic acids, α-helical structured proteins, and phosphatidylcholine compared with resting monocytes but had an increase in total lipids. FTIR spectra of MV biomolecular content will be important in shedding new light on the mechanisms of MVs and the different roles they play in physiology and disease pathogenesis.-Lee, J., Wen, B., Carter, E. A., Combes, V., Grau, G. E. R., Lay, P. A. Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation.

Lee, JYL, Brown, JJ & Ryan, LM 2017, 'Sufficiency Revisited: Rethinking Statistical Algorithms in the Big Data Era', The American Statistician, vol. 71, no. 3, pp. 202-208.
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© 2017 American Statistical Association. The big data era demands new statistical analysis paradigms, since traditional methods often break down when datasets are too large to fit on a single desktop computer. Divide and Recombine (D&R) is becoming a popular approach for big data analysis, where results are combined over subanalyses performed in separate data subsets. In this article, we consider situations where unit record data cannot be made available by data custodians due to privacy concerns, and explore the concept of statistical sufficiency and summary statistics for model fitting. The resulting approach represents a type of D&R strategy, which we refer to as summary statistics D&R; as opposed to the standard approach, which we refer to as horizontal D&R. We demonstrate the concept via an extended Gamma–Poisson model, where summary statistics are extracted from different databases and incorporated directly into the fitting algorithm without having to combine unit record data. By exploiting the natural hierarchy of data, our approach has major benefits in terms of privacy protection. Incorporating the proposed modelling framework into data extraction tools such as TableBuilder by the Australian Bureau of Statistics allows for potential analysis at a finer geographical level, which we illustrate with a multilevel analysis of the Australian unemployment data. Supplementary materials for this article are available online.

Lee, R, Comber, B, Abraham, J, Wagner, M, Lennard, C, Spindler, X & Roux, C 2017, 'Supporting fingerprint identification assessments using a skin stretch model — A preliminary study', Forensic Science International, vol. 272, pp. 41-49.
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© 2017 Elsevier B.V. To support fingerprint expert opinion, this research proposes an approach that combines subjective human analysis (as currently applied by fingerprint practitioners) with a statistical test of the result. This approach relies on the hypothesis that there are limits to the distortion caused by skin stretch. Such limits can be modelled by applying a multivariate normal probability density function to the distances and angle formed by a marked ridge characteristic and the two closest neighbouring minutiae. This study presents a model tested on 5 donors in total. The “expected range” of distortion in a within-source comparison using 10 minutiae was determined and compared to between-source comparisons. The expected range of log probability densities for within-source comparisons marked with 10 minutiae was determined to be from −33.4 to −60.0, with all between-source data falling outside this range, between −83 and −305. These results suggest that the proposed generated metric could be a powerful tool for the assessment of fingerprint expert opinion in operational casework.

Lees, T, Nassif, N, Simpson, A, Shad-Kaneez, F, Martiniello-Wilks, R, Lin, Y, Jones, A, Qu, X & Lal, S 2017, 'Recent advances in molecular biomarkers for diabetes mellitus: a systematic review', Biomarkers, vol. 22, no. 7, pp. 1-13.
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CONTEXT: Diabetes is a growing global metabolic epidemic. Current research is focussing on exploring how the biological processes and clinical outcomes of diabetes are related and developing novel biomarkers to measure these relationships, as this can subsequently improve diagnostic, therapeutic and management capacity. OBJECTIVE: The objective of this study is to identify the most recent advances in molecular biomarkers of diabetes and directions that warrant further research. METHODS: Using a systematic search strategy, the MEDLINE, CINAHL and OVID MEDLINE databases were canvassed for articles that investigated molecular biomarkers for diabetes. Initial selections were made based on article title, whilst final inclusion was informed by a critical appraisal of the full text of each article. RESULTS: The systematic search returned 246 records, of which 113 were unique. Following screening, 29 records were included in the final review. Three main research strategies (the development of novel technologies, broad biomarker panels, and targeted approaches) identified a number of potential biomarkers for diabetes including miR-126, C-reactive protein, 2-aminoadipic acid and betatrophin. CONCLUSION: The most promising research avenue identified is the detection and quantification of micro RNA. Further, the utilisation of functionalised electrodes as a means to detect biomarker compounds also warrants attention.

Lei, L, Wu, R, Zhou, J, Zhang, S, Xiao, Z, Zhang, J & Xu, S 2017, 'The enhanced 1830nm emission in Yb/Tm:NaYF4@NaYF4 active-core/inert-shell nanocrystals', Materials Letters, vol. 189, pp. 35-37.
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The strong 1830 nm emission is realized in Yb/Tm:NaYF4@Yb:NaYF4 core/shell nanocrystals for the first time. The optimal Tm3+ concentration, shell thickness and composition respectively are 2 mol%, 6.5 nm and inert NaYF4. In comparison with Yb/Tm:NaYF4 nanocrystals, the luminescence intensity of Yb/Tm:NaYF4@NaYF4 core/shell nanocrystals enhances about 160 times.

Leigh, A, Sevanto, S, Close, JD & Nicotra, AB 2017, 'The influence of leaf size and shape on leaf thermal dynamics: does theory hold up under natural conditions?', Plant, Cell & Environment, vol. 40, no. 2, pp. 237-248.
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AbstractLaboratory studies on artificial leaves suggest that leaf thermal dynamics are strongly influenced by the two‐dimensional size and shape of leaves and associated boundary layer thickness. Hot environments are therefore said to favour selection for small, narrow or dissected leaves. Empirical evidence from real leaves under field conditions is scant and traditionally based on point measurements that do not capture spatial variation in heat load. We used thermal imagery under field conditions to measure the leaf thermal time constant (τ) in summer and the leaf‐to‐air temperature difference (∆T) and temperature range across laminae (Trange) during winter, autumn and summer for 68 Proteaceae species. We investigated the influence of leaf area and margin complexity relative to effective leaf width (we), the latter being a more direct indicator of boundary layer thickness. Normalized difference of margin complexity had no or weak effects on thermal dynamics, but we strongly predicted τ and ∆T, whereas leaf area influenced Trange. Unlike artificial leaves, however, spatial temperature distribution in large leaves appeared to be governed largely by structural variation. Therefore, we agree that small size, specifically we, has adaptive value in hot environments but not with the idea that thermal regulation is the primary evolutionary driver of leaf dissection.

Leung, JM, Tiew, PY, Mac Aogáin, M, Budden, KF, Yong, VFL, Thomas, SS, Pethe, K, Hansbro, PM & Chotirmall, SH 2017, 'The role of acute and chronic respiratory colonization and infections in the pathogenesis of COPD', Respirology, vol. 22, no. 4, pp. 634-650.
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ABSTRACTCOPD is a major global concern, increasingly so in the context of ageing populations. The role of infections in disease pathogenesis and progression is known to be important, yet the mechanisms involved remain to be fully elucidated. While COPD pathogens such as Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae are strongly associated with acute exacerbations of COPD (AECOPD), the clinical relevance of these pathogens in stable COPD patients remains unclear. Immune responses in stable and colonized COPD patients are comparable to those detected in AECOPD, supporting a role for chronic colonization in COPD pathogenesis through perpetuation of deleterious immune responses. Advances in molecular diagnostics and metagenomics now allow the assessment of microbe–COPD interactions with unprecedented personalization and precision, revealing changes in microbiota associated with the COPD disease state. As microbial changes associated with AECOPD, disease severity and therapeutic intervention become apparent, a renewed focus has been placed on the microbiology of COPD and the characteriza...

Levin, RA, Suggett, DJ, Nitschke, MR, van Oppen, MJH & Steinberg, PD 2017, 'Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology', Journal of Eukaryotic Microbiology, vol. 64, no. 5, pp. 588-597.
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AbstractDinoflagellates within the genus Symbiodinium are photosymbionts of many tropical reef invertebrates, including corals, making them central to the health of coral reefs. Symbiodinium have therefore gained significant research attention, though studies have been constrained by technical limitations. In particular, the generation of viable cells with their cell walls removed (termed protoplasts) has enabled a wide range of experimental techniques for bacteria, fungi, plants, and algae such as ultrastructure studies, virus infection studies, patch clamping, genetic transformation, and protoplast fusion. However, previous studies have struggled to remove the cell walls from armored dinoflagellates, potentially due to the internal placement of their cell walls. Here, we produce the first Symbiodinium protoplasts from three genetically and physiologically distinct strains via incubation with cellulase and osmotic agents. Digestion of the cell walls was verified by a lack of Calcofluor White fluorescence signal and by cell swelling in hypotonic culture medium. Fused protoplasts were also observed, motivating future investigation into intra‐ and inter‐specific somatic hybridization of Symbiodinium. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Generation of Symbiodinium protoplasts opens exciting, new avenues for researching these crucial symbiotic dinoflagellates, including genetic modification.

Levin, RA, Voolstra, CR, Agrawal, S, Steinberg, PD, Suggett, DJ & van Oppen, MJH 2017, 'Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts', Frontiers in Microbiology, vol. 8, no. JUN, pp. 1220-1220.
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© 2017 Levin, Voolstra, Agrawal, Steinberg, Suggett and van Oppen. Elevated sea surface temperatures from a severe and prolonged El Niño event (2014-2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.

Li, D, Yang, J, Wen, S, Shen, M, Zheng, L, Zhang, G & Shi, X 2017, 'Targeted CT/MR dual mode imaging of human hepatocellular carcinoma using lactobionic acid-modified polyethyleneimine-entrapped gold nanoparticles', Journal of Materials Chemistry B, vol. 5, no. 13, pp. 2395-2401.
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Multifunctional PEI-entrapped gold nanoparticles modified with lactobionic acid enable efficient targeted dual mode CT/MR imaging of human hepatocellular carcinoma.

Li, H, Lan, R, Chan, C-F, Bao, G, Xie, C, Chu, P-H, Tai, WCS, Zha, S, Zhang, J-X & Wong, K-L 2017, 'A luminescent lanthanide approach towards direct visualization of primary cilia in living cells', Chemical Communications, vol. 53, no. 52, pp. 7084-7087.
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A simple and direct imaging tool (HGEu001) for primary cilia based on long-lived europium luminescence is firstly presented.

Li, H, Zhang, Y, Carroll, RJ, Keadle, SK, Sampson, JN & Matthews, CE 2017, 'A joint modeling and estimation method for multivariate longitudinal data with mixed types of responses to analyze physical activity data generated by accelerometers', Statistics in Medicine, vol. 36, no. 25, pp. 4028-4040.
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A mixed effect model is proposed to jointly analyze multivariate longitudinal data with continuous, proportion, count, and binary responses. The association of the variables is modeled through the correlation of random effects. We use a quasi‐likelihood type approximation for nonlinear variables and transform the proposed model into a multivariate linear mixed model framework for estimation and inference. Via an extension to the EM approach, an efficient algorithm is developed to fit the model. The method is applied to physical activity data, which uses a wearable accelerometer device to measure daily movement and energy expenditure information. Our approach is also evaluated by a simulation study.

Li, L, Wang, Y-P, Beringer, J, Shi, H, Cleverly, J, Cheng, L, Eamus, D, Huete, A, Hutley, L, Lu, X, Piao, S, Zhang, L, Zhang, Y & Yu, Q 2017, 'Responses of LAI to rainfall explain contrasting sensitivities to carbon uptake between forest and non-forest ecosystems in Australia', Scientific Reports, vol. 7, no. 1.
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AbstractNon-forest ecosystems (predominant in semi-arid and arid regions) contribute significantly to the increasing trend and interannual variation of land carbon uptake over the last three decades, yet the mechanisms are poorly understood. By analysing the flux measurements from 23 ecosystems in Australia, we found the the correlation between gross primary production (GPP) and ecosystem respiration (Re) was significant for non-forest ecosystems, but was not for forests. In non-forest ecosystems, both GPP and Re increased with rainfall, and, consequently net ecosystem production (NEP) increased with rainfall. In forest ecosystems, GPP and Re were insensitive to rainfall. Furthermore sensitivity of GPP to rainfall was dominated by the rainfall-driven variation of LAI rather GPP per unit LAI in non-forest ecosystems, which was not correctly reproduced by current land models, indicating that the mechanisms underlying the response of LAI to rainfall should be targeted for future model development.

Liana, AE, Marquis, CP, Gunawan, C, Gooding, JJ & Amal, R 2017, 'T4 bacteriophage conjugated magnetic particles for E. coli capturing: Influence of bacteriophage loading, temperature and tryptone', Colloids and Surfaces B: Biointerfaces, vol. 151, pp. 47-57.
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This work demonstrates the use of bacteriophage conjugated magnetic particles (Fe3O4) for the rapid capturing and isolation of Escherichia coli. The investigation of T4 bacteriophage adsorption to silane functionalised Fe3O4 with amine (single bondNH2), carboxylic (single bondCOOH) and methyl (single bondCH3) surface functional groups reveals the domination of net electrostatic and hydrophobic interactions in governing bacteriophage adsorption. The bare Fe3O4 and Fe3O4-NH2 with high T4 loading captured 3-fold more E. coli (∼70% capturing efficiency) compared to the low loading T4 on Fe3O4-COOH, suggesting the significance of T4 loading in E. coli capturing efficiency. Importantly, it is further revealed that E. coli capture is highly dependent on the incubation temperature and the presence of tryptone in the media. Effective E. coli capturing only occurs at 37 °C in tryptone-containing media with the absence of either conditions resulted in poor bacteria capture. The incubation temperature dictates the capturing ability of Fe3O4/T4, whereby T4 and E. coli need to establish an irreversible binding that occurred at 37 °C. The presence of tryptophan-rich tryptone in the suspending media was also critical, as shown by a 3-fold increase in E. coli capture efficiency of Fe3O4/T4 in tryptone-containing media compared to that in tryptone-free media. This highlights for the first time that successful bacteria capturing requires not only an optimum tailoring of the particle’s surface physicochemical properties for favourable bacteriophage loading, but also an in-depth understanding of how factors, such as temperature and solution chemistry influence the subsequent bacteriophage-bacteria interactions.

Liang, L, Lu, Y, Zhang, R, Care, A, Ortega, TA, Deyev, SM, Qian, Y & Zvyagin, AV 2017, 'Deep-penetrating photodynamic therapy with KillerRed mediated by upconversion nanoparticles', Acta Biomaterialia, vol. 51, pp. 461-470.
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The fluorescent protein KillerRed, a new type of biological photosensitizer, is considered as a promising substitute for current synthetic photosensitizes used in photodynamic therapy (PDT). However, broad application of this photosensitiser in treating deep-seated lesions is challenging due to the limited tissue penetration of the excitation light with the wavelength falling in the visible spectral range. To overcome this challenge, we employ upconversion nanoparticles (UCNPs) that are able to convert deep-penetrating near infrared (NIR) light to green light to excite KillerRed locally, followed by the generation of reactive oxygen species (ROS) to kill tumour cells under centimetre-thick tissue. The photosensitizing bio-nanohybrids, KillerRed-UCNPs, are fabricated through covalent conjugation of KillerRed and UCNPs. The resulting KillerRed-UCNPs exhibit excellent colloidal stability in biological buffers and low cytotoxicity in the dark. Cross-comparison between the conventional KillerRed and UCNP-mediated KillerRed PDT demonstrated superiority of KillerRed-UCNPs photosensitizing by NIR irradiation, manifested by the fact that ∼70% PDT efficacy was achieved at 1-cm tissue depth, whereas that of the conventional KillerRed dropped to ∼7%. STATEMENT OF SIGNIFICANCE: KillerRed is a protein photosensitizer that holds promise as an alternative for the existing hydrophobic photosensitizers that are widely used in clinical photodynamic therapy (PDT). However, applications of KillerRed to deep-seated tumours are limited by the insufficient penetration depth of the excitation light in highly scattering and absorbing biological tissues. Herein, we reported the deployment of upconversion nanoparticles (UCNPs) to enhance the treatment depth of KillerRed by converting the deep-penetrating near-infrared (NIR) light to upconversion photoluminescence and activating the PDT effect of KillerRed under deep tissues. This work demonstrated clear potential of UCNPs as the N...

Lin, G, Makarov, D & Schmidt, OG 2017, 'Magnetic sensing platform technologies for biomedical applications', Lab on a Chip, vol. 17, no. 11, pp. 1884-1912.
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A review highlighting the historical basis, routes and roadmap of the development of magnetic biosensing platform technologies.

Liu, G, Cooley, MA, Nair, PM, Donovan, C, Hsu, AC, Jarnicki, AG, Haw, TJ, Hansbro, NG, Ge, Q, Brown, AC, Tay, H, Foster, PS, Wark, PA, Horvat, JC, Bourke, JE, Grainge, CL, Argraves, WS, Oliver, BG, Knight, DA, Burgess, JK & Hansbro, PM 2017, 'Airway remodelling and inflammation in asthma are dependent on the extracellular matrix protein fibulin-1c', The Journal of Pathology, vol. 243, no. 4, pp. 510-523.
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Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Asthma is a chronic inflammatory disease of the airways. It is characterized by allergic airway inflammation, airway remodelling, and airway hyperresponsiveness (AHR). Asthma patients, in particular those with chronic or severe asthma, have airway remodelling that is associated with the accumulation of extracellular matrix (ECM) proteins, such as collagens. Fibulin-1 (Fbln1) is an important ECM protein that stabilizes collagen and other ECM proteins. The level of Fbln1c, one of the four Fbln1 variants, which predominates in both humans and mice, is increased in the serum and airways fluids in asthma but its function is unclear. We show that the level of Fbln1c was increased in the lungs of mice with house dust mite (HDM)-induced chronic allergic airway disease (AAD). Genetic deletion of Fbln1c and therapeutic inhibition of Fbln1c in mice with chronic AAD reduced airway collagen deposition, and protected against AHR. Fbln1c-deficient (Fbln1c–/–) mice had reduced mucin (MUC) 5 AC levels, but not MUC5B levels, in the airways as compared with wild-type (WT) mice. Fbln1c interacted with fibronectin and periostin that was linked to collagen deposition around the small airways. Fbln1c–/– mice with AAD also had reduced numbers of α-smooth muscle actin-positive cells around the airways and reduced airway contractility as compared with WT mice. After HDM challenge, these mice also had fewer airway inflammatory cells, reduced interleukin (IL)-5, IL-13, IL-33, tumour necrosis factor (TNF) and CXCL1 levels in the lungs, and reduced IL-5, IL-33 and TNF levels in lung-draining lymph nodes. Therapeutic targeting of Fbln1c reduced the numbers of GATA3-positive Th2 cells in the lymph nodes and lungs after chronic HDM challenge. Treatment also reduced the secretion of IL-5 and IL-13 from co-cultured dendritic cells and T cells restimulated with HDM extract. Human epith...

Liu, G, Zhang, K, Ma, K, Care, A, Hutchinson, MR & Goldys, EM 2017, 'Graphene quantum dot based “switch-on” nanosensors for intracellular cytokine monitoring', Nanoscale, vol. 9, no. 15, pp. 4934-4943.
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Liu, J, Ma, Y, Zhu, L & Carroll, RJ 2017, 'Estimation and inference of error-prone covariate effect in the presence of confounding variables', Electronic Journal of Statistics, vol. 11, no. 1, pp. 480-501.
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© 2017, Institute of Mathematical Statistics. All rights reserved. We introduce a general single index semiparametric measurement error model for the case that the main covariate of interest is measured with error and modeled parametrically, and where there are many other variables also important to the modeling. We propose a semiparametric bias-correction approach to estimate the effect of the covariate of interest. The resultant estimators are shown to be root-n consistent, asymptotically normal and locally efficient. Comprehensive simulations and an analysis of an empirical data set are performed to demonstrate the finite sample performance and the bias reduction of the locally efficient estimators.

Liu, MY, Worden, P, Monahan, LG, DeMaere, MZ, Burke, CM, Djordjevic, SP, Charles, IG & Darling, AE 2017, 'Evaluation of ddRADseq for reduced representation metagenome sequencing', PeerJ, vol. 5, no. 9, pp. e3837-e3837.
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BackgroundProfiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling.MethodsThis technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data.ResultsThe ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected.DiscussionAlthough ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

Liu, Y, Lu, Y, Yang, X, Zheng, X, Wen, S, Wang, F, Vidal, X, Zhao, J, Liu, D, Zhou, Z, Ma, C, Zhou, J, Piper, JA, Xi, P & Jin, D 2017, 'Amplified stimulated emission in upconversion nanoparticles for super-resolution nanoscopy', Nature, vol. 543, no. 7644, pp. 229-233.
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Lanthanide-doped glasses and crystals are attractive for laser applications because the metastable energy levels of the trivalent lanthanide ions facilitate the establishment of population inversion and amplified stimulated emission at relatively low pump power. At the nanometre scale, lanthanide-doped upconversion nanoparticles (UCNPs) can now be made with precisely controlled phase, dimension and doping level. When excited in the near-infrared, these UCNPs emit stable, bright visible luminescence at a variety of selectable wavelengths, with single-nanoparticle sensitivity, which makes them suitable for advanced luminescence microscopy applications. Here we show that UCNPs doped with high concentrations of thulium ions (Tm3+), excited at a wavelength of 980 nanometres, can readily establish a population inversion on their intermediate metastable 3H4 level: The reduced inter-emitter distance at high Tm3+ doping concentration leads to intense cross-relaxation, inducing a photon-avalanche-like effect that rapidly populates the metastable 3H4 level, resulting in population inversion relative to the 3H6 ground level within a single nanoparticle. As a result, illumination by a laser at 808 nanometres, matching the upconversion band of the 3H4 - 3H6 transition, can trigger amplified stimulated emission to discharge the 3H4 intermediate level, so that the upconversion pathway to generate blue luminescence can be optically inhibited. We harness these properties to realize low-power super-resolution stimulated emission depletion (STED) microscopy and achieve nanometre-scale optical resolution (nanoscopy), imaging single UCNPs; the resolution is 28 nanometres, that is, 1/36th of the wavelength. These engineered nanocrystals offer saturation intensity two orders of magnitude lower than those of fluorescent probes currently employed in stimulated emission depletion microscopy, suggesting a new way of alleviating the square-root law that typically limits the resolut...

Lohr, KE, Smith, DJ, Suggett, DJ, Nitschke, MR, Dumbrell, AJ, Woodcock, S & Camp, EF 2017, 'Coral Community Structure and Recruitment in Seagrass Meadows', Frontiers in Marine Science, vol. 4, no. NOV, pp. 1-13.
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© 2017 Lohr, Smith, Suggett, Nitschke, Dumbrell, Woodcock and Camp. Coral communities are increasingly found to populate non-reef habitats prone to high environmental variability. Such sites include seagrass meadows, which are generally not considered optimal habitats for corals as a result of limited suitable substrate for settlement and substantial diel and seasonal fluctuations in physicochemical conditions relative to neighboring reefs. Interest in understanding the ability of corals to persist in non-reef habitats has grown, however little baseline data exists on community structure and recruitment of scleractinian corals in seagrass meadows. To determine how corals populate seagrass meadows, we surveyed the established and recruited coral community over 25 months within seagrass meadows at Little Cayman, Cayman Islands. Simultaneous surveys of established and recruited coral communities at neighboring back-reef sites were conducted for comparison. To fully understand the amount of environmental variability to which corals in each habitat were exposed, we conducted complementary surveys of physicochemical conditions in both seagrass meadows and back-reefs. Despite overall higher variability in physicochemical conditions, particularly pH, compared to the back-reef, 14 coral taxa were capable of inhabiting seagrass meadows, and multiple coral families were also found to recruit to these sites. However, coral cover and species diversity, richness, and evenness were lower at sites within seagrass meadows compared to back-reef sites. Although questions remain regarding the processes governing recruitment, these results provide evidence that seagrass beds can serve as functional habitats for corals despite high levels of environmental variability and suboptimal conditions compared to neighboring reefs.

Luo, J, Lv, P, Zhang, J, Fane, AG, McDougald, D & Rice, SA 2017, 'Succession of biofilm communities responsible for biofouling of membrane bio-reactors (MBRs)', PLOS ONE, vol. 12, no. 7, pp. e0179855-e0179855.
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Luu, LDW, Octavia, S, Zhong, L, Raftery, M, Sintchenko, V & Lan, R 2017, 'Characterisation of the Bordetella pertussis secretome under different media', Journal of Proteomics, vol. 158, pp. 43-51.
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Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media. Proteins secreted were functionally associated with cell surface (41%), pathogenicity (16%) and transport (17%). The most abundant proteins identified were pathogenic proteins including toxins (PtxA and CyaA), adhesins (TcfA) and type III secretion (T3SS) proteins. There were 46 proteins found uniquely in THIJS including 8 virulence associated proteins. These included T3SS proteins, adhesins (FhaL and FhaS) and a putative toxin (BP1251). Nine proteins were found uniquely in SS and these were metabolic and transport-related proteins. None of the unique proteins detected in SS were known to be virulence associated. This study found that THIJS promotes secretion of virulence factors based on the number of unique virulence proteins found and may be a growth media of choice for the study of B. pertussis virulence and vaccine development. BIOLOGICAL SIGNIFICANCE: Over the past two decades, the number of B. pertussis notifications has risen despite vaccination. There is a greater need to understand the biology behind B. pertussis infections. The secretome of B. pertussis in two different media was characterised using LC-MS/MS. The results showed that THIJS promotes secretion of importance virulence factors which may be important for the development of vaccines.

Ma, C, Xu, X, Wang, F, Zhou, Z, Liu, D, Zhao, J, Guan, M, Lang, CI & Jin, D 2017, 'Optimal Sensitizer Concentration in Single Upconversion Nanocrystals', Nano Letters, vol. 17, no. 5, pp. 2858-2864.
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© 2017 American Chemical Society. Each single upconversion nanocrystal (UCNC) usually contains thousands of photon sensitizers and hundreds of photon activators to up-convert near-infrared photons into visible and ultraviolet emissions. Though in principle further increasing the sensitizers’ concentration will enhance the absorption efficiency to produce brighter nanocrystals, typically 20% of Yb3+ ions has been used to avoid the so-called “concentration quenching” effect. Here we report that the concentration quenching effect does not limit the sensitizer concentration and NaYbF4 is the most bright host matrix. Surface quenching and the large size of NaYbF4 nanocrystals are the only factors limiting this optimal concentration. Therefore, we further designed sandwich nanostructures of NaYbF4 between a small template core to allow an epitaxial growth of the size-tunable NaYbF4 shell enclosed by an inert shell to minimize surface quenching. As a result, the suspension containing 25.2 nm sandwich structure UCNCs is 1.85 times brighter than the homogeneously doped ones, and the brightness of each single 25.2 nm heterogeneous UCNC is enhanced by nearly 3 times compared to the NaYF4: 20% Yb3+, 4% Tm3+ UCNCs in similar sizes. Particularly, the blue emission intensities of the UCNCs with the sandwich structure in the size of 13.6 and 25.2 nm are 1.36 times and 3.78 times higher than that of the monolithic UCNCs in the similar sizes. Maximizing the sensitizer concentration will accelerate the development of brighter and smaller UCNCs as more efficient biomolecule probes or photon energy converters.

Ma, S, Lian, H, Liang, H & Carroll, RJ 2017, 'SiAM: A hybrid of single index models and additive models', Electronic Journal of Statistics, vol. 11, no. 1, pp. 2397-2423.
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© 2017, Institute of Mathematical Statistics. All rights reserved. While popular, single index models and additive models have potential limitations, a fact that leads us to propose SiAM, a novel hybrid combination of these two models. We first address model identifiability under general assumptions. The result is of independent interest. We then develop an estimation procedure by using splines to approximate unknown functions and establish the asymptotic properties of the resulting estimators. Furthermore, we suggest a two-step procedure for establishing confidence bands for the nonparametric additive functions. This procedure enables us to make global inferences. Numerical experiments indicate that SiAM works well with finite sample sizes, and are especially robust to model structures. That is, when the model reduces to either single-index or additive scenario, the estimation and inference results are comparable to those based on the true model, while when the model is misspecified, the superiority of our method can be very great.

Ma, S, Ma, Y, Wang, Y, Kravitz, ES & Carroll, RJ 2017, 'A Semiparametric Single-Index Risk Score Across Populations', Journal of the American Statistical Association, vol. 112, no. 520, pp. 1648-1662.
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© 2017 American Statistical Association. We consider a problem motivated by issues in nutritional epidemiology, across diseases and populations. In this area, it is becoming increasingly common for diseases to be modeled by a single diet score, such as the Healthy Eating Index, the Mediterranean Diet Score, etc. For each disease and for each population, a partially linear single-index model is fit. The partially linear aspect of the problem is allowed to differ in each population and disease. However, and crucially, the single-index itself, having to do with the diet score, is common to all diseases and populations, and the nonparametrically estimated functions of the single-index are the same up to a scale parameter. Using B-splines with an increasing number of knots, we develop a method to solve the problem, and display its asymptotic theory. An application to the NIH-AARP Study of Diet and Health is described, where we show the advantages of using multiple diseases and populations simultaneously rather than one at a time in understanding the effect of increased Milk consumption. Simulations illustrate the properties of the methods. Supplementary materials for this article are available online.

Macha, IJ, Ben-Nissan, B & Müller, W 2017, 'Kinetics and the Theoretical Aspects of Drug Release from PLA/HAp Thin Films', Key Engineering Materials, vol. 758, pp. 113-119.
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The theory of dissolution kinetics of gentamicin from polylactic acid-hydroxyapatite thin film composites is spotlighted with the combination of diffusion and polymer degradation modeling. The use of various mathematical models, characterizing diffusion, dissolution or/and erosion prevalence as well as a mix of dissolution-diffusion rate processes were employed in order to compare theory with experimental data. A number of factors influence the release kinetics of gentamicin from medical drug release systems and devices. It is difficult to have a single mathematical model that takes all these factors into account. It is shown that the degradation of the polymer matrix plays the biggest role in the release kinetics of polymer-ceramics thin film composites. It was also observed that multistage drug release form these devices depends also on the degradation kinetics of the polymer matrix. The effect of pH and device sizes were not studied but could also be of interest in future studies.

Macha, IJ, Ben-Nissan, B, Santos, J, Cazalbou, S, Stamboulis, A, Grossin, D & Giordano, G 2017, 'Biocompatibility of a new biodegradable polymer-hydroxyapatite composite for biomedical applications', Journal of Drug Delivery Science and Technology, vol. 38, pp. 72-77.
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© 2017 Elsevier B.V. The rise in the number of musculoskeletal disorders (MSDs) due to an increasingly aging population has led to a growing demand for medication to prevent and treat these diseases. An increased interest in the development of new drugs to allow treatment of these diseases in their very early stages is currently observed. The current approach on local direct delivery of medication and key minerals to support bone repair and regeneration at the defect site, from flexible degradable devices, seems to be an effective strategy. Polylactic acid (PLA) and microspheres of hydrothermally converted coralline hydroxyapatite (cHAp) were used to develop PLA thin film composites as drug delivery systems. The PLA provided flexibility and biodegradability of the systems, while coralline hydroxyapatite provided the required calcium and phosphate ions for bone regeneration. These coralline hydroxyapatite microspheres have a unique architecture of interconnected porosity, are bioactive in nature and suitable for drug loading and controlled slow drug release. The cell attachment and morphology of the PLA thin film composites were evaluated in vitro using cell cultures of human adipose derived stem cells (hADSC). It was shown that hADSC cells exhibited a strong attachment and proliferation on PLA thin film-cHAp composites, signifying high biocompatibility and a potential for osteointegration due to the presence of HAp.

Macha, IJ, Cazalbou, S, Shimmon, R, Ben-Nissan, B & Milthorpe, B 2017, 'Development and dissolution studies of bisphosphonate (clodronate)-containing hydroxyapatite-polylactic acid biocomposites for slow drug delivery', Journal of Tissue Engineering and Regenerative Medicine, vol. 11, no. 6, pp. 1723-1731.
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Copyright © 2015 John Wiley & Sons, Ltd. An increase in clinical demand on the controlled release of bisphosphonates (BPs) due to complications associated with systemic administration, has been the current driving force on the development of BP drug-release systems. Bisphosphonates have the ability to bind to divalent metal ions, such as Ca2+, in bone mineral and prevent bone resorption by influencing the apoptosis of osteoclasts. Localized delivery using biodegradable materials, such as polylactic acid (PLA) and hydroxyapatite (HAp), which are ideal in this approach, have been used in this study to investigate the dissolution of clodronate (non-nitrogen-containing bisphosphonate) in a new release system. The effects of coral structure-derived HAp and the release kinetics of the composites were evaluated. The release kinetics of clodronate from PLA–BP and PLA–HAp–BP systems seemed to follow the power law model described by Korsmeyer–Peppas. Drug release was quantified by 31P-NMR with detection and quantification limits of 9.2 and 30.7 mM, respectively. The results suggest that these biocomposite systems could be tuned to release clodronate for both relatively short and prolonged period of time. In addition to drug delivery, the degradation of HAp supplies both Ca2+ and phosphate ions that can help in bone mineralization. Copyright © 2015 John Wiley & Sons, Ltd.

MacMillan, CP, Birke, H, Chuah, A, Brill, E, Tsuji, Y, Ralph, J, Dennis, ES, Llewellyn, D & Pettolino, FA 2017, 'Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls', BMC Genomics, vol. 18, no. 1, pp. 1-18.
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Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis.Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotto...

Macreadie, PI, Nielsen, DA, Kelleway, JJ, Atwood, TB, Seymour, JR, Petrou, K, Connolly, RM, Thomson, ACG, Trevathan‐Tackett, SM & Ralph, PJ 2017, 'Can we manage coastal ecosystems to sequester more blue carbon?', Frontiers in Ecology and the Environment, vol. 15, no. 4, pp. 206-213.
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To promote the sequestration of blue carbon, resource managers rely on best‐management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment‐level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top‐down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse‐gas emissions in different settings at landscape scales.

Maeda, EE, Ma, X, Wagner, FH, Kim, H, Oki, T, Eamus, D & Huete, A 2017, 'Evapotranspiration seasonality across the Amazon Basin', Earth System Dynamics, vol. 8, no. 2, pp. 439-454.
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Abstract. Evapotranspiration (ET) of Amazon forests is a main driver of regional climate patterns and an important indicator of ecosystem functioning. Despite its importance, the seasonal variability of ET over Amazon forests, and its relationship with environmental drivers, is still poorly understood. In this study, we carry out a water balance approach to analyse seasonal patterns in ET and their relationships with water and energy drivers over five sub-basins across the Amazon Basin. We used in situ measurements of river discharge, and remotely sensed estimates of terrestrial water storage, rainfall, and solar radiation. We show that the characteristics of ET seasonality in all sub-basins differ in timing and magnitude. The highest mean annual ET was found in the northern Rio Negro basin (∼ 1497 mm year−1) and the lowest values in the Solimões River basin (∼ 986 mm year−1). For the first time in a basin-scale study, using observational data, we show that factors limiting ET vary across climatic gradients in the Amazon, confirming local-scale eddy covariance studies. Both annual mean and seasonality in ET are driven by a combination of energy and water availability, as neither rainfall nor radiation alone could explain patterns in ET. In southern basins, despite seasonal rainfall deficits, deep root water uptake allows increasing rates of ET during the dry season, when radiation is usually higher than in the wet season. We demonstrate contrasting ET seasonality with satellite greenness across Amazon forests, with strong asynchronous relationships in ever-wet watersheds, and positive correlations observed in seasonally dry watersheds. Finally, we compared our results with estimates obtained by two ET models, and we conclude that neither of the two tested models could provide a consistent representation of ET seasonal patterns across the Amazon.

Maes, W, Huete, A & Steppe, K 2017, 'Optimizing the Processing of UAV-Based Thermal Imagery', Remote Sensing, vol. 9, no. 5, pp. 476-476.
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© 2017 by the authors. The current standard procedure for aligning thermal imagery with structure-from-motion (SfM) software uses GPS logger data for the initial image location. As input data, all thermal images of the flight are rescaled to cover the same dynamic scale range, but they are not corrected for changes in meteorological conditions during the flight. This standard procedure can give poor results, particularly in datasets with very low contrast between and within images or when mapping very complex 3D structures. To overcome this, three alignment procedures were introduced and tested: camera pre-calibration, correction of thermal imagery for small changes in air temperature, and improved estimation of the initial image position by making use of the alignment of RGB (visual) images. These improvements were tested and evaluated in an agricultural (low temperature contrast data) and an afforestation (complex 3D structure) dataset. In both datasets, the standard alignment procedure failed to align the images properly, either by resulting in point clouds with several gaps (images that were not aligned) or with unrealistic 3D structure. Using initial thermal camera positions derived from RGB image alignment significantly improved thermal image alignment in all datasets. Air temperature correction had a small yet positive impact on image alignment in the low-contrast agricultural dataset, but a minor effect in the afforestation area. The effect of camera calibration on the alignment was limited in both datasets. Still, in both datasets, the combination of all three procedures significantly improved the alignment, in terms of number of aligned images and of alignment quality.

Mahmodi, H & Hashim, MR 2017, 'Effect of substrate temperature on the morphological, structural, and optical properties of RF sputtered Ge _{1− x} Sn _x films on Si substrate', Chinese Physics B, vol. 26, no. 5, pp. 056801-056801.
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In this study, Ge1-xSnx alloy films are co-sputtered on Si(100) substrates using RF magnetron sputtering at different substrate temperatures. Scanning electron micrographs, atomic force microscopy (AFM), Raman spectroscopy, and x-ray photoemission spectroscopy (XPS) are conducted to investigate the effect of substrate temperature on the structural and optical properties of grown GeSn alloy films. AFM results show that RMS surface roughness of the films increases from 1.02 to 2.30 nm when raising the substrate temperature. This increase could be due to Sn surface segregation that occurs when raising the substrate temperature. Raman spectra exhibits the lowest FWHM value and highest phonon intensity for a film sputtered at 140 °C. The spectra show that decreasing the deposition temperature to 140 °C improves the crystalline quality of the alloy films and increases nanocrystalline phase formation. The results of Raman spectra and XPS confirm GeSn bond formation. The optoelectronic characteristics of fabricated metal-semiconductor-metal photodetectors on sputtered samples at room temperature (RT) and 140 °C are studied in the dark and under illumination. The sample sputtered at 140 °C performs better than the RT sputtered sample.

Mahmud, MA, Elumalai, NK, Upama, MB, Wang, D, Puthen-Veettil, B, Haque, F, Wright, M, Xu, C, Pivrikas, A & Uddin, A 2017, 'Controlled Ostwald ripening mediated grain growth for smooth perovskite morphology and enhanced device performance', Solar Energy Materials and Solar Cells, vol. 167, pp. 87-101.
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Maitre, M, Kirkbride, KP, Horder, M, Roux, C & Beavis, A 2017, 'Current perspectives in the interpretation of gunshot residues in forensic science: A review', Forensic Science International, vol. 270, pp. 1-11.
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The traces produced when a firearm is discharged can provide important information in cases when questions regarding a possible association of the firearm with a person of interest (POI), time since discharge or shooting distance are raised. With advances in technology, the forensic challenges presented by these traces, known as gunshot residues (GSR), are moving from the analytical domain to the interpretation of the analytical results. Different interpretation frameworks are currently competing. Formal classification of particles, using standards such as that produced by ASTM, focusses only on evaluation of evidence at the sub-source level. Another approach, based on the application of Bayesian reasoning - namely the case-by-case approach - has been proposed that allows evaluation of evidence in regards to activity-related questions. This alternative approach allows an evaluation of the evidence that is more closely aligned to judicial and investigative aims. This paper critically presents the state of the art in regards to GSR interpretation in a holistic manner.

Majeed, I, Nadeem, MA, Badshah, A, Kanodarwala, FK, Ali, H, Khan, MA, Stride, JA & Nadeem, MA 2017, 'Titania supported MOF-199 derived Cu–Cu₂O nanoparticles: highly efficient non-noble metal photocatalysts for hydrogen production from alcohol–water mixtures', Catalysis Science & Technology, vol. 7, no. 3, pp. 677-686.
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Water splitting over Cu–Cu₂O/TiO₂ photocatalysts.

Majeed, I, Nadeem, MA, Kanodarwala, FK, Hussain, E, Badshah, A, Hussain, I, Stride, JA & Nadeem, MA 2017, 'Controlled Synthesis of TiO₂Nanostructures: Exceptional Hydrogen Production in Alcohol-Water Mixtures over Cu(OH)₂-Ni(OH)₂/TiO₂Nanorods', ChemistrySelect, vol. 2, no. 25, pp. 7497-7507.
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© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Development of non-noble metal photocatalysts for hydrogen (H2) generation from renewables is important towards cost effective technology. Titania nanorods with different phase compositions and surface areas were fabricated by calcination of hydrogen titanate (H2Ti3O7) precursors obtained by treating P25 (TiO2) hydrothermally in 10 M NaOH and followed by HCl washing. Subsequently the copper and nickel hydroxides were co-deposited over TiO2 nanorods and used to generate H2 from alcohol-water mixtures under UV light. Among the synthesized materials, the optimized photocatalyst 0.8Cu(OH)2-0.2Ni(OH)2/TNR130-400 showed very high H2 production rates that are 26.6 mmol h−1g−1 in 20 vol.% ethanol-water mixture and 35.1 mmol h−1g−1 in 5 vol.% glycerol-water mixtures. The amount of this H2 production is even higher than obtained from noble metal supported TiO2 photocatalysts. This exceptional photocatalytic H2 production is attributed to the high synergism among nanords mophology of support and in situ formation of Cu and Ni exclusively in metallic states during photoreactions.

Mann, R, Mediati, DG, Duggin, IG, Harry, EJ & Bottomley, AL 2017, 'Metabolic Adaptations of Uropathogenic E. coli in the Urinary Tract', Frontiers in Cellular and Infection Microbiology, vol. 7, no. JUN, pp. 1-15.
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© 2017 Mann, Mediati, Duggin, Harry and Bottomley. Escherichia coli ordinarily resides in the lower gastrointestinal tract in humans, but some strains, known as Uropathogenic E. coli (UPEC), are also adapted to the relatively harsh environment of the urinary tract. Infections of the urine, bladder and kidneys by UPEC may lead to potentially fatal bloodstream infections. To survive this range of conditions, UPEC strains must have broad and flexible metabolic capabilities and efficiently utilize scarce essential nutrients. Whole-organism (or “omics”) methods have recently provided significant advances in our understanding of the importance of metabolic adaptation in the success of UPECs. Here we describe the nutritional and metabolic requirements for UPEC infection in these environments, and focus on particular metabolic responses and adaptations of UPEC that appear to be essential for survival in the urinary tract.

Mann, R, Monahan, LG, Harry, EJ & Bottomley, AL 2017, 'We Are What We Eat: True for Bacteria Too', Frontiers for Young Minds, vol. 5, p. 54.
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MANSFIELD, DF & DOOLEY, AH 2017, 'The critical dimension for -measures', Ergodic Theory and Dynamical Systems, vol. 37, no. 3, pp. 824-836.
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The critical dimension of an ergodic non-singular dynamical system is the asymptotic growth rate of sums of consecutive Radon–Nikodým derivatives. This has been shown to equal the average coordinate entropy for product odometers when the size of individual factors is bounded. We extend this result to $G$-measures with an asymptotic bound on the size of individual factors. Furthermore, unlike von Neumann–Krieger type, the critical dimension is an invariant property on the class of ergodic $G$-measures.

Mao, Y, Nguyen, T, Tonkin, RS, Lees, JG, Warren, C, O’Carroll, SJ, Nicholson, LFB, Green, CR, Moalem-Taylor, G & Gorrie, CA 2017, 'Characterisation of Peptide5 systemic administration for treating traumatic spinal cord injured rats', Experimental Brain Research, vol. 235, no. 10, pp. 3033-3048.
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© 2017, Springer-Verlag GmbH Germany. Systemic administration of a Connexin43 mimetic peptide, Peptide5, has been shown to reduce secondary tissue damage and improve functional recovery after spinal cord injury (SCI). This study investigated safety measures and potential off-target effects of Peptide5 systemic administration. Rats were subjected to a mild contusion SCI using the New York University impactor. One cohort was injected intraperitoneally with a single dose of fluorescently labelled Peptide5 and euthanised at 2 or 4 h post-injury for peptide distribution analysis. A second cohort received intraperitoneal injections of Peptide5 or a scrambled peptide and was culled at 8 or 24 h post-injury for the analysis of connexin proteins and systemic cytokine profile. We found that Peptide5 did not cross the blood-spinal cord barrier in control animals, but reached the lesion area in the spinal cord-injured animals without entering non-injured tissue. There was no evidence that the systemic administration of Peptide5 modulates Connexin43 protein expression or hemichannel closure in the heart and lung tissue of SCI animals. The expression levels of other major connexin proteins including Connexin30 in astrocytes, Connexin36 in neurons and Connexin47 in oligodendrocytes were also unaltered by systemic delivery of Peptide5 in either the injured or non-injured spinal cords. In addition, systemic delivery of Peptide5 had no significant effect on the plasma levels of cytokines, chemokines or growth factors. These data indicate that the systemic delivery of Peptide5 is unlikely to cause any off-target or adverse effects and may thus be a safe treatment option for traumatic SCI.

Mao, Y, Tonkin, RS, Nguyen, T, O'Carroll, SJ, Nicholson, LFB, Green, CR, Moalem-Taylor, G & Gorrie, CA 2017, 'Systemic Administration of Connexin43 Mimetic Peptide Improves Functional Recovery after Traumatic Spinal Cord Injury in Adult Rats', Journal of Neurotrauma, vol. 34, no. 3, pp. 707-719.
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© Mary Ann Liebert, Inc. 2017. Blocking of Connexin43 hemichannels, the main gap junction protein located on astrocytes in the central nervous system, has been shown to reduce neural injury in a number of models. We demonstrated previously that local administration of a Connexin43 mimetic peptide, Peptide5, reduces secondary tissue damage after spinal cord injury (SCI). Here, we investigated whether acute systemic delivery of Peptide5 is also protective in a model of SCI. Rats were subjected to a mild spinal cord contusion using the Multicentre Animal Spinal Cord Injury Study impactor and were injected intraperitoneally with Peptide5 or a scrambled peptide immediately and at 2 h and 4 h post-injury. Rats were tested for locomotor recovery and pain hypersensitivity and euthanized at 8 h, 24 h, two weeks, or six weeks post-injury. Compared with control rats, Peptide5 treated rats showed significant improvement in hindlimb locomotor function between three and six weeks post-injury and reductions in at-level mechanical allodynia at weeks one and six post-injury. Immunohistochemistry showed that Peptide5 treatment led to a reduction in total Connexin43 and increased phosphorylated Connexin43 at 8 h compared with scrambled peptide. At two and six weeks, lesion size, the astrocytic and the activated macrophage, and/or microglial response were all decreased in the Peptide5 animals. In addition, neuronal cell numbers were higher in the Peptide5 animals compared with the scrambled peptide treated rats at two and six weeks. These results show for the first time that systemic administration of Peptide5 to block the pathological opening of Connexin43 hemichannels is a feasible treatment strategy in this setting, ameliorating the secondary SCI.

Maqsood, M, Nawab, Y, Umar, J, Umair, M & Shaker, K 2017, 'Comparison of compression properties of stretchable knitted fabrics and bi-stretch woven fabrics for compression garments', The Journal of The Textile Institute, vol. 108, no. 4, pp. 522-527.
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Marciniak, L, Pilch, A, Arabasz, S, Jin, D & Bednarkiewicz, A 2017, 'Heterogeneously Nd³⁺ doped single nanoparticles for NIR-induced heat conversion, luminescence, and thermometry', Nanoscale, vol. 9, no. 24, pp. 8288-8297.
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© 2017 The Royal Society of Chemistry. The current frontier in nanomaterials engineering is to intentionally design and fabricate heterogeneous nanoparticles with desirable morphology and composition, and to integrate multiple functionalities through highly controlled epitaxial growth. Here we show that heterogeneous doping of Nd3+ ions following a core-shell design already allows three optical functions, namely efficient (η > 72%) light-to-heat conversion, bright NIR emission, and sensitive (SR > 0.1% K-1) localized temperature quantification, to be built within a single ca. 25 nm nanoparticle. Importantly, all these optical functions operate within the transparent biological window of the NIR spectral region (λexc ∼ 800 nm, λemi ∼ 860 nm), in which light scattering and absorption by tissues and water are minimal. We find NaNdF4 as a core is efficient in absorbing and converting 808 nm light to heat, while NaYF4:1%Nd3+ as a shell is a temperature sensor based on the ratio-metric luminescence reading but an intermediate inert spacer shell, e.g. NaYF4, is necessary to insulate the heat convertor and thermometer by preventing the possible Nd-Nd energy relaxation. Moreover, we notice that while temperature sensitivity and luminescence intensity are optically stable, increased excitation intensity to generate heat above room temperature may saturate the sensing capacity of temperature feedback. We therefore propose a dual beam photoexcitation scheme as a solution for possible light-induced hyperthermia treatment.

Marlton, F, Standard, O, Kimpton, JA & Daniels, JE 2017, 'Phase boundaries in the ternary (Bi0.5Na0.5TiO3)x(BaTiO3)y(SrTiO3)1−x−y system', Applied Physics Letters, vol. 111, no. 20, pp. 202903-202903.
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The phase boundaries within (Bi0.5Na0.5TiO3)x(BaTiO3)y(SrTiO3)1−x−y with x ≥ 0.68 have been outlined. This was achieved using a combinatorial sample fabrication method and scanning synchrotron X-ray diffraction to rapidly characterise crystallographic structures over a large region of phase space. A parametric refinement method was used to clearly outline the phase boundaries as a function of the composition. The pseudo-cubic structure from the high strain non-ergodic Bi0.5Na0.5TiO3-BaTiO3 composition extends into the phase diagram with doping of SrTiO3, with regions of tetragonal and rhombohedral in the BaTiO3 and Bi0.5Na0.5TiO3 ends, respectively. This information can be used in conjunction with further compositional modifications to develop high strain piezoceramics that make use of electric-field-induced phase transformations and further understand the mechanisms in ergodic vs non-ergodic relaxors.

Marsh, JW, Djoko, KY, McEwan, AG & Huston, WM 2017, 'Copper(II)-bis(thiosemicarbazonato) complexes as anti-chlamydial agents', Pathogens and Disease, vol. 75, no. 7, pp. 1-4.
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Lipophilic copper (Cu)-containing complexes have shown promising antibacterial activity against a range of bacterial pathogens. To examine the susceptibility of the intracellular human pathogen Chlamydia trachomatis to copper complexes containing bis(thiosemicarbazone) ligands [Cu(btsc)], we tested the in vitro effect of CuII-diacetyl- and CuII-glyoxal-bis[N(4)-methylthiosemicarbazonato] (Cu(atsm) and Cu(gtsm), respectively) on C. trachomatis. Cu(atsm) and to a greater extent, Cu(gtsm), prevented the formation of infectious chlamydial progeny. Impacts on host cell viability and respiration were also observed in addition to the Chlamydia impacts. This work suggests that copper-based complexes may represent a new lead approach for future development of new therapeutics against chlamydial infections, although host cell impacts need to be fully explored.

Marsh, JW, Hayward, R, Shetty, A, Mahurkar, A, Humphrys, MS & Myers, GSA 2017, 'Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1115-1129.
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AbstractBacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest.

Marsh, JW, Hayward, RJ, Shetty, AC, Mahurkar, A, Humphrys, MS & Myers, GSA 2017, 'Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1115-1129.
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© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mu-tualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.

Marsh, JW, Ong, VA, Lott, WB, Timms, P, Tyndall, JDA & Huston, WM 2017, 'CtHtrA: the lynchpin of the chlamydial surface and a promising therapeutic target', Future Microbiology, vol. 12, no. 9, pp. 817-829.
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Chlamydia trachomatis is the most prevalent sexually transmitted bacterial infection worldwide and the leading cause of preventable blindness. Reports have emerged of treatment failure, suggesting a need to develop new antibiotics to battle Chlamydia infection. One possible candidate for a new treatment is the protease inhibitor JO146, which is an effective anti-Chlamydia agent that targets the CtHtrA protein. CtHtrA is a lynchpin on the chlamydial cell surface due to its essential and multifunctional roles in the bacteria's stress response, replicative phase of development, virulence and outer-membrane protein assembly. This review summarizes the current understanding of CtHtrA function and presents a mechanistic model that highlights CtHtrA as an effective target for anti-Chlamydia drug development.

Martin, AA, Bahm, A, Bishop, J, Aharonovich, I & Toth, M 2017, 'Formation of Dynamic Topographic Patterns During Electron Beam Induced Etching of Diamond', Microscopy and Microanalysis, vol. 23, no. S1, pp. 2264-2265.
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Martin, AA, Filevich, J, Straw, M, Randolph, S, Botman, A, Aharonovich, I & Toth, M 2017, 'Radiation-Induced Damage and Recovery of Ultra-Nanocrystalline Diamond: Toward Applications in Harsh Environments', ACS Applied Materials & Interfaces, vol. 9, no. 45, pp. 39790-39794.
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© 2017 American Chemical Society. Ultra-nanocrystalline diamond (UNCD) is increasingly being used in the fabrication of devices and coatings due to its excellent tribological properties, corrosion resistance, and biocompatibility. Here, we study its response to irradiation with kiloelectronvolt electrons as a controlled model for extreme ionizing environments. Real time Raman spectroscopy reveals that the radiation-damage mechanism entails dehydrogenation of UNCD grain boundaries, and we show that the damage can be recovered by annealing at 883 K. Our results have significant practical implications for the implementation of UNCD in extreme environment applications, and indicate that the films can be used as radiation sensors.

Matthews, JL, Crowder, CM, Oakley, CA, Lutz, A, Roessner, U, Meyer, E, Grossman, AR, Weis, VM & Davy, SK 2017, 'Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis', Proceedings of the National Academy of Sciences, vol. 114, no. 50, pp. 13194-13199.
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Significance Flexibility in the endosymbiotic Symbiodinium community could provide reef-building corals with the capacity to survive environmental change, but this may be restricted to compatible host-symbiont combinations. Therefore, determining the underlying molecular, cellular, and physiological processes of symbiont compatibility is of critical importance for elucidating the resilience and adaptability of coral reefs. We coupled gene expression data with high-throughput metabolite profiling to compare the effects on the sea anemone Aiptasia when colonized by the thermally tolerant, opportunistic, but comparatively unproductive Symbiodinium trenchii vs. the regular symbiont species, Symbiodinium minutum . This powerful approach revealed strong evidence that optimal nutritional exchange and the response to intracellular oxidative stress are important determinants in the success of novel cnidarian-dinoflagellate symbioses.

Mauthner, O, Claes, V, Deschodt, M, Jha, SR, Engberg, S, Macdonald, PS, Newton, PJ & De Geest, S 2017, 'Handle with care: A systematic review on frailty in cardiac care and its usefulness in heart transplantation', Transplantation Reviews, vol. 31, no. 3, pp. 218-224.
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McCoy, TM, Holt, SA, Rozario, AM, Bell, TDM & Tabor, RF 2017, 'Surfactant‐Enhanced Adsorption of Graphene Oxide for Improved Emulsification of Oil in Water', Advanced Materials Interfaces, vol. 4, no. 23, pp. 1700803-1700803.
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AbstractGraphene oxide (GO) can be enriched at the air–water interface by the adsorption of surfactant molecules to the surfaces of the GO sheets. The synergism between the surfactant and GO is shown to be responsible for the improved interfacial performance of the composite through a subtle balance of surface charge and surface activity. The use of a photoaddressable surfactant provides a unique probe for investigating the fundamental mechanisms that control adsorption, by inducing spatiotemporal modulation of the surfactant properties by irradiation with light of certain wavelengths. Tensiometry measurements uncover the interfacial activity of the materials, whereas X‐ray reflectivity serves to independently determine the interfacial structure and composition. The ratio between the surfactant and GO appears to be the key factor controlling adsorption, with pH and salt offering additional finer control of interfacial properties. This synergism between GO sheets and a surface active small molecule surfactant is utilized to stabilize oil‐in‐water emulsions with unprecedented effectiveness.

McCree-Grey, J, Cole, JM, Holt, SA, Evans, PJ & Gong, Y 2017, 'Dye⋯TiO₂ interfacial structure of dye-sensitised solar cell working electrodes buried under a solution of I⁻/I₃⁻ redox electrolyte', Nanoscale, vol. 9, no. 32, pp. 11793-11805.
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Dye-sensitised solar cells (DSCs) have niche prospects for electricity-generating windows that could equip buildings for energy-sustainable future cities.

McElroy, DJ, Hochuli, DF, Doblin, MA, Murphy, RJ, Blackburn, RJ & Coleman, RA 2017, 'Effect of copper on multiple successional stages of a marine fouling assemblage', Biofouling, vol. 33, no. 10, pp. 904-916.
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© 2017 Informa UK Limited, trading as Taylor & Francis Group. Copper based paints are used to prevent fouling on the hulls of ships. The widely documented effect of copper on hull assemblages may be primarily due to direct effects on the invertebrates themselves or indirect effects from copper absorbed into the microbial biofilm before settlement has commenced. Artificial units of habitat were exposed to varied regimes of copper to examine (1) the photosynthetic efficiency and pigments of early-colonising biofilms, and (2) subsequent macroinvertebrate assemblage change in response to the different regimes of copper. Macroinvertebrate assemblages were found to be less sensitive to the direct effects of copper than indirect effects as delivered through biofilms that have been historically exposed to copper, with some species more tolerant than others. This raises further concern for the efficacy of copper as a universal antifoulant on the hulls of ships, which may continue to assist the invasion of copper-tolerant invertebrate species.

McLeod, C, Dowsett, N, Hallegraeff, G, Harwood, DT, Hay, B, Ibbott, S, Malhi, N, Murray, S, Smith, K, Tan, J & Turnbull, A 2017, 'Accumulation and depuration of paralytic shellfish toxins by Australian abalone Haliotis rubra : Conclusive association with Gymnodinium catenatum dinoflagellate blooms', Food Control, vol. 73, pp. 971-980.
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© 2016 Elsevier Ltd Paralytic shellfish toxins (PST) were detected in abalone (Haliotis rubra) in April 2011 in south-east Tasmania, Australia, during a dinoflagellate bloom of Gymnodinium catenatum. This led to restrictions on abalone harvesting and triggered continued PST monitoring by Ultra Performance Liquid Chromatography (UPLC-FLD) of abalone and mussels (Mytilus galloprovincialis), and concurrent phytoplankton monitoring, between 2011 and 2013. PST up to 2437 μg STX eq kg−1 (three times the bivalve regulatory limit) were confirmed in abalone viscera, with toxicity up to 586 μg STX eq kg−1 in the muscular foot (mainly doSTX and minor proportions of STX and dcSTX). Mussels accumulated PST at a faster rate than abalone which suggests they can serve as sentinels of PST accumulation to inform abalone risk management protocols. Three lines of evidence for G. catenatum as the source of PST in abalone were established: (1) PST in abalone tissues increased and declined in association with dinoflagellate blooms; (2) G. catenatum DNA was detected by real-time PCR in abalone digestive tracts; and (3) the PST analogues (toxin profile) observed in both abalone viscera and mussels were similar suggesting a common PST source. This is the first time a conclusive linkage between the occurrence of PST in abalone and a dinoflagellate source has been demonstrated.

McNally, R, Alqudah, A, Obradovic, D & McClements, L 2017, 'Elucidating the Pathogenesis of Pre-eclampsia Using In Vitro Models of Spiral Uterine Artery Remodelling', Current Hypertension Reports, vol. 19, no. 11, pp. 93-93.
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© 2017, The Author(s). Purpose of Review: The aim of the study is to perform a critical assessment of in vitro models of pre-eclampsia using complementary human and cell line-based studies. Molecular mechanisms involved in spiral uterine artery (SUA) remodelling and trophoblast functionality will also be discussed. Recent Findings: A number of proteins and microRNAs have been implicated as key in SUA remodelling, which could be explored as early biomarkers or therapeutic targets for prevention of pre-eclampsia. Summary: Various 2D and 3D in vitro models involving trophoblast cells, endothelial cells, immune cells and placental tissue were discussed to elucidate the pathogenesis of pre-eclampsia. Nevertheless, pre-eclampsia is a multifactorial disease, and the mechanisms involved in its pathogenesis are complex and still largely unknown. Further studies are required to provide better understanding of the key processes leading to inappropriate placental development which is the root cause of pre-eclampsia. This new knowledge could identify novel biomarkers and treatment strategies.

McRobb, LS, McGrath, KCY, Tsatralis, T, Liong, EC, Tan, JTM, Hughes, G, Handelsman, DJ & Heather, AK 2017, 'Estrogen Receptor Control of Atherosclerotic Calcification and Smooth Muscle Cell Osteogenic Differentiation', Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 37, no. 6, pp. 1127-1137.
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Objective— Vascular calcification is associated with increased risk of myocardial infarction and stroke. The objective of this work was to examine the ability of 17β-estradiol (E2) to stimulate calcification of vascular smooth muscle cells (VSMC) in vivo, using aged apolipoprotein E-null mice with advanced atherosclerotic lesions, and subsequently to explore underlying mechanisms in vitro. Approach and Results— Silastic E2 capsules were implanted into male and female apolipoprotein E-null mice aged 34 weeks. Plaque and calcified area were measured in the aortic sinus and innominate artery after 8 weeks. Immunohistochemical analysis examined expression of the estrogen receptors (estrogen receptor alpha and estrogen receptor beta [ERβ]). VSMC expression of osteogenic markers was examined using digital polymerase chain reaction. Advanced atherosclerotic lesions were present in all mice at the end of 8 weeks. In both male and female mice, E2 increased calcified area in a site-specific manner in the aortic sinus independently of plaque growth or lipid levels and occurred in association with a site-specific decrease in the proportion of ERβ-positive intimal cells. Calcified lesions expressed collagen I and bone sialoprotein, with decreased matrix Gla protein. In vitro, E2 suppressed ERβ expression and increased VSMC mineralization, demonstrating increased collagen I and II, osteocalcin and bone sialoprotein, and reduced matrix Gla protein and osteopontin. Antagonism or RNA silencing of estrogen receptor alpha, ERβ, or both further increased VSMC mineralization. Conclusions— We have demonstrated that E2 can drive calcification in advanced atherosclerotic lesions by promoting the ...

McWalter, TA, Rudd, R, Kienitz, J & Platen, E 2017, 'Recursive Marginal Quantization of Higher-Order Schemes', Quantitative Finance, vol. 18, no. 4, pp. 693-706.
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Quantization techniques have been applied in many challenging financeapplications, including pricing claims with path dependence and early exercisefeatures, stochastic optimal control, filtering problems and efficientcalibration of large derivative books. Recursive Marginal Quantization of theEuler scheme has recently been proposed as an efficient numerical method forevaluating functionals of solutions of stochastic differential equations. Thismethod involves recursively quantizing the conditional marginals of thediscrete-time Euler approximation of the underlying process. By generalizingthis approach, we show that it is possible to perform recursive marginalquantization for two higher-order schemes: the Milstein scheme and a simplifiedweak order 2.0 scheme. As part of this generalization a simple matrixformulation is presented, allowing efficient implementation. We further extendthe applicability of recursive marginal quantization by showing how absorptionand reflection at the zero boundary may be incorporated, when this isnecessary. To illustrate the improved accuracy of the higher order schemes,various computations are performed using geometric Brownian motion and itsgeneralization, the constant elasticity of variance model. For both processes,we show numerical evidence of improved weak order convergence and we comparethe marginal distributions implied by the three schemes to the known analyticaldistributions. By pricing European, Bermudan and Barrier options, furtherevidence of improved accuracy of the higher order schemes is demonstrated.

Meakin, GE, Butcher, EV, van Oorschot, RAH & Morgan, RM 2017, 'Trace DNA evidence dynamics: An investigation into the deposition and persistence of directly- and indirectly-transferred DNA on regularly-used knives', Forensic Science International: Genetics, vol. 29, pp. 38-47.
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Empirical data on the transfer and persistence of trace DNA are crucial to the evaluation of forensic DNA evidence. This evaluation can be complicated by the occurrence of indirect DNA transfer; the possibility of which is well established, but research into such transfer is often focussed on unrealistic situations, e.g. handling of DNA-free items after participants have shaken hands for 1-2min. To simulate more realistic scenarios, this study investigated the deposition and persistence of both directly- and indirectly-transferred DNA on knives that had been artificially set up as 'regularly-used'. Each knife was handled in a prescribed manner by a specific participant over two consecutive days to simulate regular use. Each participant then shook hands for 10s with a fellow volunteer and immediately stabbed one of their knives into a foam block repeatedly for 60s. DNA was recovered by mini-taping from triplicate sets of knife handles from four pairings of volunteers after regular use, and at one hour, one day and one week after the handshaking and stabbing events. Total amounts of DNA recovered from the knives, regularly used by a single person, varied among individuals; one volunteer consistently deposited significantly greater amounts than the others, whilst another volunteer did not always leave complete profiles. DNA attributed to the regular user persisted for at least a week, declining with increasing time between DNA deposition and recovery. Non-donor DNA was co-deposited at <5% of the profiles recovered, except for one volunteer, who consistently left DNA from their romantic partner on their knives at ∼25% and ∼11% of the profiles before and after the handshaking and stabbing events, respectively. In three pairings of volunteers, after the handshaking and stabbing events, alleles that could be attributed to the respective handshakers' profiles were detected as partial minor profiles, equating to ∼10% of the profiles recovered. For the fourth pai...

Mehta, B, Daniel, R & McNevin, D 2017, 'HRM and SNaPshot as alternative forensic SNP genotyping methods', Forensic Science, Medicine and Pathology, vol. 13, no. 3, pp. 293-301.
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Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.

Mehta, B, Daniel, R, Phillips, C & McNevin, D 2017, 'Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review', International Journal of Legal Medicine, vol. 131, no. 1, pp. 21-37.
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© 2016, Springer-Verlag Berlin Heidelberg. Short tandem repeats are the gold standard for human identification but are not informative for forensic DNA phenotyping (FDP). Single-nucleotide polymorphisms (SNPs) as genetic markers can be applied to both identification and FDP. The concept of DNA intelligence emerged with the potential for SNPs to infer biogeographical ancestry (BGA) and externally visible characteristics (EVCs), which together enable the FDP process. For more than a decade, the SNaPshot® technique has been utilised to analyse identity and FDP-associated SNPs in forensic DNA analysis. SNaPshot is a single-base extension (SBE) assay with capillary electrophoresis as its detection system. This multiplexing technique offers the advantage of easy integration into operational forensic laboratories without the requirement for any additional equipment. Further, the SNP panels from SNaPshot® assays can be incorporated into customised panels for massively parallel sequencing (MPS). Many SNaPshot® assays are available for identity, BGA and EVC profiling with examples including the well-known SNPforID 52-plex identity assay, the SNPforID 34-plex BGA assay and the HIrisPlex EVC assay. This review lists the major forensically relevant SNaPshot® assays for human DNA SNP analysis and can be used as a guide for selecting the appropriate assay for specific identity and FDP applications.

Meier, P, Elsdon, D, Garvey, M, Li, WH, Loyeung, YK, Michaeil, C, Morgan, N, Walsh, S, Zheng, S & Zaslawski, C 2017, 'Moxibustion in Australia: a clinical audit of moxibustion use in a University outpatient Chinese medicine clinic', Australian Journal of Acupuncture and Chinese Medicine, vol. 11, no. 1, pp. 17-21.

Melvold, JA, Wyrsch, ER, McKinnon, J, Roy Chowdhury, P, Charles, IG & Djordjevic, SP 2017, 'Identification of a novel qnrA allele, qnrA8, in environmental Shewanella algae', Journal of Antimicrobial Chemotherapy, vol. 72, no. 10, pp. 2949-2952.
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Quinolones are recognized as one of the most widely prescribed classes of antibiotics used to treat infections caused by Gram-negative and Gram-positive bacteria.1 In humans, quinolones are used to treat infections of the urogenital, respiratory and gastroinestinal tracts as well as a range of anatomically diverse infections in swine, poultry, cattle and companion animals and in aquaculture.2 In the environment, fluoroquinolones break down slowly (half-life of ∼100 days) and it is possible to measure trace levels of the drug in exposed environments.3 The environmental impact of quinolones, particularly fluoroquinolones from humans, agriculture and pharmaceutical production facilities, is a cause of concern as residues and metabolic breakdown products released from the body of target species provides a selection pressure that impacts the ecology of non-target bacterial, invertebrate and vertebrate populations, where it can influence natural mutation rates and lateral gene transfer.2

Messer, LF, Brown, MV, Furnas, MJ, Carney, RL, McKinnon, AD & Seymour, JR 2017, 'Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters', Frontiers in Microbiology, vol. 8, no. JUN, pp. 1-16.
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© 2017 Messer, Brown, Furnas, Carney, McKinnon and Seymour. Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N2) fixation through the activity of 'diazotrophic' bacterioplankton. Here, we investigated N2 fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N2 fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L-1 d-1. Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N2 fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N2 fixing assemblages as a potentially significant source of dissolved N within the water column.

Miao, S, He, S, Liang, M, Lin, G, Cai, B & Schmidt, OG 2017, 'Microtubular Fuel Cell with Ultrahigh Power Output per Footprint', Advanced Materials, vol. 29, no. 34, pp. 1607046-1607046.
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A novel realization of microtubular direct methanol fuel cells (µDMFC) with ultrahigh power output is reported by using “rolled‐up” nanotechnology. The microtube (Pt‐RuO2‐RUMT) is prepared by rolling up Ru2O layers coated with magnetron‐sputtered Pt nanoparticles (cat‐NPs). The µDMFC is fabricated by embedding the tube in a fluidic cell. The footprint of per tube is as small as 1.5 × 10−4 cm2. A power density of ≈257 mW cm−2 is obtained, which is three orders of magnitude higher than the present microsized DFMCs. Atomic layer deposition technique is applied to alleviate the methanol crossover as well as improve stability of the tube, sustaining electrolyte flow for days. A laminar flow driven mechanism is proposed, and the kinetics of the fuel oxidation depends on a linear‐diffusion‐controlled process. The electrocatalytic performance on anode and cathode is studied by scanning both sides of the tube wall as an ex situ working electrode, respectively. This prototype µDFMC is extremely interesting for integration with micro‐ and nanoelectronics systems.

Michelot, H, Fu, S, Stuart, B, Shimmon, R, Raymond, T, Crandell, T & Roux, C 2017, 'Effect of drug precursors and chemicals relevant to clandestine laboratory investigation on plastic bags used for collection and storage', Forensic Science International, vol. 273, pp. 106-112.
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© 2017 Elsevier B.V. In the area of clandestine laboratory investigations, plastic bags are used to collect and store evidence, such as solvents, precursors, and other compounds usually employed for the manufacturing of drugs (although liquids may be stored in glass containers within the bags first). In this study, three different types of plastic bags were provided by the NSW Police Force and investigated for their suitability for evidence collection: two different types of low-density polyethylene (LDPE) bags and one type of polyvinyl chloride (PVC) bag. Three different experiments were carried out: (1) storing relevant chemicals in the bags for up to three months; (2) exposing the bags including their content to accelerated conditions using a weatherometer, and (3) simulating an expected real case scenario. This study indicates that drugs and related chemicals stored in plastic bags may lead to a change in the composition of the chemical and an alteration or degradation of the plastic bag. All experiments led to the same conclusion: the polyvinyl chloride bags appeared to be the most affected. LDPE bags seem to be more appropriate for routine use, although it has been established they are not suitable for the collection of liquids (unless pre-packaged in, for instance, a glass container).

Michelot, H, Stuart, B, Fu, S, Shimmon, R, Raymond, T, Crandell, T & Roux, C 2017, 'The mechanical properties of plastic evidence bags used for collection and storage of drug chemicals relevant to clandestine laboratory investigations', Forensic Sciences Research, vol. 2, no. 4, pp. 198-202.
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The effectiveness of three types of plastic bags used by the New South Wales Police Force for the storage of clandestine drug evidence has been investigated through a comparison of mechanical properties. The tensile and tear properties of 'as received' low-density polyethylene (LDPE) and poly(vinyl chloride) (PVC) bags do not show major differences such that one type would be favoured over the other. However, the mechanical properties of the bags once exposed to a range of chemicals routinely collected as drug evidence have been shown to be influenced as a result of different chemical interactions. Although an interaction of reagents/solvents with an additive within the LDPE bags is proposed to influence the mechanical properties of the bags, the change in properties has been shown to be less severe than that observed for the PVC bag, where softening and damage of the bags results due to absorption of reagents.

Mirnaziry, SR, Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 2017, 'Stimulated Brillouin scattering in integrated ring resonators', Journal of the Optical Society of America B, vol. 34, no. 5, pp. 937-937.
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© 2017 Optical Society of America. We investigate stimulated Brillouin scattering (SBS) in ring resonators that exhibit linear and nonlinear losses. We present both analytic and numerical tools that can be used to compute the amplification and lasing threshold for the SBS-induced Stokes line. We show that, for both linear and nonlinear losses, there is a maximum achievable SBS amplification, and we show how this depends on the parameters of the ring and on the material parameters. We also study the relation between the critical coupling and input pump power to achieve amplification in various situations. We present simplified models that can be used to accurately predict the nonlinear behavior of the ring and consequently estimate the pump power required to achieve the optimum gain in a range of technologically important situations.

Mirnaziry, SR, Wolff, C, Steel, MJ, Morrison, B, Eggleton, BJ & Poulton, CG 2017, 'Lasing in ring resonators by stimulated Brillouin scattering in the presence of nonlinear loss', Optics Express, vol. 25, no. 20, pp. 23619-23619.
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© 2017 Optical Society of America. We theoretically investigate lasing due to stimulated Brillouin scattering in integrated ring resonators. We give analytic expressions and numerical calculations for the lasing threshold for rings in the presence of for both linear and nonlinear loss. We demonstrate the operation of the ring in the different regimes of amplification and lasing, and show how these regimes depend on the coupling to the ring and on the nonlinear parameters. In the case of nonlinear losses, we find that there can exist an upper threshold to the lasing regime where the losses are dominated by free-carrier absorption. We also find that nonlinear losses can inhibit Brillouin lasing entirely for certain ranges of coupling parameters, and we show how the correct ranges of coupling parameters can be calculated and optimized for the design of integrated Brillouin lasers.

Mitchell, AB, Mourad, B, Malouf, MA, Benzimra, M, Morgan, LC, Oliver, BG & Glanville, AR 2017, 'Transplanting the Human Respiratory Virome', The Journal of Heart and Lung Transplantation, vol. 36, no. 4, pp. S148-S149.
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Mittra, R, Pavy, M, Subramanian, N, George, AM, O'Mara, ML, Kerr, ID & Callaghan, R 2017, 'Location of contact residues in pharmacologically distinct drug binding sites on P-glycoprotein', Biochemical Pharmacology, vol. 123, pp. 19-28.
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The multidrug resistance P-glycoprotein (P-gp) is characterised by the ability to bind and/or transport an astonishing array of drugs. This poly-specificity is imparted by at least four pharmacologically distinct binding sites within the transmembrane domain. Whether or not these sites are spatially distinct has remained unclear. Biochemical and structural investigations have implicated a central cavity as the likely location for the binding sites. In the present investigation, a number of contact residues that are involved in drug binding were identified through biochemical assays using purified, reconstituted P-gp. Drugs were selected to represent each of the four pharmacologically distinct sites. Contact residues important in rhodamine123 binding were identified in the central cavity of P-gp. However, contact residues for the binding of vinblastine, paclitaxel and nicardipine were located at the lipid-protein interface rather than the central cavity. A key residue (F978) within the central cavity is believed to be involved in coupling drug binding to nucleotide hydrolysis. Data observed in this investigation suggest the presence of spatially distinct drug binding sites connecting through to a single translocation pore in the central cavity.

Miyaji, N, Shimizu, M, Miyazaki, J, Osabe, K, Sato, M, Ebe, Y, Takada, S, Kaji, M, Dennis, ES, Fujimoto, R & Okazaki, K 2017, 'Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa L.', Plant Cell Reports, vol. 36, no. 12, pp. 1841-1854.
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Mondal, AK, Kretschmer, K, Zhao, Y, Liu, H, Fan, H & Wang, G 2017, 'Naturally nitrogen doped porous carbon derived from waste shrimp shells for high-performance lithium ion batteries and supercapacitors', Microporous and Mesoporous Materials, vol. 246, pp. 72-80.
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© 2017 Elsevier Inc. Transformation of biomass wastes into sustainable low cost carbon materials is now a topic of great interest. Here, we describe porous carbon from biomass derived waste shrimp shells and its application in two different energy storage systems. The unique porous structure with the presence of heteroatoms (O, N) makes it promising material for both lithium ion batteries and supercapacitors. When applied as anode materials for lithium ion batteries, the as-prepared carbon showed a specific capacity as high as 1507 mA h g−1 and 1014 mA h g−1 at current densities of 0.1 A g−1 and 0.5 A g−1, respectively, good rate performance and superior cycling stability. The porous carbon-based supercapacitor also delivered a specific capacitance of 239 F g−1 at a current density of 0.5 A g−1 in 6 M KOH electrolyte. The specific capacitance retention is 99.4% even after 5000 charge-discharge cycles, indicating excellent cycling stability. The superior electrochemical performances for both lithium ion batteries and supercapacitors could be ascribed to the high specific surface area, porous structure and nitrogen doping effect.

Mondal, AK, Kretschmer, K, Zhao, Y, Liu, H, Wang, C, Sun, B & Wang, G 2017, 'Nitrogen‐Doped Porous Carbon Nanosheets from Eco‐Friendly Eucalyptus Leaves as High Performance Electrode Materials for Supercapacitors and Lithium Ion Batteries', Chemistry – A European Journal, vol. 23, no. 15, pp. 3683-3690.
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AbstractNitrogen‐doped porous carbon nanosheets were prepared from eucalyptus tree leaves by simply mixing the leaf powders with KHCO3 and subsequent carbonisation. Porous carbon nanosheets with a high specific surface area of 2133 m2 g−1 were obtained and applied as electrode materials for supercapacitors and lithium ion batteries. For supercapacitor applications, the porous carbon nanosheet electrode exhibited a supercapacitance of 372 F g−1 at a current density of 500 mA g−1 in 1 m H2SO4 aqueous electrolyte and excellent cycling stability over 15 000 cycles. In organic electrolyte, the nanosheet electrode showed a specific capacitance of 71 F g−1 at a current density of 2 Ag−1 and stable cycling performance. When applied as the anode material for lithium ion batteries, the as‐prepared porous carbon nanosheets also demonstrated a high specific capacity of 819 mA h g−1 at a current density of 100 mA g−1, good rate capability, and stable cycling performance. The outstanding electrochemical performances for both supercapacitors and lithium ion batteries are derived from the large specific surface area, porous nanosheet structure and nitrogen doping effects. The strategy developed in this paper provides a novel route to utilise biomass‐derived materials for low‐cost energy storage systems.

Moosavi, SM, Prabhala, P & Ammit, AJ 2017, 'Role and regulation of MKP-1 in airway inflammation', Respiratory Research, vol. 18, no. 1, pp. 154-12.
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Mitogen-activated protein kinase (MAPK) phosphatase 1 (MKP-1) is a protein with anti-inflammatory properties and the archetypal member of the dual-specificity phosphatases (DUSPs) family that have emerged over the past decade as playing an instrumental role in the regulation of airway inflammation. Not only does MKP-1 serve a critical role as a negative feedback effector, controlling the extent and duration of pro-inflammatory MAPK signalling in airway cells, upregulation of this endogenous phosphatase has also emerged as being one of the key cellular mechanism responsible for the beneficial actions of clinically-used respiratory medicines, including β2-agonists, phosphodiesterase inhibitors and corticosteroids. Herein, we review the role and regulation of MKP-1 in the context of airway inflammation. We initially outline the structure and biochemistry of MKP-1 and summarise the multi-layered molecular mechanisms responsible for MKP-1 production more generally. We then focus in on some of the key in vitro studies in cell types relevant to airway disease that explain how MKP-1 can be regulated in airway inflammation at the transcriptional, post-translation and post-translational level. And finally, we address some of the potential challenges with MKP-1 upregulation that need to be explored further to fully exploit the potential of MKP-1 to repress airway inflammation in chronic respiratory disease.

Mor, D, Kendig, MD, Kang, JWM, Gemikonakli, G, Austin, PJ, Kalman, E & Corbit, LH 2017, 'Peripheral nerve injury impairs the ability to maintain behavioural flexibility following acute stress in the rat', Behavioural Brain Research, vol. 328, pp. 123-129.
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Morelato, M, Barash, M, Blanes, L, Chadwick, S, Dilag, J, Kuzhiumparambil, U, Nizio, KD, Spindler, X & Moret, S 2017, 'Forensic Science: Current State and Perspective by a Group of Early Career Researchers', Foundations of Science, vol. 22, no. 4, pp. 799-825.
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© 2016, Springer Science+Business Media Dordrecht. Forensic science and its influence on policing and the criminal justice system have increased since the beginning of the twentieth century. While the philosophies of the forensic science pioneers remain the pillar of modern practice, rapid advances in technology and the underpinning sciences have seen an explosion in the number of disciplines and tools. Consequently, the way in which we exploit and interpret the remnant of criminal activity are adapting to this changing environment. In order to best exploit the trace, an interdisciplinary approach to both research and investigation is required. In this paper, nine postdoctoral research fellows from a multidisciplinary team discuss their vision for the future of forensic science at the crime scene, in the laboratory and beyond. This paper does not pretend to be exhaustive of all fields of forensic science, but describes a portion of the postdoctoral fellows’ interests and skills.

Mostyn, SN, Carland, JE, Shimmon, S, Ryan, RM, Rawling, T & Vandenberg, RJ 2017, 'Synthesis and Characterization of Novel Acyl-Glycine Inhibitors of GlyT2', ACS Chemical Neuroscience, vol. 8, no. 9, pp. 1949-1959.
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© 2017 American Chemical Society. It has been demonstrated previously that the endogenous compound N-arachidonyl-glycine inhibits the glycine transporter GlyT2, stimulates glycinergic neurotransmission, and provides analgesia in animal models of neuropathic and inflammatory pain. However, it is a relatively weak inhibitor with an IC50 of 9 μM and is subject to oxidation via cyclooxygenase, limiting its therapeutic value. In this paper we describe the synthesis and testing of a novel series of monounsaturated C18 and C16 acyl-glycine molecules as inhibitors of the glycine transporter GlyT2. We demonstrate that they are up to 28 fold more potent that N-arachidonyl-glycine with no activity at the closely related GlyT1 transporter at concentrations up to 30 μM. This novel class of compounds show considerable promise as a first generation of GlyT2 transport inhibitors.

Mowe, MAD, Porojan, C, Abbas, F, Mitrovic, SM, Lim, RP, Furey, A & Yeo, DCJ 2017, 'Corrigendum to “Rising temperatures may increase growth rates and microcystin production in tropical Microcystis species” [Harmful Algae 50 88–98]', Harmful Algae, vol. 63, pp. 205-206.
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Munday, R, Murray, S, Rhodes, L, Larsson, M & Harwood, D 2017, 'Ciguatoxins and Maitotoxins in Extracts of Sixteen Gambierdiscus Isolates and One Fukuyoa Isolate from the South Pacific and Their Toxicity to Mice by Intraperitoneal and Oral Administration', Marine Drugs, vol. 15, no. 7, pp. 208-208.
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© 2017 by the authors. Licensee MDPI. Ciguatoxins (CTXs), and possibly maitotoxins (MTXs), are responsible for Ciguatera Fish Poisoning, an important health problem for consumers of reef fish (such as inhabitants of islands in the South Pacific Ocean). The habitational range of the Gambierdiscus species is expanding, and new species are being discovered. In order to provide information on the potential health risk of the Gambierdiscus species, and one Fukuyoa species (found in the Cook Islands, the Kermadec Islands, mainland New Zealand, and New South Wales, Australia), 17 microalgae isolates were collected from these areas. Unialgal cultures were grown and extracts of the culture isolates were analysed for CTXs and MTXs by liquid chromatography tandem mass spectrometry (LC-MS/MS), and their toxicity to mice was determined by intraperitoneal and oral administration. An isolate of G. carpenteri contained neither CTXs nor MTXs, while 15 other isolates (including G. australes, G. cheloniae, G. pacificus, G. honu, and F. paulensis) contained only MTX-1 and/or MTX-3. An isolate of G. polynesiensis contained both CTXs and MTX-3. All the extracts were toxic to mice by intraperitoneal injection, but those containing only MTX-1 and/or -3 were much less toxic by oral administration. The extract of G. polynesiensis was highly toxic by both routes of administration.

Murphy, CD, Ni, G, Li, G, Barnett, A, Xu, K, Grant‐Burt, J, Liefer, JD, Suggett, DJ & Campbell, DA 2017, 'Quantitating active photosystem II reaction center content from fluorescence induction transients', Limnology and Oceanography: Methods, vol. 15, no. 1, pp. 54-69.
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AbstractPhotosystem II (PSII) is a pigment‐protein complex that photochemically extracts electrons from water, generating the reductant that supports biological productivity in all biomes. Estimating the content of active PSII reaction centers in a liquid sample is a key input for estimating aquatic photosynthesis rates, as well as for analyzing phytoplankton stress responses. Established procedures for PSII content quantification based on oxygen evolution are slow, imprecise and require dense cell suspensions, and are thus inapplicable to many laboratory or field studies. A new approach uses baseline chlorophyll fluorescence emission divided by the effective absorbance cross section for PSII photochemistry, with both variables derivable from single turnover fluorescence induction protocols. This approach has not been widely tested and is potentially subject to variation in samples suffering progressive photoinactivation or induction of non‐photochemical quenching under variable light. We evaluated the validity of this approach for a marine picocyanobacteria, low and high light Prochlorococcus ecotypes, arctic and temperate prasinophyte green alga and two centric diatoms, generating 209 paired determinations from a range of growth and treatment conditions. We successfully calibrated the fluorescence derived estimator for PSII reaction center content, and demonstrate a modification that corrects for the short term influence of photoinactivation. The modified parameter shows little response to induction of non‐photochemical quenching. In doing so we show the potential and limitations of an estimator of active PSII reaction center content that is sufficiently robust to support rapid, time‐resolved autonomous measures of primary productivity from lakes and oceans.

Murray, M, Choucair, H, Allison, S, Bourget, K, Chen, Y, Dunstan, C & Rawling, T 2017, 'O25 A novel synthetic ω-3 fatty acid epoxide analogue activates breast cancer cell killing in vitro and in vivo', Biochemical Pharmacology, vol. 139, pp. 117-117.
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Murray, SA, Ajani, P, Kretzschmar, AL & Verma, A 2017, 'Response to “More surprises in the global greenhouse: Human health impacts form recent toxic marine aerosol formulations, due to centennial alterations or world-wide coastal food webs”', Marine Pollution Bulletin, vol. 123, no. 1-2, pp. 415-417.
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Nair, HAS, Periasamy, S, Yang, L, Kjelleberg, S & Rice, SA 2017, 'Real Time, Spatial, and Temporal Mapping of the Distribution of c-di-GMP during Biofilm Development', Journal of Biological Chemistry, vol. 292, no. 2, pp. 477-487.
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© 2017 by The American Society for Biochemistry and Molecular Biology, Inc. Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di- GMP) is a dynamic intracellular signaling molecule that plays a central role in the biofilm life cycle. Current methodologies for the quantification of c-di-GMP are typically based on chemical extraction, representing end point measurements. Chemical methodologies also fail to take into consideration the physiological heterogeneity of the biofilm and thus represent an average c-di-GMP concentration across the entire biofilm. To address these problems, a ratiometric, image-based quantification method has been developed based on expression of the green fluorescence protein (GFP) under the control of the c-di-GMPresponsive cdrA promoter (Rybtke, M. T., Borlee, B. R., Murakami, K., Irie, Y., Hentzer, M., Nielsen, T. E., Givskov, M., Parsek, M. R., and Tolker-Nielsen, T. (2012) Appl. Environ. Microbiol. 78, 5060-5069). The methodology uses the cyan fluorescent protein (CFP) as a biomass indicator and the GFP as a c-di-GMP reporter. Thus, the CFP/GFP ratio gives the effective c-di-GMP per biomass. A binary mask was applied to alleviate background fluorescence, and fluorescence was calibrated against known c-di-GMP concentrations. Using flow cells for biofilm formation, c-di-GMP showed a non-uniform distribution across the biofilm, with concentrated hot spots of c-di- GMP. Additionally, c-di-GMP was found to be localized at the outer boundary of mature colonies in contrast to a uniform distribution in early stage, small colonies. These data demonstrate the application of a method for the in situ, real time quantification of c-di-GMP and show that the amount of this biofilmregulating second messenger was dynamic with time and colony size, reflecting the extent of biofilm heterogeneity in real time.

Nair, PM, Starkey, MR, Haw, TJ, Liu, G, Horvat, JC, Morris, JC, Verrills, NM, Clark, AR, Ammit, AJ & Hansbro, PM 2017, 'Targeting PP2A and proteasome activity ameliorates features of allergic airway disease in mice', Allergy, vol. 72, no. 12, pp. 1891-1903.
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AbstractBackgroundAsthma is an allergic airway disease (AAD) caused by aberrant immune responses to allergens. Protein phosphatase‐2A (PP2A) is an abundant serine/threonine phosphatase with anti‐inflammatory activity. The ubiquitin proteasome system (UPS) controls many cellular processes, including the initiation of inflammatory responses by protein degradation. We assessed whether enhancing PP2A activity with fingolimod (FTY720) or 2‐amino‐4‐(4‐(heptyloxy) phenyl)‐2‐methylbutan‐1‐ol (AAL(S)), or inhibiting proteasome activity with bortezomib (BORT), could suppress experimental AAD.MethodsAcute AAD was induced in C57BL/6 mice by intraperitoneal sensitization with ovalbumin (OVA) in combination with intranasal (i.n) exposure to OVA. Chronic AAD was induced in mice with prolonged i.n exposure to crude house dust mite (HDM) extract. Mice were treated with vehicle, FTY720,

Najafpour, MM, Heidari, S, Balaghi, SE, Hołyńska, M, Sadr, MH, Soltani, B, Khatamian, M, Larkum, AW & Allakhverdiev, SI 2017, 'Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1858, no. 2, pp. 156-174.
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Plants, algae and cyanobacteria capture sunlight, extracting electrons from H2O to reduce CO2 into sugars while releasing O2 in the oxygenic photosynthetic process. Because of the important role of water oxidation in artificial photosynthesis and many solar fuel systems, understanding the structure and function of this unique biological catalyst forms a requisite research field. Herein the structure of the water-oxidizing complex and its ligand environment are described with reference to the 1.9Å resolution X-ray-derived crystallographic model of the water-oxidizing complex from the cyanobacterium Thermosynechococcus vulcanus. Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides are also reviewed and discussed in the paper.

Naser, IB, Hoque, MM, Abdullah, A, Bari, SMN, Ghosh, AN & Faruque, SM 2017, 'Environmental bacteriophages active on biofilms and planktonic forms of toxigenic Vibrio cholerae: Potential relevance in cholera epidemiology', PLOS ONE, vol. 12, no. 7, pp. e0180838-e0180838.
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METHODS: Phages isolated from environmental waters in Bangladesh were tested for their host specificity towards V. cholerae O1 and O139, and the ability to disperse V. cholerae biofilms formed in the laboratory. Representative phages were further characterized by electron microscopy and whole genome sequencing. Selected phages were then introduced in various combinations to biofilms of toxigenic V. cholerae added to samples of river water, and the dispersion of biofilms as well as the growth kinetics of V. cholerae and the phages were monitored. RESULTS: A phage cocktail composed of three different phages isolated from surface waters in Bangladesh and designated as JSF7, JSF4, and JSF3 could significantly influence the distribution and concentration of the active planktonic form and biofilm associated form of toxigenic V. cholerae in water. While JSF7 showed a biofilm degrading activity and dispersed cells from both V. cholerae O1 and O139 derived biofilms thus increasing the concentration of planktonic V. cholerae in water, JSF4 and JSF3 showed strong bactericidal activity against V. cholerae O1 and O139 respectively. A mixture of all three phages could effectively reduce both biofilm-associated and planktonic V. cholerae in river water microcosms. SIGNIFICANCE: Besides potential applicability in phage-mediated control of cholera, our results have relevance in appreciating possible intricate role of diverse environmental phages in the epidemiology of the disease, since both biofilms and phages influence the prevalence and infectivity of V. cholerae in a variety of ways.

Naser, IB, Hoque, MM, Nahid, MA, Tareq, TM, Rocky, MK & Faruque, SM 2017, 'Analysis of the CRISPR-Cas system in bacteriophages active on epidemic strains of Vibrio cholerae in Bangladesh', Scientific Reports, vol. 7, no. 1, p. 14880.
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AbstractCRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated proteins) are microbial nuclease systems involved in defense against phages. Bacteria also resist phages by hosting phage-inducible chromosomal islands (PICI) which prevent phage reproduction. Vibrio cholerae which causes cholera epidemics, interacts with numerous phages in the environment and in cholera patients. Although CRISPR-Cas systems are usually carried by bacteria and archea, recently V. cholerae specific ICP1 phages were found to host a CRISPR-Cas system that inactivates PICI-like elements (PLE) in V. cholerae. We analyzed a collection of phages and V. cholerae isolated during seasonal cholera epidemics in Bangladesh, to study the distribution, and recent evolution of the phage-encoded CRISPR-Cas system. Five distinct but related phages carrying the CRISPR-Cas system, and possible CRISPR-Cas negative progenitor phages were identified. Furthermore, CRISPR arrays in the phages were found to have evolved by acquisition of new spacers targeting diverse regions of PLEs carried by the V. cholerae strains, enabling the phages to efficiently grow on PLE positive strains. Our results demonstrate a continuing arms-race involving genetic determinants of phage-resistance in V. cholerae, and the phage-encoded CRISPR-Cas system in the co-evolution of V. cholerae and its phages, presumably fostered by their enhanced interactions during seasonal epidemics of cholera.

Neira, V, Brito, B, Mena, J, Culhane, M, Apel, MI, Max, V, Perez, P, Moreno, V, Mathieu, C, Johow, M, Badia, C, Torremorell, M, Medina, R & Ortega, R 2017, 'Epidemiological investigations of the introduction of porcine reproductive and respiratory syndrome virus in Chile, 2013-2015', PLOS ONE, vol. 12, no. 7, pp. e0181569-e0181569.
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© 2017 Neira 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. Porcine reproductive and respiratory syndrome (PRRS) is endemic in most pork producing countries. In Chile, eradication of PRRS virus (PRRSV) was successfully achieved in 2009 as a result of the combined efforts of producers and the animal health authorities. In October 2013, after several years without detecting PRRSV under surveillance activities, suspected cases were confirmed on a commercial swine farm. Here, we describe the PRRS epidemic in Chile between October 2013 and April 2015, and we studied the origins and spread of PRRSV throughout the country using official surveillance data and Bayesian phylogenetic analysis. Our results indicate that the outbreaks were caused by a PRRSV closely related to viruses present in swine farms in North America, and different from the strain that circulated in the country before 2009. Using divergence time estimation analysis, we found that the 2013–2015 PRRSV may have been circulating in Chile for at least one month before the first detection. A single strain of PRRSV spread into a limited number of commercial and backyard swine farms. New infections in commercial systems have not been reported since October 2014, and eradication is underway by clearing the disease from the few commercial and backyard farms that remain positive. This is one of the few documented experiences of PRRSV introduction into a disease-free country.

Ng Kee Kwong, F, Nicholson, AG, Harrison, CL, Hansbro, PM, Adcock, IM & Chung, KF 2017, 'Is mitochondrial dysfunction a driving mechanism linking COPD to nonsmall cell lung carcinoma?', European Respiratory Review, vol. 26, no. 146, pp. 170040-170040.
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Chronic obstructive pulmonary disease (COPD) patients are at increased risk of developing nonsmall cell lung carcinoma, irrespective of their smoking history. Although the mechanisms behind this observation are not clear, established drivers of carcinogenesis in COPD include oxidative stress and sustained chronic inflammation. Mitochondria are critical in these two processes and recent evidence links increased oxidative stress in COPD patients to mitochondrial damage. We therefore postulate that mitochondrial damage in COPD patients leads to increased oxidative stress and chronic inflammation, thereby increasing the risk of carcinogenesis.The functional state of the mitochondrion is dependent on the balance between its biogenesis and degradation (mitophagy). Dysfunctional mitochondria are a source of oxidative stress and inflammasome activation. In COPD, there is impaired translocation of the ubiquitin-related degradation molecule Parkin following activation of the Pink1 mitophagy pathway, resulting in excessive dysfunctional mitochondria. We hypothesise that deranged pathways in mitochondrial biogenesis and mitophagy in COPD can account for the increased risk in carcinogenesis. To test this hypothesis, animal models exposed to cigarette smoke and developing emphysema and lung cancer should be developed. In the future, the use of mitochondria-based antioxidants should be studied as an adjunct with the aim of reducing the risk of COPD-associated cancer.

Nguyen, LT, Chen, H, Pollock, C & Saad, S 2017, 'SIRT1 reduction is associated with sex-specific dysregulation of renal lipid metabolism and stress responses in offspring by maternal high-fat diet', Scientific Reports, vol. 7, no. 1, pp. 1-13.
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AbstractRodent models of maternal obesity have been associated with kidney damage and dysfunction in offspring. However, the underlying mechanisms are yet to be elucidated. In this study, female rats were fed a high-fat diet (HFD) for 6 weeks prior to mating, throughout gestation and lactation; both male and female offspring were examined at weaning. Our results demonstrate that renal lipid deposition was increased in male offspring only, which is associated with reduced protein expression of Sirtuin (SIRT) 1, an essential regulator of lipid metabolism and stress response. Other components in its signalling network including phosphorylated 5′-AMP-activated protein kinase (pAMPKα), Forkhead box FOXO3a and Peroxisome proliferator-activated receptor (PPAR)γ coactivator 1-alpha (PGC-1α) were also downregulated. By contrast, in female offspring, renal fat/lipid distribution was unchanged in coupling with normal SIRT1 regulation. Specific autophagy and antioxidant markers were suppressed in both sexes. On the other hand, fibronectin and Collagen type IV protein expression was significantly higher in the offspring born HFD-fed dams, particularly in the males. Collectively, these findings suggest that maternal HFD consumption can induce sex-specific changes in offspring kidney lipid metabolism and stress responses at early ages, which may underpin the risk of kidney diseases later in life.

Nguyen, LT, Saad, S, Tan, Y, Pollock, C & Chen, H 2017, 'Maternal high-fat diet induces metabolic stress response disorders in offspring hypothalamus', Journal of Molecular Endocrinology, vol. 59, no. 1, pp. 81-92.
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Maternal obesity has been shown to increase the risk of obesity and related disorders in the offspring, which has been partially attributed to changes of appetite regulators in the offspring hypothalamus. On the other hand, endoplasmic reticulum (ER) stress and autophagy have been implicated in hypothalamic neuropeptide dysregulation, thus may also play important roles in such transgenerational effect. In this study, we show that offspring born to high-fat diet-fed dams showed significantly increased body weight and glucose intolerance, adiposity and plasma triglyceride level at weaning. Hypothalamic mRNA level of the orexigenic neuropeptide Y (NPY) was increased, while the levels of the anorexigenic pro-opiomelanocortin (POMC), NPY1 receptor (NPY1R) and melanocortin-4 receptor (MC4R) were significantly downregulated. In association, the expression of unfolded protein response (UPR) markers including glucose-regulated protein (GRP)94 and endoplasmic reticulum DNA J domain-containing protein (Erdj)4 was reduced. By contrast, protein levels of autophagy-related genes Atg5 and Atg7, as well as mitophagy marker Parkin, were slightly increased. The administration of 4-phenyl butyrate (PBA), a chemical chaperone of protein folding and UPR activator, in the offspring from postnatal day 4 significantly reduced their body weight, fat deposition, which were in association with increased activating transcription factor (ATF)4, immunoglobulin-binding protein (BiP) and Erdj4 mRNA as well as reduced Parkin, PTEN-induced putative kinase (PINK)1 and dynamin-related protein (Drp)1 protein expression levels. These results suggest that hypothalamic ER stress and mitophagy are among the regulatory factors of offspring metabolic changes due to maternal obesity.

Nguyen, M, Kim, S, Tran, TT, Xu, Z-Q, Kianinia, M, Toth, M & Aharonovich, I 2017, 'Nanoassembly of quantum emitters in hexagonal boron nitride and gold nanospheres', Nanoscale, vol. 10, no. 5, pp. 2267-2274.
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Assembly of quantum nanophotonic systems with plasmonic resonators areimportant for fundamental studies of single photon sources as well as foron-chip information processing. In this work, we demonstrate controllablenanoassembly of gold nanospheres with ultra-bright quantum emitters in 2Dlayered hexagonal boron nitride (hBN). We utilize an atomic force microscope(AFM) tip to precisely position gold nanospheres to close proximity of thequantum emitters and observe the resulting emission enhancement andfluorescence lifetime reduction. A fluorescence enhancement of over 300% isachieved experimentally for quantum emitters in hBN, with a radiative quantumefficiency of up to 40% and a saturated count rate in excess of 5 millioncounts/s. Our results are promising for future employment of quantum emittersin hBN for integrated nanophotonic devices and plasmonic based nanosensors.

Nguyen, TV, Ho-Le, TP & Le, UV 2017, 'International collaboration in scientific research in Vietnam: an analysis of patterns and impact', Scientometrics, vol. 110, no. 2, pp. 1035-1051.
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Nizalapur, S, Kimyon, O, Yee, E, Ho, K, Berry, T, Manefield, M, Cranfield, CG, Willcox, M, Black, DS & Kumar, N 2017, 'Amphipathic guanidine-embedded glyoxamide-based peptidomimetics as novel antibacterial agents and biofilm disruptors', Organic & Biomolecular Chemistry, vol. 15, no. 9, pp. 2033-2051.
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Novel antibacterial peptidomimetics that inhibit the growth of planktonic cells and reduce biofilm formation in both Gram-positive and Gram-negative bacteria.

Nizio, KD, Ueland, M, Stuart, BH & Forbes, SL 2017, 'The analysis of textiles associated with decomposing remains as a natural training aid for cadaver-detection dogs', Forensic Chemistry, vol. 5, pp. 33-45.
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© 2017 Elsevier B.V. Cadaver-detection dogs are employed by law enforcement agencies to locate human remains in cases of missing persons, suspected homicides and following natural or man-made disasters. The ability of cadaver-detection dogs to locate human remains relies heavily on the use of effective and reliable training aids. Cadaver-detection dogs may be trained using a variety of materials ranging from natural scent sources (e.g. flesh, bone, blood or decomposition soil) to synthetic materials (e.g. Pseudo™ Scents). Commercially available synthetic scents often have an overly simplistic chemical composition that is inconsistent with decomposition odour. Therefore, natural scent sources are typically considered to be the most effective training aids; however, there is concern that using individual tissue types as natural training aids may not be indicative of the scent of an intact human cadaver. The objective of this work was to determine how well textiles associated with decomposing remains retain and mimic the odour of natural training aids. To test this, the chemical odour profile of textile samples collected from decomposing porcine remains that were buried clothed in 100% cotton t-shirts was examined. Throughout various stages of decomposition, the pig carcasses were exhumed and cotton samples were obtained. The volatile organic compound (VOC) profile of the textiles was collected using headspace solid phase microextraction (HS-SPME) and analysed using comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC×GC-TOFMS). This study provides evidence that textiles associated with decomposing remains may represent a useful natural training aid with a VOC profile reflective of a large subset of cadaveric decomposition odour. The odour profile is dynamic and changes over time suggesting that obtaining textiles from different postmortem intervals would be useful for providing training aids that represent the full spectrum of dec...

Nolan, RH, Fairweather, KA, Tarin, T, Santini, NS, Cleverly, J, Faux, R & Eamus, D 2017, 'Divergence in plant water-use strategies in semiarid woody species', Functional Plant Biology, vol. 44, no. 11, pp. 1134-1134.
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Partitioning of water resources amongst plant species within a single climate envelope is possible if the species differ in key hydraulic traits. We examined 11 bivariate trait relationships across nine woody species found in the Ti-Tree basin of central Australia. We found that species with limited access to soil moisture, evidenced by low pre-dawn leaf water potential, displayed anisohydric behaviour (e.g. large seasonal fluctuations in minimum leaf water potential), had greater sapwood density and lower osmotic potential at full turgor. Osmotic potential at full turgor was positively correlated with the leaf water potential at turgor loss, which was, in turn, positively correlated with the water potential at incipient stomatal closure. We also observed divergent behaviour in two species of Mulga, a complex of closely related Acacia species which range from tall shrubs to low trees and dominate large areas of arid and semiarid Australia. These Mulga species had much lower minimum leaf water potentials and lower specific leaf area compared with the other seven species. Finally, one species, Hakea macrocarpa A.Cunn ex.R.Br., had traits that may allow it to tolerate seasonal dryness (through possession of small specific leaf area and cavitation resistant xylem) despite exhibiting cellular water relations that were similar to groundwater-dependent species. We conclude that traits related to water transport and leaf water status differ across species that experience differences in soil water availability and that this enables a diversity of species to exist in this low rainfall environment.

Nolan, RH, Tarin, T, Fairweather, KA, Cleverly, J & Eamus, D 2017, 'Variation in photosynthetic traits related to access to water in semiarid Australian woody species', Functional Plant Biology, vol. 44, no. 11, pp. 1087-1087.
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Low soil water content can limit photosynthesis by reducing stomatal conductance. Here, we explore relationships among traits pertaining to carbon uptake and pre-dawn leaf water potential (as an index of soil water availability) across eight species found in semiarid central Australia. We found that as pre-dawn leaf water potential declined, stomatal limitations to photosynthesis increased, as did foliar nitrogen, which enhanced photosynthesis. Nitrogen-fixing Acacia species had higher foliar nitrogen concentrations compared with non-nitrogen fixing species, although there was considerable variability of traits within the Acacia genus. From principal component analysis we found that the most dissimilar species was Acacia aptaneura Maslin&J.E.Reid compared with both Eucalyptus camaldulensis Dehnh. and Corymbia opaca. (D.J.Carr & S.G.M.Carr)K.D.Hill&L.A.S.Johnson, having both the largest foliar N content, equal largest leaf mass per area and experiencing the lowest pre-dawn water potential of all species. A. aptaneura has shallow roots and grows above a hardpan that excludes access to groundwater, in contrast to E. camaldulensis and C. opaca, which are known to access groundwater. We conclude that ecohydrological niche separation is an important factor driving the variability of within-biome traits related to carbon gain. These observations have important implications for global vegetation models, which are parameterised with many of the traits measured here, but are often limited by data availability.

Nolan, RH, Tarin, T, Santini, NS, McAdam, SAM, Ruman, R & Eamus, D 2017, 'Differences in osmotic adjustment, foliar abscisic acid dynamics, and stomatal regulation between an isohydric and anisohydric woody angiosperm during drought', Plant, Cell & Environment, vol. 40, no. 12, pp. 3122-3134.
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AbstractSpecies are often classified along a continuum from isohydric to anisohydric, with isohydric species exhibiting tighter regulation of leaf water potential through stomatal closure in response to drought. We investigated plasticity in stomatal regulation in an isohydric (Eucalyptus camaldulensis) and an anisohydric (Acacia aptaneura) angiosperm species subject to repeated drying cycles. We also assessed foliar abscisic acid (ABA) content dynamics, aboveground/belowground biomass allocation and nonstructural carbohydrates. The anisohydric species exhibited large plasticity in the turgor loss point (ΨTLP), with plants subject to repeated drying exhibiting lower ΨTLP and correspondingly larger stomatal conductance at low water potential, compared to plants not previously exposed to drought. The anisohydric species exhibited a switch from ABA to water potential‐driven stomatal closure during drought, a response previously only reported for anisohydric gymnosperms. The isohydric species showed little osmotic adjustment, with no evidence of switching to water potential‐driven stomatal closure, but did exhibit increased root:shoot ratios. There were no differences in carbohydrate depletion between species. We conclude that a large range in ΨTLP and biphasic ABA dynamics are indicative of anisohydric species, and these traits are associated with exposure to low minimum foliar water potential, dense sapwood and large resistance to xylem embolism.

Nolan, TH & Wand, MP 2017, 'Accurate logistic variational message passing: algebraic and numerical details', Stat, vol. 6, no. 1, pp. 102-112.
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We provide full algebraic and numerical details required for fitting accurate logistic likelihood regression‐type models via variational message passing with factor graph fragments. Existing methodology of this type involves the Jaakkola–Jordan device, which is prone to poor accuracy. We examine two alternatives: the Saul–Jordan tilted bound device and conjugacy enforcement via multivariate normal prespecification of a key message. Both of these approaches appear in related literature. Our contributions facilitate immediate implementation within variational message passing schemes. Copyright © 2017 John Wiley & Sons, Ltd.

Noorian, P, Hu, J, Chen, Z, Kjelleberg, S, Wilkins, MR, Sun, S & McDougald, D 2017, 'Pyomelanin produced by Vibrio cholerae confers resistance to predation by Acanthamoeba castellanii', FEMS Microbiology Ecology, vol. 93, no. 12, pp. 1-10.
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© FEMS 2017. Protozoan predation is one of the main environmental factors constraining bacterial growth in aquatic environments, and thus has led to the evolution of a number of defence mechanisms that protect bacteria from predation. These mechanisms may also function as virulence factors in infection of animal and human hosts. Whole transcriptome shotgun sequencing of Vibrio cholerae biofilms during predation by the amoebae, Acanthamoeba castellanii, revealed that 131 transcripts were significantly differentially regulated when compared to the non-grazed control. Differentially regulated transcripts included those involved in biosynthetic and metabolic pathways. The transcripts of genes involved in tyrosine metabolism were down-regulated in the grazed population, which indicates that the tyrosine metabolic regulon may have a role in the response of V. cholerae biofilms to A. castellanii predation. Homogentisate 1, 2-dioxygenase (HGA) is the main intermediate of the normal L-tyrosine catabolic pathway which is known to auto-oxidize, leading to the formation of the pigment, pyomelanin. Indeed, a pigmented mutant, disrupted in hmgA, was more resistant to amoebae predation than the wild type. Increased grazing resistance was correlated with increased production of pyomelanin and thus reactive oxygen species (ROS), suggesting that ROS production is a defensive mechanism used by bacterial biofilms against predation by amoebae A. castellanii.

Novikov, A & Kaji, S 2017, 'On distibutions of first passage times of martingales arising in some gambling problems', Japan Journal of Industrial and Applied Mathematics, vol. 34, no. 3, pp. 859-871.
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© 2017, The JJIAM Publishing Committee and Springer Japan KK. Using a martingale technique we derive bounds and asymptotics for tail distributions of first passage times τb associated with crossing a level b for some gambling strategies. In particilar, for the case of martingale games with so-called “Oscar strategy” we show that P{τb>n}≤Cn-3/2 for any level b> 0.

Novikov, A, Alexander, S, Kordzakhia, N & Ling, T 2017, 'Pricing of Asian-Type and Basket Options via Bounds', Theory of Probability & Its Applications, vol. 61, no. 1, pp. 94-106.
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© 2017 Society for Industrial and Applied Mathematics. This paper sets out to provide a general framework for the pricing of average-type options via lower and upper bounds. This class of options includes Asian, basket, and options on the volume-weighted average price. The use of lower and upper bounds is proposed in response to the inherent difficulty in finding analytical representations for the true price of these options and the requirement for numerical procedures to be fast and efficient. We demonstrate that in some cases lower bounds allow for the dimensionality of the problem to be reduced and that these methods provide reasonable approximations to the price of the option.

O’Rourke, MB, Raymond, BBA & Padula, MP 2017, 'The Characterization of Laser Ablation Patterns and a New Definition of Resolution in Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS)', Journal of the American Society for Mass Spectrometry, vol. 28, no. 5, pp. 895-900.
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© 2017, American Society for Mass Spectrometry. Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) is a technique that has seen a sharp rise in both use and development. Despite this rapid adoption, there have been few thorough investigations into the actual physical mechanisms that underlie the acquisition of IMS images. We therefore set out to characterize the effect of IMS laser ablation patterns on the surface of a sample. We also concluded that the governing factors that control spatial resolution have not been correctly defined and therefore propose a new definition of resolution. [Figure not available: see fulltext.]

O'Connor, JJ, Booth, DJ, Swearer, SE, Fielder, DS & Leis, JM 2017, 'Ontogenetic milestones of chemotactic behaviour reflect innate species-specific response to habitat cues in larval fish', Animal Behaviour, vol. 132, pp. 61-71.
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© 2017 The Association for the Study of Animal Behaviour The distribution and connectivity of marine populations are largely dependent on biophysical factors affecting pelagic larval dispersal between spawning at adult spawning sites and settlement to juvenile nursery habitats. Behaviour and swimming ability of pelagic larvae are increasingly understood to influence patterns of dispersal, but it is unclear which sensory cues are involved and when during ontogeny these abilities first develop. Here we studied the early ontogenetic development of responses to olfactory cues from coastal and estuarine waters in larvae of two temperate estuarine-associated fish species, Australian bass, Macquaria novemaculeata, and mulloway, Argyrosomus japonicus, to determine when olfaction begins to influence dispersal. Olfactory responses to habitat-associated cues were not present when larvae first transitioned from nonswimming to swimming (indicated by flexion of the notochord), but emerged after ca. 7 days in a species-specific manner that was consistent across different cohorts. Based on general additive models (GAMs), age (in days posthatch) best explained the ontogenetic pattern in both species. The emergence of chemotactic responses coincides with an exponential increase in swimming endurance reported for these species. This suggests the existence of ontogenetic milestones during larval development that, once reached, trigger active influence on dispersal. Salinity and pH did not influence choice behaviour after these ontogenetic milestones; however, the presence of cues generated by seagrass harvested from the estuary habitat elicited strong responses in fish larvae consistent with species-specific habitat preferences, indicating an important role for aquatic vegetation in driving these behaviours.

Oh, B, Lee, KJ, Zaslawski, C, Yeung, A, Rosenthal, D, Larkey, L & Back, M 2017, 'Health and well-being benefits of spending time in forests: systematic review', Environmental Health and Preventive Medicine, vol. 22, no. 1, pp. 1-11.
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© The Author(s) 2017. Background: Numerous studies have reported that spending time in nature is associated with the improvement of various health outcomes and well-being. This review evaluated the physical and psychological benefits of a specific type of exposure to nature, forest therapy. Method: A literature search was carried out using MEDLINE, PubMed, ScienceDirect, EMBASE, and ProQuest databases and manual searches from inception up to December 2016. Key words: 'Forest' or 'Shinrin -Yoku' or 'Forest bath' AND 'Health' or 'Wellbeing'. The methodological quality of each randomized controlled trials (RCTs) was assessed according to the Cochrane risk of bias (ROB) tool. Results: Six RCTs met the inclusion criteria. Participants' ages ranged from 20 to 79 years. Sample size ranged from 18 to 99. Populations studied varied from young healthy university students to elderly people with chronic disease. Studies reported the positive impact of forest therapy on hypertension (n = 2), cardiac and pulmonary function (n = 1), immune function (n = 2), inflammation (n= 3), oxidative stress (n = 1), stress (n = 1), stress hormone (n= 1), anxiety (n= 1), depression (n = 2), and emotional response (n = 3). The quality of all studies included in this review had a high ROB. Conclusion: Forest therapy may play an important role in health promotion and disease prevention. However, the lack of high-quality studies limits the strength of results, rendering the evidence insufficient to establish clinical practice guidelines for its use. More robust RCTs are warranted.

Oh, H-S, Tan, CH, Low, JH, Rzechowicz, M, Siddiqui, MF, Winters, H, Kjelleberg, S, Fane, AG & Rice, SA 2017, 'Quorum quenching bacteria can be used to inhibit the biofouling of reverse osmosis membranes', Water Research, vol. 112, pp. 29-37.
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Ong, M, Peng, J, Jin, X & Qu, X 2017, 'Chinese Herbal Medicine for the Optimal Management of Polycystic Ovary Syndrome', The American Journal of Chinese Medicine, vol. 45, no. 03, pp. 405-422.
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Polycystic ovary syndrome (PCOS) is a complex heterogeneous disorder characterized by androgen excess and ovulatory dysfunction; it is now known to be closely linked to metabolic syndrome. Recent research suggests that insulin resistance plays an important role in the pathogenesis of PCOS which may lead to the excessive production of androgens by ovarian theca cells. Currently there is no single drug that can treat both the reproductive and metabolic complications of the disorder. Existing pharmaceutical agents such as hormonal therapies have been associated with side effects and are not appropriate for PCOS women with infertility. Additionally, insulin sensitizing agents useful for treating the metabolic abnormalities in PCOS have limited efficacy for treating reproductive aspects of the disorder. Chinese herbal medicines have a long history of treating gynaecological problems and infertility and therefore may be a novel approach to the treatment of PCOS. Current research demonstrates that the compounds isolated from herbs have shown beneficial effects for PCOS and when combined in an herbal formula can target both reproductive and metabolic defects simultaneously. Therefore, further investigation into Chinese herbal medicine in the treatment of PCOS is warranted.

O'Rourke, MB & Padula, MP 2017, 'A new standard of visual data representation for imaging mass spectrometry', PROTEOMICS – Clinical Applications, vol. 11, no. 3-4, pp. 1600098-1600098.
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PurposeMALDI imaging MS (IMS) is principally used for cancer diagnostics. In our own experience with publishing IMS data, we have been requested to modify our protocols with respect to the areas of the tissue that are imaged in order to comply with the wider literature. In light of this, we have determined that current methodologies lack effective controls and can potentially introduce bias by only imaging specific areas of the targeted tissueExperimental designA previously imaged sample was selected and then cropped in different ways to show the potential effect of only imaging targeted areas.ResultsBy using a model sample, we were able to effectively show how selective imaging of samples can misinterpret tissue features and by changing the areas that are acquired, according to our new standard, an effective internal control can be introduced.Conclusions and clinical relevanceCurrent IMS sampling convention relies on the assumption that sample preparation has been performed correctly. This prevents users from checking whether molecules have moved beyond borders of the tissue due to delocalization and consequentially products of improper sample preparation could be interpreted as biological features that are of critical importance when encountered in a visual diagnostic.

Osei, ET, Florez-Sampedro, L, Tasena, H, Faiz, A, Noordhoek, JA, Timens, W, Postma, DS, Hackett, TL, Heijink, IH & Brandsma, C-A 2017, 'miR-146a-5p plays an essential role in the aberrant epithelial–fibroblast cross-talk in COPD', European Respiratory Journal, vol. 49, no. 5, pp. 1602538-1602538.
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We previously reported that epithelial-derived interleukin (IL)-1α drives fibroblast-derived inflammation in the lung epithelial–mesenchymal trophic unit. Since miR-146a-5p has been shown to negatively regulate IL-1 signalling, we investigated the role of miR-146a-5p in the regulation of IL-1α-driven inflammation in chronic obstructive pulmonary disease (COPD).Human bronchial epithelial (16HBE14o-) cells were co-cultured with control and COPD-derived primary human lung fibroblasts (PHLFs), and miR-146a-5p expression was assessed with and without IL-1α neutralising antibody. Genomic DNA was assessed for the presence of the single nucleotide polymorphism (SNP) rs2910164. miR-146a-5p mimics were used for overexpression studies to assess IL-1α-induced signalling and IL-8 production by PHLFs.Co-culture of PHLFs with airway epithelial cells significantly increased the expression of miR-146a-5p and this induction was dependent on epithelial-derived IL-1α. miR-146a-5p overexpression decreased IL-1α-induced IL-8 secretion in PHLFs via downregulation of IL-1 receptor-associated kinase-1. In COPD PHLFs, the induction of miR-146a-5p was significantly less compared with controls and was associated with the SNP rs2910164 (GG allele) in the miR-146a-5p gene.Our results suggest that induction of miR-146a-5p is involved in epithelial–fibroblast communication in the lungs and negatively regulates epithelial-derived IL-1α induction of IL-8 by fibroblasts. The decreased levels of miR-146a-5p in COPD fibroblasts may induce a more pro-inflammatory phenotype, contributing to chronic inflammation in COPD.

Pacheco, JM, Brito, B, Hartwig, E, Smoliga, GR, Perez, A, Arzt, J & Rodriguez, LL 2017, 'Early Detection of Foot‐And‐Mouth Disease Virus from Infected Cattle Using A Dry Filter Air Sampling System', Transboundary and Emerging Diseases, vol. 64, no. 2, pp. 564-573.
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Padula, M, Berry, I, O′Rourke, M, Raymond, B, Santos, J & Djordjevic, SP 2017, 'A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis', Proteomes, vol. 5, no. 4, pp. 11-11.
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© 2017 by the authors. Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O'Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single 'spots' in a polyacrylamide gel, allowing the quantitation of changes in a proteoform0s abundance to ascertain changes in an organism's phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the 'Top-Down'. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O'Farrell's paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism0s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.

Pan, C, Lv, W, Wang, G, Niu, X, Guo, H & Chen, X 2017, 'Simultaneous separation of neutral and cationic analytes by one dimensional open tubular capillary electrochromatography using zeolitic imidazolate framework-8 as stationary phase', Journal of Chromatography A, vol. 1484, pp. 98-106.
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Developing simple methods for separation of analytes that belong to different classes is of great importance. Herein, we developed a simple one-dimensional (1-D) capillary electrochromatography method to demonstrate the simultaneous separation of target fractions that belong to two different classes (i.e., cationic and neutral analytes) without switching buffer solution by a zeolitic imidazolate framework ZIF-8 coated capillary column. Owing to the difference of charge-to-mass ratio of the cationic analytes, the interaction of the cationic analytes and coating material ZIF-8 and the hydrophobic interactions between the neutral analytes and the microporous framework of ZIF-8, six cationic analytes and four neutral analytes were simultaneously separated in a single run by 1-D capillary electrochromatography. The relative standard deviations (RSDs) of the analytes migration time for intra-day, inter-day and column-to-column were in the range of 0.11-0.87%, 0.54-2.04% and 2.00-6.89% and the RSDs of the analytes peak area for intra-day, inter-day and column-to-column were in the range of 0.70-4.45%, 1.33-6.20% and 2.27-11.88%. Additionally, the developed method was employed in the analysis of urine samples with satisfactory recoveries.

Pandey, AK, Mishra, AK, Kumar, R, Berwal, S, Devadas, R, Huete, A & Kumar, K 2017, 'CO variability and its association with household cooking fuels consumption over the Indo-Gangetic Plains', Environmental Pollution, vol. 222, pp. 83-93.
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© 2017 Elsevier Ltd This study examines the spatio-temporal trends obtained from decade long (Jan 2003–Dec 2014) satellite observational data of Atmospheric Infrared Sounder (AIRS) and Measurements of Pollution in the Troposphere (MOPITT) on carbon monoxide (CO) concentration over the Indo-Gangetic Plains (IGP) region. The time sequence plots of columnar CO levels over the western, central and eastern IGP regions reveal marked seasonal behaviour, with lowest CO levels occurring during the monsoon months and the highest CO levels occurring during the pre-monsoon period. A negative correlation between CO levels and rainfall is observed. CO vertical profiles show relatively high values in the upper troposphere at ∼200 hPa level during the monsoon months, thus suggesting the role of convective transport and advection in addition to washout behind the decreased CO levels during this period. MOPITT and AIRS observations show a decreasing trend of 9.6 × 1015and 1.5 × 1016molecules cm−2yr−1, respectively, in columnar CO levels over the IGP region. The results show the existence of a spatial gradient in CO from the eastern (higher levels) to western IGP region (lower levels). Data from the Census of India on the number of households using various cooking fuels in the IGP region shows the prevalence of biomass-fuel (i.e. firewood, crop residue, cowdung etc.) use over the eastern and central IGP regions and that of liquefied petroleum gas over the western IGP region. CO emission estimates from cooking activity over the three IGP regions are found to be in the order east > central > west, which support the existence of the spatial gradient in CO from eastern to the western IGP region. Our results support the intervention of present Indian government on limiting the use of biomass-fuels in domestic cooking to achieve the benefits in terms of the better air quality, household health and regional/global climate change mitigation.

Pang, CT, Ammit, AJ, Ong, YQE & Wheate, NJ 2017, 'para -Sulfonatocalix[4]arene and polyamidoamine dendrimer nanocomplexes as delivery vehicles for a novel platinum anticancer agent', Journal of Inorganic Biochemistry, vol. 176, pp. 1-7.
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Novel para-sulfonatocalix[4]arene (sCX[4]) and polyamidoamine (PAMAM) dendrimer nanocomplexes were evaluated as delivery vehicles for the platinum anticancer agent [(1,10-phenanthroline)(1S,2S-diaminocyclohexane)platinum(II)] chloride (PHENSS). Different ratios of sCX[4] to PHENSS were tested for their compatibility, with a ratio of 6:1 sCX[4]:PHENSS having the best solubility. The loading of sCX[4], and sCX[4]-bound PHENSS, onto three different generations of PAMAM dendrimers (G3.0-5.0) was examined using UV-visible spectrophotometry. The quantity of sCX[4] bound was found to increase exponentially with dendrimer size: G3, 15 sCX[4] molecules per dendrimer; G4, 37; and G5, 78. Similarly, the loading of sCX[4]-bound PHENSS also increased with increasing dendrimer size: G3, 7 PHENSS molecules per dendrimer; G4, 14; and G5, 28.5. The loading of sCX[4]-bound PHENSS molecules is significantly lower when compared with that of sCX[4], which indicates that less than half of the binding sites were occupied (45, 44, and 44%, respectively). By 1H NMR and UV-vis analysis, the nanocomplex was found to be stable in NaCl solutions at concentrations up to 150mM. While PHENSS is more active in vitro than cisplatin against the human breast cancer cell line, MCF-7, delivery of PHENSS using the sCX[4]-dendrimer nanocomplexes, regardless of dendrimer generation, had little effect on PHENSS cytotoxicity. The results of this study may have application in the delivery of a variety of small molecule metal-based drugs for which chemical conjugation to a nanoparticle is undesired or not feasible.

Panth, N, Manandhar, B & Paudel, KR 2017, 'Anticancer Activity ofPunica granatum(Pomegranate): A Review', Phytotherapy Research, vol. 31, no. 4, pp. 568-578.
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Copyright © 2017 John Wiley & Sons, Ltd. Cancer is a pathological condition where excessive and abnormal cell growth leads to widespread invasion within the body to affect various organ functions. It is known that chemotherapeutic agents are themselves possible candidate of cancer generation as they can kill normal cells. So, therapeutic approach for cancer treatment and prevention is weighed in terms of benefit to risk ratio. Nowadays, there is an immense interest for the search herbal formulation with cancer preventive effect because of the problems, generated with existing chemotherapeutic regimens. Research interest in fruits rich in polyphenols is increasing because of their anticancer potential. In this review, we highlight the potential health benefits of pomegranate (Punica granatum) fruit and the underlying mechanism of its inhibition of cancer progression. Pomegranate has demonstrated anti-proliferative, anti-metastatic and anti-invasive effects on various cancer cell line in vitro as well as in vivo animal model or human clinical trial. Although several clinical trials are in progress for identifying the pomegranate as a candidate for various cancer treatment. It is necessary to replicate and validate its therapeutic efficacy by multiple clinical studies in order to formulate pomegranate products as an integral part of the dietary and pharmacological intervention in anticancer therapy. Copyright © 2017 John Wiley & Sons, Ltd.

Parker, LM, O'Connor, WA, Byrne, M, Coleman, RA, Virtue, P, Dove, M, Gibbs, M, Spohr, L, Scanes, E & Ross, PM 2017, 'Adult exposure to ocean acidification is maladaptive for larvae of the Sydney rock oyster Saccostrea glomerata in the presence of multiple stressors', Biology Letters, vol. 13, no. 2, pp. 20160798-20160798.
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Parental effects passed from adults to their offspring have been identified as a source of rapid acclimation that may allow marine populations to persist as our surface oceans continue to decrease in pH. Little is known, however, whether parental effects are beneficial for offspring in the presence of multiple stressors. We exposed adults of the oyster Saccostrea glomerata to elevated CO 2 and examined the impacts of elevated CO 2 (control = 392; 856 µatm) combined with elevated temperature (control = 24; 28°C), reduced salinity (control = 35; 25) and reduced food concentration (control = full; half diet) on their larvae. Adult exposure to elevated CO 2 had a positive impact on larvae reared at elevated CO 2 as a sole stressor, which were 8% larger and developed faster at elevated CO 2 compared with larvae from adults exposed to ambient CO 2 . These larvae, however, had significantly reduced survival in all multistressor treatments. This was particularly evident for larvae reared at elevated CO 2 combined with elevated temperature or reduced food concentration, with no larvae surviving in some treatment combinations. Larvae from CO 2 -exposed adults had a higher standard metabolic rate. Our results provide evidence that parental exposure to ocean acidification may be maladaptive when larvae experience multiple stressors.

Parker, LM, Scanes, E, O'Connor, WA, Coleman, RA, Byrne, M, Pörtner, H-O & Ross, PM 2017, 'Ocean acidification narrows the acute thermal and salinity tolerance of the Sydney rock oyster Saccostrea glomerata', Marine Pollution Bulletin, vol. 122, no. 1-2, pp. 263-271.
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Coastal and estuarine environments are characterised by acute changes in temperature and salinity. Organisms living within these environments are adapted to withstand such changes, yet near-future ocean acidification (OA) may challenge their physiological capacity to respond. We tested the impact of CO2-induced OA on the acute thermal and salinity tolerance, energy metabolism and acid-base regulation capacity of the oyster Saccostrea glomerata. Adult S. glomerata were acclimated to three CO2 levels (ambient 380μatm, moderate 856μatm, high 1500μatm) for 5weeks (24°C, salinity 34.6) before being exposed to a series of acute temperature (15-33°C) and salinity (34.2-20) treatments. Oysters acclimated to elevated CO2 showed a significant metabolic depression and extracellular acidosis with acute exposure to elevated temperature and reduced salinity, especially at the highest CO2 of 1500μatm. Our results suggest that the acute thermal and salinity tolerance of S. glomerata and thus its distribution will reduce as OA continues to worsen.

Pascali, G, Matesic, L, Zhang, B, King, AT, Robinson, AJ, Ung, AT & Fraser, BH 2017, 'Sulfur - fluorine bond in PET radiochemistry', EJNMMI Radiopharmacy and Chemistry, vol. 2, no. 1, pp. 2-18.
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The importance of the sulfur-fluorine bond is starting to increase in modern medicinal chemistry literature. This is due to a better understanding of the stability and reactivity of this moiety depending on the various oxidation states of sulfur. Furthermore, several commercial reagents used for mild and selective fluorination of organic molecules are based on the known reactivity of S-F groups. In this review, we will show how these examples are translating into the 18F field, both for use as stable tags in finished radiopharmaceuticals and as mildly reactive fluoride-relay intermediates. Finally, we also discuss current opportunities where examples of non-radioactive S-F applications/chemistry may be translated into future 18F radiochemistry applications.

Pasin, D, Cawley, A, Bidny, S & Fu, S 2017, 'Characterization of hallucinogenic phenethylamines using high‐resolution mass spectrometry for non‐targeted screening purposes', Drug Testing and Analysis, vol. 9, no. 10, pp. 1620-1629.
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Hallucinogenic phenethylamines such as 2,5‐dimethoxyphenethylamines (2C–X) and their N‐(2‐methoxybenzyl) derivatives (25X–NBOMe) have seen an increase in novel analogues in recent years. These rapidly changing analogues make it difficult for laboratories to rely on traditional targeted screening methods to detect unknown new psychoactive substances (NPS). In this study, twelve 2C–X, six 2,5‐dimethoxyamphetamines (DOX), and fourteen 25X–NBOMe derivatives, including two deuterated derivatives (2C–B‐d6 and 25I–NBOMe‐d9), were analyzed using ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry (UPLC‐QTOF‐MS). Collision‐induced dissociation (CID) experiments were performed using collision energies set at 10, 20, and 40 eV. For 2C–X and DOX derivatives, common losses were observed including neutral and radical losses such as NH3 (17.0265 Da), •CH6N (32.0500 Da), C2H7N (45.0578 Da) and C2H9N (47.0735 Da). 2C–X derivatives displayed common product ions at m/z 164.0837 ([C10H12O2]+•), 149.0603 ([C9H9O2]+), and 134.0732 ([C9H10O]+•) while DOX derivatives had common product ions at m/z 178.0994 ([C11H14O2]+•), 163.0754 ([C10H11O2]+), 147.0804 ([C10H11O]+), and 13...

Pasin, D, Cawley, A, Bidny, S & Fu, S 2017, 'Current applications of high-resolution mass spectrometry for the analysis of new psychoactive substances: a critical review', Analytical and Bioanalytical Chemistry, vol. 409, no. 25, pp. 5821-5836.
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© 2017, Springer-Verlag Berlin Heidelberg. The proliferation of new psychoactive substances (NPS) in recent years has resulted in the development of numerous analytical methods for the detection and identification of known and unknown NPS derivatives. High-resolution mass spectrometry (HRMS) has been identified as the method of choice for broad screening of NPS in a wide range of analytical contexts because of its ability to measure accurate masses using data-independent acquisition (DIA) techniques. Additionally, it has shown promise for non-targeted screening strategies that have been developed in order to detect and identify novel analogues without the need for certified reference materials (CRMs) or comprehensive mass spectral libraries. This paper reviews the applications of HRMS for the analysis of NPS in forensic drug chemistry and analytical toxicology. It provides an overview of the sample preparation procedures in addition to data acquisition, instrumental analysis, and data processing techniques. Furthermore, it gives an overview of the current state of non-targeted screening strategies with discussion on future directions and perspectives of this technique. [Figure not available: see fulltext.].

Patel, BS, Kugel, MJ, Baehring, G & Ammit, AJ 2017, 'Doxofylline does not increase formoterol-induced cAMP nor MKP-1 expression in ASM cells resulting in lack of anti-inflammatory effect', Pulmonary Pharmacology & Therapeutics, vol. 45, pp. 34-39.
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© 2017 The xanthine doxofylline has been examined in clinical trials and shown to have efficacy and greater tolerability than theophylline in asthma and chronic obstructive pulmonary disease. The ‘novofylline’ doxofylline has demonstrated bronchodilatory and anti-inflammatory actions in in vivo and ex vivo experimental models of respiratory disease. However, there are limited studies in vitro. We address this herein and examine whether doxofylline has anti-inflammatory impact on primary cultures of airway smooth muscle (ASM) cells. We conduct a series of investigations comparing and contrasting doxofylline with the archetypal xanthine, theophylline, and the specific phosphodiesterase (PDE) 4 inhibitor, cilomilast. We confirm that the xanthine drugs do not have action as PDE inhibitors in ASM cells. Unlike cilomilast, doxofylline (and theophylline) do not increase cAMP production in ASM cells induced by long-acting β2-agonist formoterol. Similar to theophylline, and consistent with the lack of cAMP potentiation, doxofylline does not augment formoterol-induced upregulation of the anti-inflammatory protein mitogen-activated protein kinase phosphatase 1 (MKP-1). However, when we examine the effect of doxofylline on secretion of the interleukin 8 from ASM cells stimulated by tumour necrosis factor (an in vitro surrogate measure of inflammation), there was no repression of inflammation. This is in contrast to the anti-inflammatory impact exerted by theophylline and cilomilast in confirmatory experiments. In summary, our study is the first to examine the effect of doxofylline on ASM cells in vitro and highlights some distinct differences between two key members of xanthine drug family, doxofylline and theophylline.

Patel, BS, Rahman, MM, Baehring, G, Xenaki, D, Tang, FS-M, Oliver, BG & Ammit, AJ 2017, 'Roflumilast N-Oxide in Combination with Formoterol Enhances the Antiinflammatory Effect of Dexamethasone in Airway Smooth Muscle Cells', American Journal of Respiratory Cell and Molecular Biology, vol. 56, no. 4, pp. 532-538.
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Roflumilast is an orally active phosphodiesterase 4 inhibitor approved for use in chronic obstructive pulmonary disease. RoflumilastN-oxide (RNO) is the active metabolite of roflumilast and has a demonstrated antiinflammatory impact in vivo and in vitro. To date, the effect of RNO on the synthetic function of airway smooth muscle (ASM) cells is unknown. We address this herein and investigate the effect of RNO on β2-adrenoceptor-mediated, cAMPdependent responses in ASM cells in vitro, and whether RNO enhances steroid-induced repression of inflammation. RNO (0.001-1,000 nM) alone had no effect onAMPproduction fromASM cells, and significant potentiation of the long-acting β2-agonist formoterol-induced cAMP could only be achieved at the highest concentration ofRNOtested (1,000 nM). At this concentration,RNO exerted a small, but not significantly different, potentiation of formoterol-induced expression of antiinflammatory mitogenactivated protein kinase phosphatase 1. Consequently, tumor necrosis factor-induced IL-8 secretion was unaffected by RNO in combination with formoterol. However, because there was the potential for phosphodiesterase 4 inhibitors and long-acting β2-agonists to interact with corticosteroids to achieve superior antiinflammatory efficacy, we examined whether RNO, alone or in combination with formoterol, enhanced the antiinflammatory effect of dexamethasone by measuring the impact on IL-8 secretion. Although RNO alone did not significantly enhance the cytokine repression achieved with steroids, RNO in combination with formoterol significantly enhanced the antiinflammatory effect of dexamethasone in ASM cells. This was linked to increased mitogen-activated protein kinase phosphatase 1 expression in ASM cells, suggesting that a molecular mechanism is responsible for augmented antiinflammatory actions of combination therapeutic approaches that include RNO.

Paul, B, Kim, HS, Kerr, MC, Huston, WM, Teasdale, RD & Collins, BM 2017, 'Structural basis for the hijacking of endosomal sorting nexin proteins by Chlamydia trachomatis', eLife, vol. 6, pp. 1-23.
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During infection chlamydial pathogens form an intracellular membrane-bound replicative niche termed the inclusion, which is enriched with bacterial transmembrane proteins called Incs. Incs bind and manipulate host cell proteins to promote inclusion expansion and provide camouflage against innate immune responses. Sorting nexin (SNX) proteins that normally function in endosomal membrane trafficking are a major class of inclusion-associated host proteins, and are recruited by IncE/CT116. Crystal structures of the SNX5 phox-homology (PX) domain in complex with IncE define the precise molecular basis for these interactions. The binding site is unique to SNX5 and related family members SNX6 and SNX32. Intriguingly the site is also conserved in SNX5 homologues throughout evolution, suggesting that IncE captures SNX5-related proteins by mimicking a native host protein interaction. These findings thus provide the first mechanistic insights both into how chlamydial Incs hijack host proteins, and how SNX5-related PX domains function as scaffolds in protein complex assembly.

Pauszek, SJ, Bertram, MR, Vu, LT, Hartwig, EJ, Smoliga, GR, Brito, B, Stenfeldt, C, VanderWaal, K, Fish, IH, Hung, VV, Phuong, NT, Hoang, BH, Rodriguez, LL, Dung, DH & Arzt, J 2017, 'Genome Sequences of Seven Foot-and-Mouth Disease Virus Isolates Collected from Serial Samples from One Persistently Infected Carrier Cow in Vietnam', Genome Announcements, vol. 5, no. 34, pp. 1-3.
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ABSTRACT Several foot-and-mouth disease virus (FMDV) carrier cattle were identified in Vietnam by the recovery of infectious virus from oropharyngeal fluid. This report contains the first near-complete genome sequences of seven viruses from sequential samples from one carrier animal collected over the course of 1 year. The characterization of within-host viral evolution has implications for FMDV control strategies.

Pellegrino, G, Taraschi, V, Vercellotti, T, Ben-Nissan, B & Marchetti, C 2017, 'Three-Dimensional Implant Positioning with a Piezosurgery Implant Site Preparation Technique and an Intraoral Surgical Navigation System: Case Report', The International Journal of Oral & Maxillofacial Implants, vol. 32, no. 3, pp. e163-e165.
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© 2017 by Quintessence Publishing Co Inc. This case report describes new implant site preparation techniques joining the benefits of using an intraoral navigation system to optimize three-dimensional implant site positioning in combination with an ultrasonic osteotomy. A report of five patients is presented, and the implant positions as planned in the navigation software with the postoperative scan image were compared. The preliminary results are useful, although further clinical studies with larger populations are needed to confirm these findings.

Peng, D, Zhang, B, Wu, C, Huete, AR, Gonsamo, A, Lei, L, Ponce-Campos, GE, Liu, X & Wu, Y 2017, 'Country-level net primary production distribution and response to drought and land cover change', Science of The Total Environment, vol. 574, pp. 65-77.
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© 2016 Elsevier B.V. Carbon sequestration by terrestrial ecosystems can offset emissions and thereby offers an alternative way of achieving the target of reducing the concentration of CO2 in the atmosphere. Net primary production (NPP) is the first step in the sequestration of carbon by terrestrial ecosystems. This study quantifies moderate-resolution imaging spectroradiometer (MODIS) NPP from 2000 to 2014 at the country level along with its response to drought and land cover change. Our results indicate that the combined NPP for 53 countries represents > 90% of global NPP. From 2000 to 2014, 29 of these 53 countries had increasing NPP trends, most notably the Central African Republic (23 g C/m2/y). The top three and top 12 countries accounted for 30% and 60% of total global NPP, respectively, whereas the mean national NPP per unit area in the countries with the 12 lowest values was only around ~ 300 g C/m2/y - the exception to this was Brazil, which had an NPP of 850 g C/m2/y. Large areas of Russia, Argentina, Peru and several countries in southeast Asia showed a marked decrease in NPP (~ 15 g C/m2/y). About 37% of the NPP decrease was caused by drought while ~ 55% of NPP variability was attributed to changes in water availability. Land cover change explained about 20% of the NPP variability. Our findings support the idea that government policies should aim primarily to improve water management in drought-afflicted countries; land use/land cover change policy could also be used as an alternative method of increasing NPP.

Peng, D, Zhang, X, Wu, C, Huang, W, Gonsamo, A, Huete, AR, Didan, K, Tan, B, Liu, X & Zhang, B 2017, 'Intercomparison and evaluation of spring phenology products using National Phenology Network and AmeriFlux observations in the contiguous United States', Agricultural and Forest Meteorology, vol. 242, pp. 33-46.
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© 2017 Elsevier B.V. Many remote sensing based spring phenology products have been developed to monitor and study vegetation phenology at regional and global scales. It is important to understand how these products perform relative to each other and to ground observations. In this study, we extracted spring green-up onset dates (GUD) over the contiguous United States (CONUS) from six major land surface phenology (LSP) products: (1) Moderate Resolution Imaging Spectroradiometer (MODIS) Land Cover Dynamics Phenology (MCD12Q2); (2) Vegetation Index and Phenology Multi-sensor Phenology (VIPPHENEVI2); (3) Global Long-Term Climate Modeling Grid Land Surface Phenology (CMGLSP); (4 and 5) North American Carbon Program (NACP) Phenology (MOD09Q1PEVI and MOD15PHN); and (6) USGS/EROS advanced very high resolution radiometer (AVHRR) phenology (AVHRRP). We characterized and compared the GUD data in these LSP products, and evaluated their accuracy using ground-based phenology observations [i.e., human observations of first leaf and sensor readings of gross primary productivity (GPP)] from the USA National Phenology Network (USA-NPN) and AmeriFlux. The results revealed the consistencies and discrepancies of GUD estimates among LSP products. Intercomparison of the six products indicated that the root mean square error (RMSE) of these products range from 17.8 days to 31.5 days, whereas AVHRRP GUD has the lowest correlation and largest RMSE (∼30 days) relative to other products. When compared to ground observations, GUD estimates in six LSP products generally have RMSE values of ∼20 days and significant correlations (p < 0.001). For the products (MCD12Q2, AVHRRP, MOD09Q1PEVI, and MOD15PHN) available for comparisons in the short-term period (from 2001–2007), AVHRRP GUD presented relatively weaker correlations and a lower index of agreement (IOA), however, MCD12Q2 GUD showed overall slightly better consistencies with ground observations. In the two long-term products (CMGLS...

Peng, D, Zhang, X, Zhang, B, Liu, L, Liu, X, Huete, AR, Huang, W, Wang, S, Luo, S, Zhang, X & Zhang, H 2017, 'Scaling effects on spring phenology detections from MODIS data at multiple spatial resolutions over the contiguous United States', ISPRS Journal of Photogrammetry and Remote Sensing, vol. 132, pp. 185-198.
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© 2017 Land surface phenology (LSP) has been widely retrieved from satellite data at multiple spatial resolutions, but the spatial scaling effects on LSP detection are poorly understood. In this study, we collected enhanced vegetation index (EVI, 250 m) from collection 6 MOD13Q1 product over the contiguous United States (CONUS) in 2007 and 2008, and generated a set of multiple spatial resolution EVI data by resampling 250 m to 2 × 250 m and 3 × 250 m, 4 × 250 m, …, 35 × 250 m. These EVI time series were then used to detect the start of spring season (SOS) at various spatial resolutions. Further the SOS variation across scales was examined at each coarse resolution grid (35 × 250 m ≈ 8 km, refer to as reference grid) and ecoregion. Finally, the SOS scaling effects were associated with landscape fragment, proportion of primary land cover type, and spatial variability of seasonal greenness variation within each reference grid. The results revealed the influences of satellite spatial resolutions on SOS retrievals and the related impact factors. Specifically, SOS significantly varied lineally or logarithmically across scales although the relationship could be either positive or negative. The overall SOS values averaged from spatial resolutions between 250 m and 35 × 250 m at large ecosystem regions were generally similar with a difference less than 5 days, while the SOS values within the reference grid could differ greatly in some local areas. Moreover, the standard deviation of SOS across scales in the reference grid was less than 5 days in more than 70% of area over the CONUS, which was smaller in northeastern than in southern and western regions. The SOS scaling effect was significantly associated with heterogeneity of vegetation properties characterized using land landscape fragment, proportion of primary land cover type, and spatial variability of seasonal greenness variation, but the latter was the most important impact factor.

Petrou, K, Ralph, PJ & Nielsen, DA 2017, 'A novel mechanism for host-mediated photoprotection in endosymbiotic foraminifera', The ISME Journal, vol. 11, no. 2, pp. 453-462.
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Abstract Light underpins the health and function of coral reef ecosystems, where symbiotic partnerships with photosynthetic algae constitute the life support system of the reef. Decades of research have given us detailed knowledge of the photoprotective capacity of phototrophic organisms, yet little is known about the role of the host in providing photoprotection in symbiotic systems. Here we show that the intracellular symbionts within the large photosymbiotic foraminifera Marginopora vertebralis exhibit phototactic behaviour, and that the phototactic movement of the symbionts is accomplished by the host, through rapid actin-mediated relocation of the symbionts deeper into the cavities within the calcium carbonate test. Using a photosynthetic inhibitor, we identified that the infochemical signalling for host regulation is photosynthetically derived, highlighting the presence of an intimate communication between the symbiont and the host. Our results emphasise the central importance of the host in photosymbiotic photoprotection via a new mechanism in foraminifera that can serve as a platform for exploring host–symbiont communication in other photosymbiotic organisms.

Pettit, T, Irga, PJ, Abdo, P & Torpy, FR 2017, 'Do the plants in functional green walls contribute to their ability to filter particulate matter?', Building and Environment, vol. 125, pp. 299-307.
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© 2017 Elsevier Ltd Indoor air quality has become a growing concern as people are spending more time indoors, combined with the construction of highly sealed buildings that promote thermal efficiency. Particulate matter (PM) is a common indoor air pollutant, with exposure to high concentrations associated with several detrimental health outcomes. Active botanical biofilters or functional green walls are becoming increasingly efficient and have the potential to mitigate high suspended PM concentrations. These systems, however, require further development before they become competitive with industry standard in-room air filters. Whilst the plant growth substrate in active biofilters can act as a filter medium, it was previously not known whether the plant component of these systems played a function in PM filtration. This study thus examines the influence of the botanical component on active green wall PM single pass removal efficiency (SPRE), with a focus on evaluating the air filtration features of different plant species in green wall modules. All tested botanical biofilters outperformed biofilters that consisted only of substrate. Green walls using different plant species had different single pass removal efficiencies, with fern species recording the highest removal efficiencies across all measured particle sizes (Nephrolepis exaltata bostoniensis SPRE for PM0.3-0.5 and PM5-10 = 45.78% and 92.46% respectively). Higher removal efficiencies were associated with increased pressure drop across the biofilter. An assessment of plant morphological data suggested that the root structure of the plants strongly influenced removal efficiency. These findings demonstrate the potential to enhance active botanical biofiltration technology with appropriate plant species selection.

Pfeiffer, RM, Redd, A & Carroll, RJ 2017, 'On the impact of model selection on predictor identification and parameter inference', Computational Statistics, vol. 32, no. 2, pp. 667-690.
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© 2016, The Author(s). We assessed the ability of several penalized regression methods for linear and logistic models to identify outcome-associated predictors and the impact of predictor selection on parameter inference for practical sample sizes. We studied effect estimates obtained directly from penalized methods (Algorithm 1), or by refitting selected predictors with standard regression (Algorithm 2). For linear models, penalized linear regression, elastic net, smoothly clipped absolute deviation (SCAD), least angle regression and LASSO had a low false negative (FN) predictor selection rates but false positive (FP) rates above 20 % for all sample and effect sizes. Partial least squares regression had few FPs but many FNs. Only relaxo had low FP and FN rates. For logistic models, LASSO and penalized logistic regression had many FPs and few FNs for all sample and effect sizes. SCAD and adaptive logistic regression had low or moderate FP rates but many FNs. 95 % confidence interval coverage of predictors with null effects was approximately 100 % for Algorithm 1 for all methods, and 95 % for Algorithm 2 for large sample and effect sizes. Coverage was low only for penalized partial least squares (linear regression). For outcome-associated predictors, coverage was close to 95 % for Algorithm 2 for large sample and effect sizes for all methods except penalized partial least squares and penalized logistic regression. Coverage was sub-nominal for Algorithm 1. In conclusion, many methods performed comparably, and while Algorithm 2 is preferred to Algorithm 1 for estimation, it yields valid inference only for large effect and sample sizes.

Pham, HM, Nguyen, SC, Ho-Le, TP, Center, JR, Eisman, JA & Nguyen, TV 2017, 'Association of Muscle Weakness With Post-Fracture Mortality in Older Men and Women: A 25-Year Prospective Study', Journal of Bone and Mineral Research, vol. 32, no. 4, pp. 698-707.
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ABSTRACT   Osteoporotic fracture increases the risk of premature mortality. Muscle weakness is associated with both increased fracture risk and low bone mineral density (BMD). However, the role of muscle strength in post-fracture mortality is not well understood. This study examines the change of muscle strength measured at quadriceps (QS) before and after fracture and defines the relationship between muscle strength and post-fracture mortality. The study involved 889 women and 295 men (who were participating in the Dubbo Osteoporosis Study) who had at least one low-trauma fracture (ascertained from X-ray reports) after the age of 50 years. Median follow-up time was 11 years (range 1 to 24). To determine the change in muscle strength before and after a fracture, we selected a subset of 344 women and 99 men who had had at least two muscle strength measurements before the fracture event and a subset of 407 women and 105 men who had had at least two measurements after the fracture. During the follow-up period, 366 (41.2%) women and 150 (50.9%) men died. The annual rate of decrease in height-adjusted muscle strength before fracture was 0.27 kg/m (1.85%) in women and 0.40 kg/m (1.79%) in men. Strength loss after fracture was not significantly different from that before fracture. In women, after adjusting for baseline age and BMD, each SD (5 kg/m) lower height-adjusted pre- and post-fracture quadriceps strength was associated with a 27% (hazard ratio [HR] = 1.27; 95% confidence interval [CI] 1.07, 1.50) and 18% (HR = 1.18; 95% CI 1.01, 1.38) increase in post-fracture mortality risk, respectively. Similarly, in men, each SD (5 kg/m) lower height-adjusted pre- and post-fracture QS was associated with increased mortality before fracture (HR = 1.33; 95% CI 1.09, 1.63) and after fracture (HR = 1.43; 95% CI 1.16, 1.78). Muscle weakness accounted f...

Pinkerton, JW, Kim, RY, Robertson, AAB, Hirota, JA, Wood, LG, Knight, DA, Cooper, MA, O’Neill, LAJ, Horvat, JC & Hansbro, PM 2017, 'Inflammasomes in the lung', Molecular Immunology, vol. 86, pp. 44-55.
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© 2017 Elsevier Ltd Innate immune responses act as first line defences upon exposure to potentially noxious stimuli. The innate immune system has evolved numerous intracellular and extracellular receptors that undertake surveillance for potentially damaging particulates. Inflammasomes are intracellular innate immune multiprotein complexes that form and are activated following interaction with these stimuli. Inflammasome activation leads to the cleavage of pro-IL-1β and release of the pro-inflammatory cytokine, IL-1β, which initiates acute phase pro-inflammatory responses, and other responses are also involved (IL-18, pyroptosis). However, excessive activation of inflammasomes can result in chronic inflammation, which has been implicated in a range of chronic inflammatory diseases. The airways are constantly exposed to a wide variety of stimuli. Inflammasome activation and downstream responses clears these stimuli. However, excessive activation may drive the pathogenesis of chronic respiratory diseases such as severe asthma and chronic obstructive pulmonary disease. Thus, there is currently intense interest in the role of inflammasomes in chronic inflammatory lung diseases and in their potential for therapeutic targeting. Here we review the known associations between inflammasome-mediated responses and the development and exacerbation of chronic lung diseases.

Pires Da Silva, IED, Wang, KYX, Wilmott, JS, Holst, J, Park, JJ, Quek, C, Wongchenko, M, Yan, Y, Mann, GJ, Carlino, MS, Kefford, R, Scolyer, RA, Yang, J, Long, GV, Rizos, H & Menzies, AM 2017, 'Distinct gene expression, mutational profile and clinical outcomes of V600E and V600K/R BRAF-mutant metastatic melanoma (MM).', Journal of Clinical Oncology, vol. 35, no. 15_suppl, pp. 9541-9541.
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9541 Background: BRAF V600E and V600K/R mm have distinct clinicopathologic features suggesting different etiology. V600K/R mm appears less responsive to MAPK inhibitors (MAPKi) compared to V600E MM. We investigated potential mechanisms for this by comparing the gene expression and mutation profiles of these two melanoma subgroups. Methods: BRAF V600 mutant mm patients (pts) treated with MAPKi (BRAFi +/- MEKi) between July/2009 and July/2013 were selected. Demographics, clinicopathologic features and clinical outcomes were examined. Pre-treatment FFPE tumors underwent RNA expression profiling (795-gene nanostring panel) and DNA sequencing (239 gene NGS panel). Molecular results were validated using an independent cohort from the The Cancer Genome Atlas (TCGA). Results: 95 mm pts were included (78 V600E, 17 V600K/R), with median (med) follow-up of 18.4 months (mo). 74 (78%) had BRAFi, 21 (22%) had BRAF/MEKi. At MAPKi start, there were no differences between subgroups regarding age, gender, ECOG, AJCC stage or LDH level. V600K/R pts had a trend to less tumour regression by RECIST (med 30% vs 51%, p = 0.08) and shorter PFS (med 5.1 vs 7.1mo, p = 0.08) than V600E, with no difference in OS (20.8mo vs 17.9mo, p = 0.64). V600K/R had lower expression of the MAPK-pathway feedback regulator DUSP6 and glycosyltransferase GCNT1, compared to V600E (p < 0.05). Analysis of TCGA data (122 V600E, 21 V600K/R) confirmed these findings. There was a trend toward higher mutational load in V600K/R than V600E, confirmed with TCGA data (p < 0.05). V600K/R had a higher proportion of mutations in PIK3CA and several tumour suppressor genes (FBXW7, NF2, RB1 and SMAD4), with only FBXW7 confirmed using TCGA data. Conclusions: V600K/R mm has inferior response and shorter survival with MAPKi than V600E, potentially due to less reliance on MAPK pathway activation (lower DUSP6 expression) and greater use of alternative drivers of oncogenesis (higher mutati...

Pirotta, V, Smith, A, Ostrowski, M, Russell, D, Jonsen, ID, Grech, A & Harcourt, R 2017, 'An Economical Custom-Built Drone for Assessing Whale Health', Frontiers in Marine Science, vol. 4, no. DEC, pp. 1-12.
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Drones or Unmanned Aerial Vehicles (UAVs) have huge potential to improve the safety and efficiency of sample collection from wild animals under logistically challenging circumstances. Here we present a method for surveying population health that uses UAVs to sample respiratory vapor, 'whale blow,' exhaled by free-swimming humpback whales (Megaptera novaeangliae), and coupled this with amplification and sequencing of respiratory tract microbiota. We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated 'blow' to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and drone-captured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa. Whale-specific taxa included species and genera previously associated with the respiratory tracts or oral cavities of mammals (e.g., Pseudomonas, Clostridia, Cardiobacterium), as well as species previously isolated from dolphin or killer whale blowholes (Corynebacteria, others). Many examples of exogenous marine species were identified, including Tenacibaculum and Psychrobacter spp. that have been associated with the skin microbiota of marine mammals and fish and may include pathogens. This information provides a baseline of respiratory tract microbiota profiles of contemporary whale health. Customized UAVs are a promising new tool for marine megafauna research and may have broad application in cost-ef...

Poh, WH, Barraud, N, Guglielmo, S, Lazzarato, L, Rolando, B, Fruttero, R & Rice, SA 2017, 'Furoxan Nitric Oxide Donors Disperse Pseudomonas aeruginosa Biofilms, Accelerate Growth, and Repress Pyoverdine Production', ACS Chemical Biology, vol. 12, no. 8, pp. 2097-2106.
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The use of nitric oxide (NO) as a signal for biofilm dispersal has been shown to increase the susceptibility of many biofilms to antibiotics, promoting their eradication. The delivery of NO to biofilms can be achieved by using NO donors with different kinetics and properties of NO release that can influence their efficacy as biofilm control agents. In this study, the kinetics of three furoxan derivatives were evaluated. The effects of these NO donors, which have an advantageous pharmacological profile of slower onset with an extended duration of action, on Pseudomonas aeruginosa growth, biofilm development, and dispersal were also characterized. Compound LL4254, which showed a fast rate of NO release, induced biofilm dispersal at approximately 200 μM. While LL4212 and LL4216 have a slower rate of NO release, both compounds could induce biofilm dispersal, under the same treatment conditions, when used at higher concentrations. In addition, LL4212 and LL4216 were found to promote P. aeruginosa growth in iron-limited minimal medium, leading to a faster rate of biofilm formation and glucose utilization, and ultimately resulted in early dispersal of biofilm cells through carbon starvation. High concentrations of LL4216 also repressed production of the siderophore pyoverdine by more than 50-fold, via both NOx-dependent and NOx-independent mechanisms. The effects on growth and pyoverdine levels exerted by the furoxans appeared to be mediated by NO-independent mechanisms, suggesting functional activities of furoxans in addition to their release of NO and nitrite. Overall, this study reveals that secondary effects of furoxans are important considerations for their use as NO-releasing dispersal agents and that these compounds could be potentially redesigned as pyoverdine inhibitors.

Pokharel, D, Roseblade, A, Oenarto, V, Lu, JF & Bebawy, M 2017, 'Proteins regulating the intercellular transfer and function of P-glycoprotein in multidrug-resistant cancer', ecancermedicalscience, vol. 11.
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© the authors; Chemotherapy is an essential part of anticancer treatment. However, the overexpression of P-glycoprotein (P-gp) and the subsequent emergence of multidrug resistance (MDR) hampers successful treatment clinically. P-gp is a multidrug efflux transporter that functions to protect cells from xenobiotics by exporting them out from the plasma membrane to the extracellular space. P-gp inhibitors have been developed in an attempt to overcome P-gp-mediated MDR; however, lack of specificity and dose limiting toxicity have limited their effectiveness clinically. Recent studies report on accessory proteins that either directly or indirectly regulate P-gp expression and function and which are necessary for the establishment of the functional phenotype in cancer cells. This review discusses the role of these proteins, some of which have been recently proposed to comprise an interactive complex, and discusses their contribution towards MDR. We also discuss the role of other pathways and proteins in regulating P-gp expression in cells. The potential for these proteins as novel therapeutic targets provides new opportunities to circumvent MDR clinically.

Portbury, SD, Hare, DJ, Finkelstein, DI & Adlard, PA 2017, 'Trehalose improves traumatic brain injury-induced cognitive impairment', PLOS ONE, vol. 12, no. 8, pp. e0183683-e0183683.
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© 2017 Portbury 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. Traumatic brain Injury (TBI) is a significant cause of death and long-term disability for which there are currently no effective pharmacological treatment options. In this study then, we utilized a mouse model of TBI to assess the therapeutic potential of the stable disaccharide trehalose, which is known to protect against oxidative stress, increase levels of chaperone molecules and enhance autophagy. Furthermore, trehalose has demonstrated neuroprotective properties in numerous animal models and has been proposed as a potential treatment for neurodegeneration. As TBI (and associated neurodegenerative disorders) is complicated by a sudden and dramatic change in brain metal concentrations, including iron (Fe) and zinc (Zn), the collective accumulation and translocation of which has been hypothesized to contribute to the pathogenesis of TBI, then we also sought to determine whether trehalose modulated the metal dyshomeostasis associated with TBI. In this study three-month-old C57Bl/6 wildtype mice received a controlled cortical impact TBI, and were subsequently treated for one month with trehalose. During this time animals were assessed on multiple behavioral tasks prior to tissue collection. Results showed an overall significant improvement in the Morris water maze, Y-maze and open field behavioral tests in trehalose-treated mice when compared to controls. These functional benefits occurred in the absence of any change in lesion volume or any significant modulation of biometals, as assessed by laser ablation inductively coupled plasma mass spectrometry. Western blot analysis, however, revealed an upregulation of synaptophysin, doublecortin and brain derived neurotrophic factor protein in trehalose tr...

Portbury, SD, Hare, DJ, Sgambelloni, C, Perronnes, K, Portbury, AJ, Finkelstein, DI & Adlard, PA 2017, 'Trehalose Improves Cognition in the Transgenic Tg2576 Mouse Model of Alzheimer’s Disease', Journal of Alzheimer's Disease, vol. 60, no. 2, pp. 549-560.
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This study assessed the therapeutic utility of the autophagy enhancing stable disaccharide trehalose in the Tg2576 transgenic mouse model of Alzheimer's disease (AD) via an oral gavage of a 2% trehalose solution for 31 days. Furthermore, as AD is a neurodegenerative condition in which the transition metals, iron, copper, and zinc, are understood to be intricately involved in the cellular cascades leading to the defining pathologies of the disease, we sought to determine any parallel impact of trehalose treatment on metal levels. Trehalose treatment significantly improved performance in the Morris water maze, consistent with enhanced learning and memory. The improvement was not associated with significant modulation of full length amyloid-β protein precursor or other amyloid-β fragments. Trehalose had no effect on autophagy as assessed by western blot of the LC3-1 to LC3-2 protein ratio, and no alteration in biometals that might account for the improved cognition was observed. Biochemical analysis revealed a significant increase in the hippocampus of both synaptophysin, a synaptic vesicle protein and surrogate marker of synapses, and doublecortin, a reliable marker of neurogenesis. The growth factor progranulin was also significantly increased in the hippocampus and cortex with trehalose treatment. This study suggests that trehalose might invoke a suite of neuroprotective mechanisms that can contribute to improved cognitive performance in AD that are independent of more classical trehalose-mediated pathways, such as Aβ reduction and activation of autophagy. Thus, trehalose may have utility as a potential AD therapeutic, with conceivable implications for the treatment of other neurodegenerative disorders.

Portbury, SD, Hare, DJ, Sgambelloni, CJ, Bishop, DP, Finkelstein, DI, Doble, PA & Adlard, PA 2017, 'Age modulates the injury-induced metallomic profile in the brain', Metallomics, vol. 9, no. 4, pp. 402-410.
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© 2017 The Royal Society of Chemistry. The biological transition metals iron (Fe), copper (Cu) and zinc (Zn) are thought to contribute to the neuronal pathologies that occur following traumatic brain injury (TBI), and indeed our previously published work in young (3 month-old) mice clearly demonstrates a significant spatiotemporal modulation of metals following TBI. Of note, however, is the literature observation that there is both an apparent detrimental effect of aging on TBI outcomes and an alteration in metals and their various transporters with normal advancing age. Therefore, to determine whether there was an interaction between aging, metals and TBI, we have utilised laser ablation-inductively coupled plasma-mass spectrometry to examine the spatial and temporal distribution of Fe, Zn and Cu following an acute controlled cortical impact brain injury in aged (24 months) rodents. The relative abundance of metals in corresponding regions within the ipsilateral and contralateral hemispheres as well as the hippocampus was assessed. Substantial region and time point specific alterations in Fe, Zn and Cu were identified immediately and up to 28 days post-TBI. The data from this follow-up study has also been compared to our previous data from young animals, and aged mice exhibit an appreciably enhanced and persistent elevation of all metals in every region surveyed, with individual metal disparities at various time points observed post-injury. This may potentially contribute to the acceleration in the onset of cognitive decline and neurological disease that has been observed in the aged population following head trauma.

Pouwels, SD, Faiz, A, den Boef, LE, Gras, R, van den Berge, M, Boezen, HM, Korstanje, R, ten Hacken, NHT, van Oosterhout, AJM, Heijink, IH & Nawijn, MC 2017, 'Genetic variance is associated with susceptibility for cigarette smoke-induced DAMP release in mice', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 313, no. 3, pp. L559-L580.
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Chronic obstructive pulmonary disease (COPD) is characterized by unresolved neutrophilic airway inflammation and is caused by chronic exposure to toxic gases, such as cigarette smoke (CS), in genetically susceptible individuals. Recent data indicate a role for damage-associated molecular patterns (DAMPs) in COPD. Here, we investigated the genetics of CS-induced DAMP release in 28 inbred mouse strains. Subsequently, in lung tissue from a subset of strains, the expression of the identified candidate genes was analyzed. We tested whether small interfering RNA-dependent knockdown of candidate genes altered the susceptibility of the human A549 cell line to CS-induced cell death and DAMP release. Furthermore, we tested whether these genes were differentially regulated by CS exposure in bronchial brushings obtained from individuals with a family history indicative of either the presence or absence of susceptibility for COPD. We observed that, of the four DAMPs tested, double-stranded DNA (dsDNA) showed the highest correlation with neutrophilic airway inflammation. Genetic analyses identified 11 candidate genes governing either CS-induced or basal dsDNA release in mice. Two candidate genes ( Elac2 and Ppt1) showed differential expression in lung tissue on CS exposure between susceptible and nonsusceptible mouse strains. Knockdown of ELAC2 and PPT1 in A549 cells altered susceptibility to CS extract-induced cell death and DAMP release. In bronchial brushings, CS-induced expression of ENOX1 and ARGHGEF11 was significantly different between individuals susceptible or nonsusceptible for COPD. Our study shows that genetic variance in a mouse model is associated with CS-induced DAMP release, and that this might contribute to susceptibility for COPD.

Prakash, YS, Halayko, AJ, Gosens, R, Panettieri, RA, Camoretti-Mercado, B & Penn, RB 2017, 'An Official American Thoracic Society Research Statement: Current Challenges Facing Research and Therapeutic Advances in Airway Remodeling', American Journal of Respiratory and Critical Care Medicine, vol. 195, no. 2, pp. e4-e19.
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BACKGROUND: Airway remodeling (AR) is a prominent feature of asthma and other obstructive lung diseases that is minimally affected by current treatments. The goals of this Official American Thoracic Society (ATS) Research Statement are to discuss the scientific, technological, economic, and regulatory issues that deter progress of AR research and development of therapeutics targeting AR and to propose approaches and solutions to these specific problems. This Statement is not intended to provide clinical practice recommendations on any disease in which AR is observed and/or plays a role. METHODS: An international multidisciplinary group from within academia, industry, and the National Institutes of Health, with expertise in multimodal approaches to the study of airway structure and function, pulmonary research and clinical practice in obstructive lung disease, and drug discovery platforms was invited to participate in one internet-based and one face-to-face meeting to address the above-stated goals. Although the majority of the analysis related to AR was in asthma, AR in other diseases was also discussed and considered in the recommendations. A literature search of PubMed was performed to support conclusions. The search was not a systematic review of the evidence. RESULTS: Multiple conceptual, logistical, economic, and regulatory deterrents were identified that limit the performance of AR research and impede accelerated, intensive development of AR-focused therapeutics. Complementary solutions that leverage expertise of academia and industry were proposed to address them. CONCLUSIONS: To date, numerous factors related to the intrinsic difficulty in performing AR research, and economic forces that are disincentives for the pursuit of AR treatments, have thwarted the ability to understand AR pathology and mechanisms and to address it clinically. This ATS Research Statement identifies potential solutions for each of these factors and emphasizes the importance of educ...

Pravadali-Cekic, S, Jones, A, Kazarian, AA, Paull, B, Soliven, A, Ritchie, H, Camenzuli, M, Leung, L, Dennis, GR & Shalliker, RA 2017, 'Postcolumn derivatization of amino acids using reaction flow chromatography columns with fluorescence detection: A fast new approach to selective derivatization techniques', Journal of Liquid Chromatography & Related Technologies, vol. 40, no. 2, pp. 83-92.
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Prior, J & Rai, T 2017, 'Engaging with residents' perceived risks and benefits about technologies as a way of resolving remediation dilemmas', Science of The Total Environment, vol. 601-602, pp. 1649-1669.
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© 2017 Elsevier B.V. In recent decades the diversity of remediation technologies has increased significantly, with the breadth of technologies ranging from dig and dump to emergent technologies like phytoremediation and nanoremediation. The benefits of these technologies to the environment and human health are believed to be substantial. However, they also potentially constitute risks. Whilst there is a growing body of knowledge about the risks and benefits of these technologies from the perspective of experts, little is known about how residents perceive the risks and benefits of the application of these technologies to address contaminants in their local environment. This absence of knowledge poses a challenge to remediation practitioners and policy makers who are increasingly seeking to engage these affected local residents in choosing technology applications. Building on broader research into the perceived benefits and risks of technologies, and data from a telephone survey of 2009 residents living near 13 contaminated sites in Australia, regression analysis of closed-ended survey questions and coding of open-ended questions are combined to identify the main predictors of resident's perceived levels of risk and benefit to resident's health and to their local environment from remediation technologies. This research identifies a range of factors associated with the residents’ physical context, their engagement with institutions during remediation processes, and the technologies which are associated with residents’ level of perceived risk and benefit for human health and the local environment. The analysis found that bioremediation technologies were perceived as less risky and more beneficial than chemical, thermal and physical technologies. The paper also supports broader technology research that reports an inverse correlation between levels of perceived risks and benefits. In addition, the paper reveals the types of risks and benefits to human health...

Prior, J, Hubbard, P & Rai, T 2017, 'Using residents' worries about technology as a way of resolving environmental remediation dilemmas', Science of The Total Environment, vol. 580, pp. 882-899.
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© 2016 Elsevier B.V. The choice of technologies used to remediate contaminated environments are increasingly made via engagement with affected local residents. Despite this, little is known about how residents perceive remediation technology applications. Building on the findings of broader technology worry research, and drawing on data from a telephone survey of 2009 residents living near thirteen contaminated sites in Australia, regression analysis of closed-ended survey questions and coding analysis of open-ended survey questions are combined to identify the main predictors of worries concerning particular remediation technologies, and how worry affects them. This suggests respondents are more worried about the application of chemical remediation technologies than the application of physical and thermal technologies, which in turn caused more worry than the application of biotechnology. The paper suggests that these worries can be reduced via direct engagement with residents about remediation technologies, suggesting that such engagement can provide knowledge that improves remediation technology decisions.

Promsawat, M, Promsawat, N, Jiansirisomboon, S, Namsar, O, Marlton, F, Daniels, J & Pojprapai, S 2017, 'Investigation of frequency effect on electrical fatigue and crack tip domain-switching behaviors in Pb(Mg1/3Nb2/3)0.65Ti0.35O3 ceramics via synchrotron X-ray diffraction', Journal of the European Ceramic Society, vol. 37, no. 15, pp. 4609-4616.
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Pu, Y, Du, Y, Khin, MM, Ravikumar, V, Rice, SA, Duan, H & Chan-Park, MB 2017, 'Using Diphenylphosphoryl Azide (DPPA) for the Facile Synthesis of Biodegradable Antiseptic Random Copolypeptides', Macromolecular Rapid Communications, vol. 38, no. 7, pp. 1600601-1600601.
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A facile method has been developed for the large-scale synthesis of random copolypeptides composed of multiple (i.e., cationic, hydrophobic, and hydrophilic) amino acids and their relative ratios have been optimized for broad-spectrum antibacterial effect. The copolypeptides obtained have measured compositions close to the design ratios in spite of the differing reactivities of the different amino acids. An optimized random copolypeptide of lysine, leucine, and serine (denoted as KLS-3) mimicking the composition of LL-37 host defense peptide gives broad spectrum antibacterial activity against clinically relevant Gram-negative and Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PAO1) with minimum inhibitory concentrations (MICs) of 32-64 μg mL-1 , as well as good MICs against multidrug resistant Gram-negative bacteria of Escherichia coli EC 958 (64 μg mL-1 ) and Klebseilla pneumoniae PTR3 (128 μg mL-1 ). This method can be applied to the facile large-scale copolymerization of multiple amino acids, including unnatural amino acids, to make effective antibacterial copolypeptides.

Pyne, SG, Jatisatienr, A, Mungkornasawakul, P, Ung, AT, Limtrakul, P, Sastraruji, T, Sastraruji, K, Chaiyong, S, Umsumarng, S, Baird, MC, Dau, XD & Ramli, RA 2017, 'Phytochemical, Synthetic and Biological Studies on Stemona and Stichoneuron Plants and Alkaloids: A Personal Perspective', Natural Product Communications, vol. 12, no. 8, pp. 1934578X1701200-1934578X1701200.
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This report is an overview of our research on phytochemical, synthetic and biological studies of the Stemona and Stichoneuron species of plants.

Quince, C, Delmont, TO, Raguideau, S, Alneberg, J, Darling, AE, Collins, G & Eren, AM 2017, 'DESMAN: a new tool for de novo extraction of strains from metagenomes', Genome Biology, vol. 18, no. 1.
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© 2017 The Author(s). We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

R. Cardoso, B, Hare, DJ, Lind, M, McLean, CA, Volitakis, I, Laws, SM, Masters, CL, Bush, AI & Roberts, BR 2017, 'The APOE ε4 Allele Is Associated with Lower Selenium Levels in the Brain: Implications for Alzheimer’s Disease', ACS Chemical Neuroscience, vol. 8, no. 7, pp. 1459-1464.
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© 2017 American Chemical Society. The antioxidant activity of selenium, which is mainly conferred by its incorporation into dedicated selenoproteins, has been suggested as a possible neuroprotective approach for mitigating neuronal loss in Alzheimer's disease. However, there is inconsistent information with respect to selenium levels in the Alzheimer's disease brain. We examined the concentration and cellular compartmentalization of selenium in the temporal cortex of Alzheimer's disease and control brain tissue. We found that Alzheimer's disease was associated with decreased selenium concentration in both soluble (i.e., cytosolic) and insoluble (i.e., plaques and tangles) fractions of brain homogenates. The presence of the APOE ϵ4 allele correlated with lower total selenium levels in the temporal cortex and a higher concentration of soluble selenium. Additionally, we found that age significantly contributed to lower selenium concentrations in the peripheral membrane-bound and vesicular fractions. Our findings suggest a relevant interaction between APOE ϵ4 and selenium delivery into brain, and show changes in cellular selenium distribution in the Alzheimer's disease brain.

Rabi, R, Turnbull, L, Whitchurch, CB, Awad, M & Lyras, D 2017, 'Structural Characterization of Clostridium sordellii Spores of Diverse Human, Animal, and Environmental Origin and Comparison to Clostridium difficile Spores', mSphere, vol. 2, no. 5, pp. 1-12.
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Clostridium sordellii is a significant pathogen with mortality rates approaching 100%. It is the bacterial spore that is critical in initiating infection and disease. An understanding of spore structures as well as spore morphology across a range of strains may lead to a better understanding of C. sordellii infection and disease. However, the structural characteristics of the C. sordellii spores are limited. In this work, we have addressed this lack of detail and characterized the C. sordellii spore morphology. The use of traditional and advanced microscopy techniques has provided detailed new observations of C. sordellii spore structural features, which serve as a reference point for structural studies of spores from other bacterial species.

Raghuwanshi, VS, Su, J, Garvey, CJ, Holt, SA, Holden, PJ, Batchelor, WJ & Garnier, G 2017, 'Visualization and Quantification of IgG Antibody Adsorbed at the Cellulose–Liquid Interface', Biomacromolecules, vol. 18, no. 8, pp. 2439-2445.
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Raghuwanshi, VS, Su, J, Garvey, CJ, Holt, SA, Raverty, W, Tabor, RF, Holden, PJ, Gillon, M, Batchelor, W & Garnier, G 2017, 'Bio-deuterated cellulose thin films for enhanced contrast in neutron reflectometry', Cellulose, vol. 24, no. 1, pp. 11-20.
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Rahimi, MA, Ramazani S.A, A, Alijani Alijanvand, H, Ghazanfari, MH & Ghanavati, M 2017, 'Effect ­­­­­of ultrasonic irradiation treatment on rheological behaviour of extra heavy crude oil: A solution method for transportation improvement', The Canadian Journal of Chemical Engineering, vol. 95, no. 1, pp. 83-91.
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AbstractThe highly viscous property of heavy oil often causes problems in its transportation in pipelines. Mixing heavy oil with light oil as well as ultrasound treatment are viable solutions to this problem. In this study, extra heavy crude oil samples were first diluted with 0, 0.05, 0.1, and 0.15 mL/mL (0, 5, 10, and 15 vol%) of a light crude oil; then the mixture was irradiated by ultrasonic waves for 0, 5, 10, 15, and 20 min; finally the viscous shear functions of all mixtures was measured at different values of shear rate at different temperature levels. The results revealed that the minimum viscosity of the diluted extra heavy crude oil samples was obtained at 10 min of ultrasonic irradiation. Moreover, the viscosity reduction rate in relation to temperature decreases as temperature increases. In other words, the maximum viscosity reduction rate occurred at 0.05 mL/mL (5 vol%) of light crude oil. Using the experimental data, the parameters of common rheological models were obtained and a new modified Power Law model was presented to calculate the effect of shear rate and temperature simultaneously.

Rahman, MA, Phillips, MR & Ton-That, C 2017, 'Efficient multi-coloured Li-doped ZnO thin films fabricated by spray pyrolysis', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 691, pp. 339-342.
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© 2016 Elsevier B.V. Undoped and Li-doped ZnO films with bright visible luminescence have been fabricated by the spray pyrolysis technique at 400 °C. The pyrolytic films exhibit multi-coloured emissions of yellow, green and blue, which can be tuned by varying the Li concentration. Simulation of the cathodoluminescence spectra from the Li-doped films using the Huang-Rhys model reveals the energies of the luminescence centres and their electron-phonon coupling strength. These centres are attributable to either VZnor LiZnacceptor states. This work presents a practical route to fabricate inexpensive multi-coloured light emitting coatings on any substrate.

Rahman, MA, Westerhausen, MT, Nenstiel, C, Choi, S, Hoffmann, A, Gentle, A, Phillips, MR & Ton-That, C 2017, 'Charge state switching of Cu acceptors in ZnO nanorods', Applied Physics Letters, vol. 110, no. 12, pp. 121907-121907.
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Undoped and Ga-doped ZnO nanorods both exhibit an intense green luminescence (GL) band centered at ∼2.4 eV. Unlike the defect-related GL in undoped nanorods, the GL band in Ga-doped nanorods displays a periodic fine structure separated by 72 meV, which consists of doublets with an energy spacing of 30 ± 3 meV. The emergence of the structured GL is due to the Cu+ state being stabilized by the rise in the Fermi level above the 0/- (Cu2+/Cu+) charge transfer level as a result of Ga donor incorporation. From a combination of optical characterization and simulation using the Brownian oscillator model, the doublet fine structures are shown to originate from two hole transitions with the Cu+ state located at 390 meV above the valence band.

Raina, J-B, Clode, PL, Cheong, S, Bougoure, J, Kilburn, MR, Reeder, A, Forêt, S, Stat, M, Beltran, V, Thomas-Hall, P, Tapiolas, D, Motti, CM, Gong, B, Pernice, M, Marjo, CE, Seymour, JR, Willis, BL & Bourne, DG 2017, 'Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria', eLife, vol. 6, pp. 1-17.
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Phytoplankton-bacteria interactions drive the surface ocean sulfur cycle and local climatic processes through the production and exchange of a key compound: dimethylsulfoniopropionate (DMSP). Despite their large-scale implications, these interactions remain unquantified at the cellular-scale. Here we use secondary-ion mass spectrometry to provide the first visualization of DMSP at sub-cellular levels, tracking the fate of a stable sulfur isotope (34S) from its incorporation by microalgae as inorganic sulfate to its biosynthesis and exudation as DMSP, and finally its uptake and degradation by bacteria. Our results identify for the first time the storage locations of DMSP in microalgae, with high enrichments present in vacuoles, cytoplasm and chloroplasts. In addition, we quantify DMSP incorporation at the single-cell level, with DMSP-degrading bacteria containing seven times more 34S than the control strain. This study provides an unprecedented methodology to label, retain, and image small diffusible molecules, which can be transposable to other symbiotic systems.

Ramsay, HA, Richman, MB & Leslie, LM 2017, 'The Modulating Influence of Indian Ocean Sea Surface Temperatures on Australian Region Seasonal Tropical Cyclone Counts', Journal of Climate, vol. 30, no. 13, pp. 4843-4856.
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The Australian region seasonal tropical cyclone count (TCC) maintained a robust statistical relationship with El Niño–Southern Oscillation (ENSO), with skillful forecasts of above (below) average TCC during La Niña (El Niño) years from 1969 until about 1998, weakening thereafter. The current study identifies an additional climate driver that mitigates the loss of predictive skill for Australian TCC after about 1998. It is found that the seasonal Australian TCC is strongly modulated by a southwest-to-northeast-oriented dipole in Indian Ocean sea surface temperature anomalies (SSTAs), referred to here as the transverse Indian Ocean dipole (TIOD). The TIOD emerges as the leading mode of detrended Indian Ocean SSTAs in the Southern Hemisphere during late winter and spring. Active (inactive) TC seasons are linked to positive (negative) TIOD phases, most notably during August–October immediately preceding the TC season, when SSTAs northwest of Australia, in the northeast pole of the TIOD, are positive (negative). To provide a physical interpretation of the TIOD–TCC relationship, 850-hPa zonal winds, 850-hPa relative vorticity, and 600-hPa relative humidity are composited for positive and negative TIOD phases, providing results consistent with observed TCC modulation. Correlations between ENSO and TCC weaken from 1998 onward, becoming statistically insignificant, whereas the TIOD–TCC correlation remains statistically significant until 2003. Overall, TIOD outperforms Niño-4 SSTA as a TCC predictor (46% skill increase since about 1998), when used individually or with Niño-4. The combination of TIOD and Niño 4 provide a skill increase (up to 33%) over climatology, demonstrating reliably accurate seasonal predictions of Australian region TCC.

Rawling, T, Choucair, H, Koolaji, N, Bourget, K, Allison, SE, Chen, Y-J, Dunstan, CR & Murray, M 2017, 'A Novel Arylurea Fatty Acid That Targets the Mitochondrion and Depletes Cardiolipin To Promote Killing of Breast Cancer Cells', Journal of Medicinal Chemistry, vol. 60, no. 20, pp. 8661-8666.
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© 2017 American Chemical Society. Cancer cell mitochondria are promising anticancer drug targets because they control cell death and are structurally and functionally different from normal cell mitochondria. We synthesized arylurea fatty acids and found that the analogue 16-({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)hexadecanoic acid (13b) decreased proliferation and activated apoptosis in MDA-MB-231 breast cancer cells in vitro and in vivo. In mechanistic studies 13b emerged as the prototype of a novel class of mitochondrion-targeted agents that deplete cardiolipin and promote cancer cell death.

Razavy, S, Gadau, M, Zhang, SP, Wang, FC, Bangrazi, S, Berle, C, Harahap, M, Li, T, Li, WH & Zaslawski, C 2017, 'Investigation of the Phenomenon of Propagated Sensation along the Channels in the Upper Limb Following Administration of Acupuncture and Mock Laser', Journal of Acupuncture and Meridian Studies, vol. 10, no. 5, pp. 307-316.
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© 2017 Background Similar to De Qi psychophysical responses, propagated sensation along the channels (PSC) is considered an important phenomenon in traditional Chinese acupuncture. In acupuncture clinical trials, different acupuncture manipulation techniques are used to enhance the propagation of sensation along the channels to facilitate an optimum therapeutic result. Aim To examine and compare the PSC reported by participants in a clinical trial following the administration of acupuncture and inactive mock laser. Methods The study was embedded in a two-arm parallel design multicenter, randomized clinical trial, the Tennis Elbow Acupuncture—International Study—China, Hong Kong, Australia, Italy (TEA IS CHAI). Needle sensations were measured using a validated instrument, the Massachusetts General Hospital Acupuncture Sensation Spreading Scale. Ninety-six participants with lateral elbow pain were randomly allocated into two groups in a 1:1 ratio; the acupuncture treatment group (n = 47) and the mock laser control group (n = 49). Participants in both groups received the intervention at two acupoints, LI10 and LI11, consisting of 2 minutes of either standardized needle manipulation or mock laser at each acupoint with a rest period between each intervention period. Data were collected immediately following the interventions at the first and the ninth session within the clinical trial. Results Although participants in both groups perceived PSC radiating to similar sites along the upper limb, the frequency of the reported radiation sites among the two intervention groups for both radiation up the limb (p < 0.05) and radiation down the limb (p < 0.001) were statistically significantly different. Among the radiating sensation sites recorded within the two study groups, the sensations were reported as radiating a greater distance down the forearm to the wrist compared to up the arm. Evaluation of PSC across the four study sites revealed a statistically significa...

Razavy, S, Gadau, M, Zhang, SP, Wang, FC, Bangrazi, S, Berle, C, Harahap, M, Li, T, Li, WH & Zaslawski, C 2017, 'Psychophysical responses in patients receiving a mock laser within context of an acupuncture clinical trial: an interoceptive perspective', BMC Complementary and Alternative Medicine, vol. 17, no. 1.
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© 2017 The Author(s). Background: The psychophysical responses induced by verum acupuncture are characterized by a constellation of unique subjective sensory responses commonly termed De Qi. Furthermore, a variety of sham interventions have been used as a control for acupuncture clinical trials. Indeed, one such control has been mock laser which has been used as control intervention in several acupuncture clinical controlled trials. The current study aim was to examine the De Qi sensory responses and its related characteristics elicited from acupuncture and compare them to those reported following sham laser in participants enrolled in a clinical trial. Methods: The study was embedded in a multi-center, two-arm randomised clinical trial, which evaluated the effect of acupuncture on lateral elbow pain. De Qi was assessed using the Massachusetts General Hospital Acupuncture Sensation Scale (MASS). Ninety-six participants were randomly allocated to receive either acupuncture (n = 47) or mock laser (n = 49) at the acupoints LI 10 and LI 11. Results: Participants in both intervention groups reported similar De Qi psychophysical characteristics; however, both intensity and frequency of the individually perceived De Qi characteristics were significantly higher in the acupuncture group. 'Soreness', 'deep pressure', and 'fullness-distension' in the acupuncture group and 'tingling', and 'sharp pain' in mock laser group, were identified as the leading characteristics. Similar level of MASS De Qi Index (MDI) scores were reported for 'Hong Kong-China' and 'Australia-Italy' with a significantly higher level of De Qi reported by 'Hong Kong-China'. Furthermore, two distinct De Qi categories were identified, namely De Qi (in line with classical sensory responses of Suan, Ma, Zhang, and Zhong) and pain. Conclusions: Subjective 'somatic or interoceptive awareness' should be taken into account when De Qi psychophysical responses are examined. The study accentuates the nece...

Reid, CJ, Wyrsch, ER, Chowdhury, PR, Zingali, T, Liu, M, Darling, A, Chapman, TA & Djordjevic, SP 2017, 'Porcine commensalEscherichia coli: A reservoir for class 1 integrons associated with IS26'.
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AbstractPorcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensalEscherichia colifrom swine is largely unknown. Furthermore, little is known about the role of commensalE. colias contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141E. colifrom the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genesblaTEM, aphAl, cmlA, strAB, tet(A)A,dfrA12, dfrA5, sul1, sul2, sul3; iv)IS26;and v) heavy metal resistance genes (merA, cusA, terA). Carriage of the sulphonamide resistance genesul3was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenicE. coli(ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensalE. coliof porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry.Conflict of Interest StatementNone to declare.

Reid, CJ, Wyrsch, ER, Roy Chowdhury, P, Zingali, T, Liu, M, Darling, AE, Chapman, TA & Djordjevic, SP 2017, 'Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26', Microbial Genomics, vol. 3, no. 12, pp. 1-13.
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Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.

Reimers, JR & Hush, NS 2017, 'Relating transition-state spectroscopy to standard chemical spectroscopic processes', Chemical Physics Letters, vol. 683, pp. 467-477.
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© 2017 Elsevier B.V. Transition-state spectra are mapped out using generalized adiabatic electron-transfer theory. This simple model depicts diverse chemical properties, from aromaticity, through bound reactions such as isomerizations and atom-transfer processes with classic transition states, to processes often described as being “non-adiabatic”, to those in the “inverted” region that become slower as they are made more exothermic. Predictably, the Born-Oppenheimer approximation is found inadequate for modelling transition-state spectra in the weak-coupling limit. In this limit, the adiabatic Born-Huang approximation is found to perform much better than non-adiabatic surface-hopping approaches. Transition-state spectroscopy is shown to involve significant quantum entanglement between electronic and nuclear motion.

Reimers, JR & Hush, NS 2017, 'The critical role of the transition-state cusp diameter in understanding adiabatic and non-adiabatic electron transfer', Russian Journal of Electrochemistry, vol. 53, no. 9, pp. 1042-1053.
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© 2017, Pleiades Publishing, Ltd. The equation of Levich and Dogonadze describing the rate of electron-transfer processes in the weak-coupling “non-adiabatic” limit is understood in terms of the properties of general adiabatic electron-transfer theory. The cusp diameter describing the continuous changeover of Born–Oppenheimer adiabatic surfaces from donor-like to acceptor-like character is shown to be the critical property controlling reaction rates and intervalence spectra. Their work is presented in the context of general Born–Oppenheimer breakdown phenomena and linked to the overarching cusp catastrophe.

Reimers, JR, Ford, MJ, Marcuccio, SM, Ulstrup, J & Hush, NS 2017, 'Competition of van der Waals and chemical forces on gold–sulfur surfaces and nanoparticles', Nature Reviews Chemistry, vol. 1, no. 2, pp. 1-12.
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Chemists generally believe that covalent and ionic bonds form much stronger links between atoms than the van der Waals force does. However, this is not always so. We present cases in which van der Waals dispersive forces introduce new competitive bonding possibilities rather than just modulating traditional bonding scenarios. Although the new possibilities could arise from any soft–soft chemical interaction, we focus on bonding between gold atoms and alkylor arylsulfur ligands, RS. Consideration of all the interactions at play in sulfur-protected gold surfaces and gold nanoparticles is necessary to understand their structural, chemical and spectroscopic properties. In turn, such knowledge opens pathways to new chemical entities and innovative nanotechnological devices. Such experimentation is complemented by modern theory, and presented here is a broad overview of computational methods appropriate to fields ranging from gas-phase chemistry to device physics and biochemistry.

Reimers, JR, Ford, MJ, Marcuccio, SM, Ulstrup, J & Hush, NS 2017, 'Erratum: Competition of van der Waals and chemical forces on gold–sulfur surfaces and nanoparticles', Nature Reviews Chemistry, vol. 1, no. 4.
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© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Errors existed in the originally published version of figure 5 in this Review. Thiolate RS-, generated from thiol RSH and NaBH 4, reacts with HAuCl2 to afford Au(i) thiolates. Au(0) thiyls can form on treating Au metal with RSH or RSSR, or from a mixture containing HAuCl2, RSSR and acid. The amended figure 5 appears in both the HTML and PDF versions.

Ren, J, Song, J, Ellis, J & Li, J 2017, 'Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences', BMC Genomics, vol. 18, no. S2.
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© 2017 The Author(s). Background: The broad heterogeneity of antigen-antibody interactions brings tremendous challenges to the design of a widely applicable learning algorithm to identify conformational B-cell epitopes. Besides the intrinsic heterogeneity introduced by diverse species, extra heterogeneity can also be introduced by various data sources, adding another layer of complexity and further confounding the research. Results: This work proposed a staged heterogeneity learning method, which learns both characteristics and heterogeneity of data in a phased manner. The method was applied to identify antigenic residues of heterogenous conformational B-cell epitopes based on antigen sequences. In the first stage, the model learns the general epitope patterns of each kind of propensity from a large data set containing computationally defined epitopes. In the second stage, the model learns the heterogenous complementarity of these propensities from a relatively small guided data set containing experimentally determined epitopes. Moreover, we designed an algorithm to cluster the predicted individual antigenic residues into conformational B-cell epitopes so as to provide strong potential for real-world applications, such as vaccine development. With heterogeneity well learnt, the transferability of the prediction model was remarkably improved to handle new data with a high level of heterogeneity. The model has been tested on two data sets with experimentally determined epitopes, and on a data set with computationally defined epitopes. This proposed sequence-based method achieved outstanding performance - about twice that of existing methods, including the sequence-based predictor CBTOPE and three other structure-based predictors. Conclusions: The proposed method uses only antigen sequence information, and thus has much broader applications.

Ren, NN, Chen, HJ, Li, Y, Mcgowan, GW & Lin, YG 2017, '[A clinical study on the effect of nattokinase on carotid artery atherosclerosis and hyperlipidaemia].', Zhonghua Yi Xue Za Zhi, vol. 97, no. 26, pp. 2038-2042.
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Objective: To evaluate the efficacy of oral nattokinase (NK) in the reduction of common carotid artery intimal medial thickness (CCA-IMT) and carotid artery plaque size and in lowering blood lipids, and to explore the underlying mechanism of actions of NK and its potential clinical use. Methods: All enrolled patients were from the Out-Patient Clinic of the Department of TCM at the 3(rd) Affiliated Hospital of Sun Yat-sen University. Using randomised picking method, all patients were randomly assigned to one of two groups, NK and Statin (ST) group. NK Group-patients were given NK at a daily dose of 6 000 FU and ST Group-patients were treated with statin (simvastatin 20 mg) daily. The treatment course was 26 weeks. CCA-IMT, carotid plaque size and blood lipid profile of the patients were measured before and after treatment. Results: A total of 82 patients were enrolled in the study and 76 patients (NK 39, ST 37) completed the study. Following the treatments for 26 weeks, there was a significant reduction in CCA-IMT and carotid plaque size in both groups compared with the baseline before treatment. The carotid plaque size and CCA-IMT reduced from(0.25±0.12)cm(2) to (0.16±0.10)cm(2) and from (1.13±0.12)mm to (1.01±0.11)mm, repectively. The reduction in the NK group was significantly profound (P<0.01, 36.6% reduction in plaque size in NK group versus 11.5% change in ST group). Both treatments reduced total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG). While the reduction in both groups was shown to be statistically significant (P<0.01), the reduction of TC, LDL-C and TG in ST group was significantly greater (P<0.05). In addition, NK significantly increased the level of high-density lipoprotein cholesterol (HDL-C) (P<0.05), in contrast, HDL-C in the ST group did not change. The lipid lowering effect observed in the NK group was not correlated to the reduction of CCA-IMT and carotid artery plaque size (r=0.35, P=0.09). Co...

Reyna, J, Hanham, J & Meier, P 2017, 'A taxonomy of digital media types for Learner-Generated Digital Media assignments', E-Learning and Digital Media, vol. 14, no. 6, pp. 309-322.
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The notion of students as co-creators of content in higher education is gaining popularity, with an ever-increasing emphasis on the development of digital media assignments. In a separate paper, the authors introduced the Digital Media Literacies Framework, which is composed of three interrelated domains: (1) conceptual, (2) functional, and (3) audiovisual, each of which defines a set of prosumer principles used to create digital artefacts. This framework fills a gap in the literature and is the first step towards the provision of a systematic approach to designing digital media assignments. This paper expands on the Digital Media Literacies Framework through the incorporation of Technological Proxies and proposes a taxonomy of digital media types to help educators and students to visualise the skills needed to complete Learner-Generated Digital Media assignments. A taxonomy of digital media types is presented considering the conceptual, functional, and audiovisual domains of the Digital Media Literacies Framework. The taxonomy spans a range of Learner-Generated Digital Media assignments, from the creation of an audio podcast to the complexity of blended media or game development. Implications of the taxonomy for teaching and learning in higher education are discussed.

Rhodes, L, Smith, KF, Verma, A, Curley, BG, Harwood, DT, Murray, S, Kohli, GS, Solomona, D, Rongo, T, Munday, R & Murray, SA 2017, 'A new species of Gambierdiscus (Dinophyceae) from the south-west Pacific: Gambierdiscus honu sp. nov.', Harmful Algae, vol. 65, pp. 61-70.
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© 2017 Elsevier B.V. Two isolates of a new tropical, epiphytic dinoflagellate species, Gambierdiscus honu sp. nov., were obtained from macroalgae sampled in Rarotonga, Cook Islands, and from North Meyer Island, Kermadec Islands. Gambierdiscus honu sp. nov. had the common Gambierdiscus Kofoidian plate formula: Po, 3′, 6″, 6C?, 6 or 7S, 5‴, 1p and 2⁗. The characteristic morphological features of this species were its relatively small short dorsoventral length and width and the shape of individual plates, in particular the combination of the hatchet-shaped 2′ and pentagonal 3′ plates and the length to width ratio of the antapical 1p plate. The combination of these characteristics plus the smooth thecal surface and equal sized 1⁗ and 2⁗ plates differentiated this species from other Gambierdiscus species. The phylogenetic analyses supported the unique description. Both isolates of G. honu produced the putative maitotoxin (MTX)-3 analogue, but neither produced ciguatoxin (CTX) or MTX. Extracts of G. honu were shown to be highly toxic to mice by intraperitoneal injection (0.2 mg/kg), although less toxic by gavage. It is possible that toxins other than putative MTX-3 are produced.

Rhodes, LL, Smith, KF, Verma, A, Murray, S, Harwood, DT & Trnski, T 2017, 'The dinoflagellate genera Gambierdiscus and Ostreopsis from subtropical Raoul Island and North Meyer Island, Kermadec Islands', New Zealand Journal of Marine and Freshwater Research, vol. 51, no. 4, pp. 490-504.
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© 2016 The Royal Society of New Zealand. An expedition to North Meyer Island, Kermadec Islands, in November 2015, resulted in the isolation of two Gambierdiscus species, G. australes and a previously unknown Gambierdiscus species maintained in the Cawthron Institute Culture Collection of Micro-algae as CAWD242. Identifications were based on morphology and DNA sequence data analysis. Nine isolates of G. australes produced maitotoxin-1 (MTX-1) ranging from present (detectable but below the confidence level) to 36.6 pg per cell. One further isolate did not produce MTX-1, but all G. australes isolates produced putative MTX-3. Isolate CAWD242 was negative for MTX-1 but produced MTX-3. Ostreopsis sp. 3 isolated from samples collected during an earlier expedition in 2013 produced low concentrations of palytoxin (PLTX)-like compounds (0.013 pg per cell), but an isolate of the same species from samples collected in 2015 was non-toxic. Other dinoflagellates isolated and identified were Coolia malayensis, Amphidinium carterae and Prorocentrum hoffmannianum.

Ribaux, O, Roux, C & Crispino, F 2017, 'Expressing the value of forensic science in policing', Australian Journal of Forensic Sciences, vol. 49, no. 5, pp. 489-501.
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© 2016 Australian Academy of Forensic SciencesOnly a small part of forensic science activities scattered across criminal justice systems is the object of scientific scrutiny, and is taken into account when evaluating the added-value brought by this discipline. Even in its more restricted definition, forensic science faces many embarrassing questions about its capacity to provide valid and reliably interpreted information in court. The inflation of control mechanisms increases costs and reduces the scope or availability of forensic information. The viability of forensic science, viewed through this lens, is questioned. To address this challenge, it is imperative to validly express forensic science contributions that are otherwise diluted across earlier processes. These include abductive and inductive species of inferences used in crime investigation, crime analysis and criminal intelligence. The ‘scientificity’ of these processes may be questioned, but it is not contested that they largely determine the global outcome of justice systems. As a result, they cannot be ignored. To unlock the debate, it is proposed to turn the forensic science focus from means (instruments, techniques, methods) to ends (what is the problem, what are the objectives?). This perspective naturally leads to proactive models of policing. It also provides possible frameworks to express various uses of the information conveyed by traces for solving problems. Reframed forensic science contributions are more validly expressed and the current debate can ultimately be transcended.

Rice, SA 2017, 'Interactions between microbial community members', Environmental Microbiology Reports, vol. 9, no. 5, pp. 471-473.
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Rice, SA & Verboncoeur, JP 2017, 'Migration of Multipactor Trajectories via Higher-Order Mode Perturbation', IEEE Transactions on Plasma Science, vol. 45, no. 7, pp. 1739-1745.
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Richman, MB, Leslie, LM, Ramsay, HA & Klotzbach, PJ 2017, 'Reducing Tropical Cyclone Prediction Errors Using Machine Learning Approaches', Procedia Computer Science, vol. 114, pp. 314-323.
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Ritchie, L, Taddeo, S, Weeks, B, Carroll, R, Dykes, L, Rooney, L & Turner, N 2017, 'Impact of Novel Sorghum Bran Diets on DSS-Induced Colitis', Nutrients, vol. 9, no. 4, pp. 330-330.
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We have demonstrated that polyphenol-rich sorghum bran diets alter fecal microbiota; however, little is known regarding their effect on colon inflammation. Our aim was to characterize the effect of sorghum bran diets on intestinal homeostasis during dextran sodium sulfate (DSS)-induced colitis. Male Sprague-Dawley rats (N = 20/diet) were provided diets containing 6% fiber from cellulose, or Black (3-deoxyanthocyanins), Sumac (condensed tannins) or Hi Tannin Black (both) sorghum bran. Colitis was induced (N = 10/diet) with three separate 48-h exposures to 3% DSS, and feces were collected. On Day 82, animals were euthanized and the colon resected. Only discrete mucosal lesions, with no diarrhea or bloody stools, were observed in DSS rats. Only bran diets upregulated proliferation and Tff3, Tgfβ and short chain fatty acids (SCFA) transporter expression after a DSS challenge. DSS did not significantly affect fecal SCFA concentrations. Bran diets alone upregulated repair mechanisms and SCFA transporter expression, which suggests these polyphenol-rich sorghum brans may suppress some consequences of colitis.

Rivas, J, Neira, V, Mena, J, Brito, B, Garcia, A, Gutierrez, C, Sandoval, D & Ortega, R 2017, 'Identification of a divergent genotype of equine arteritis virus from South American donkeys', Transboundary and Emerging Diseases, vol. 64, no. 6, pp. 1655-1660.
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A novel equine arteritis virus (EAV) was isolated and sequenced from feral donkeys in Chile. Phylogenetic analysis indicates that the new virus and South African asinine strains diverged at least 100 years from equine EAV strains. The results indicate that asinine strains belonged to a different EAV genotype.

Robinson, CM, Cherukuru, N, Hardman-Mountford, NJ, Everett, JD, McLaughlin, MJ, Davies, KP, Van Dongen-Vogels, V, Ralph, PJ & Doblin, MA 2017, 'Phytoplankton absorption predicts patterns in primary productivity in Australian coastal shelf waters', Estuarine, Coastal and Shelf Science, vol. 192, pp. 1-16.
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© 2017 Elsevier Ltd The phytoplankton absorption coefficient (aPHY) has been suggested as a suitable alternate first order predictor of net primary productivity (NPP). We compiled a dataset of surface bio-optical properties and phytoplankton NPP measurements in coastal waters around Australia to examine the utility of an in-situ absorption model to estimate NPP. The magnitude of surface NPP (0.20–19.3 mmol C m−3 d−1) across sites was largely driven by phytoplankton biomass, with higher rates being attributed to the microplankton (>20 μm) size class. The phytoplankton absorption coefficient aPHY for PAR (photosynthetically active radiation; āPHY)) ranged from 0.003 to 0.073 m-1, influenced by changes in phytoplankton community composition, physiology and environmental conditions. The aPHY coefficient also reflected changes in NPP and the absorption model-derived NPP could explain 73% of the variability in measured surface NPP (n = 41; RMSE = 2.49). The absorption model was applied to two contrasting coastal locations to examine NPP dynamics: a high chlorophyll-high variation (HCHV; Port Hacking National Reference Station) and moderate chlorophyll-low variation (MCLV; Yongala National Reference Station) location in eastern Australia using the GIOP-DC satellite aPHY product. Mean daily NPP rates between 2003 and 2015 were higher at the HCHV site (1.71 ± 0.03 mmol C m−3 d−1) with the annual maximum NPP occurring during the austral winter. In contrast, the MCLV site annual NPP peak occurred during the austral wet season and had lower mean daily NPP (1.43 ± 0.03 mmol C m−3 d−1) across the time-series. An absorption-based model to estimate NPP is a promising approach for exploring the spatio-temporal dynamics in phytoplankton NPP around the Australian continental shelf.

Rodriguez, GM, Bowen, J, Grossin, D, Ben-Nissan, B & Stamboulis, A 2017, 'Functionalisation of Ti6Al4V and hydroxyapatite surfaces with combined peptides based on KKLPDA and EEEEEEEE peptides', Colloids and Surfaces B: Biointerfaces, vol. 160, pp. 154-160.
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Surface modifications are usually performed on titanium alloys to improve osteo-integration and surface bioactivity. Modifications such as alkaline and acid etching, or coating with bioactive materials such as hydroxyapatite, have previously been demonstrated. The aim of this work is to develop a peptide with combined titanium oxide and hydroxyapatite binders in order to achieve a biomimetic hydroxyapatite coating on titanium surfaces. The technology would also be applicable for the functionalisation of titanium and hydroxyapatite surfaces for selective protein adsorption, conjugation of antimicrobial peptides, and adsorption of specialised drugs for drug delivery. In this work, functionalisation of Ti6Al4V and hydroxyapatite surfaces was achieved using combined titanium-hydroxyapatite (Ti-Hap) peptides based on titanium peptide binder (KKLPDA) and hydroxyapatite peptide binder (EEEEEEEE). Homogeneous peptide coatings on Ti6Al4V surfaces were obtained after surface chemical treatments with a 30wt% aqueous solution of H2O2 for 24 and 48h. The treated titanium surfaces presented an average roughness of Sa=197nm (24h) and Sa=128nm (48h); an untreated mirror polished sample exhibited an Sa of 13nm. The advancing water contact angle of the titanium oxide layer after 1h of exposure to 30wt% aqueous solution of H2O2 was around 65°, decreasing gradually with time until it reached 35° after a 48h exposure, suggesting that the surface hydrophilicity increased over etching time. The presence of a lysine (L) amino acid in the sequence of the titanium binder resulted in fluorescence intensity roughly 16% higher compared with the arginine (R) amino acid analogue and therefore the lysine containing titanium peptide binder was used in this work. The Ti-Hap peptide KKLPDAEEEEEEEE (Ti-Hap1) was not adsorbed by the treated Ti6Al4V surfaces and therefore was modified. The modifications involved the inclusion of a glycine spacer between the binding terminals (Ti-Hap2) and the additio...

Rong, Y, Wang, D, Xu, C, Ji, Y, Jin, D, Wu, W, Xu, X, Kuang, T & Lou, W 2017, 'Prognostic value of histological subtype in intraductal papillary mucinous neoplasm of the pancreas', Medicine, vol. 96, no. 15, pp. e6599-e6599.
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Roseblade, A, Ung, A & Bebawy, M 2017, 'Synthesis and in vitro biological evaluation of thiosulfinate derivatives for the treatment of human multidrug-resistant breast cancer', Acta Pharmacologica Sinica, vol. 38, no. 10, pp. 1353-1368.
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© 2017 CPS and SIMM All rights reserved. Organosulfur compounds derived from Allium vegetables have long been recognized for various therapeutic effects, including anticancer activity. Allicin, one of the main biologically active components of garlic, shows promise as an anticancer agent; however, instability makes it unsuitable for clinical application. The aim of this study was to investigate the effect of stabilized allicin derivatives on human breast cancer cells in vitro. In this study, a total of 22 stabilized thiosulfinate derivatives were synthesized and screened for their in vitro antiproliferative activities against drug-sensitive (MCF-7) and multidrug-resistant (MCF-7/Dx) human adenocarcinoma breast cancer cells. Assays for cell death, apoptosis, cell cycle progression and mitochondrial bioenergetic function were performed. Seven compounds (4b, 7b, 8b, 13b, 14b, 15b and 18b) showed greater antiproliferative activity against MCF-7/Dx cells than allicin. These compounds were also selective towards multidrug-resistant (MDR) cells, a consequence attributed to collateral sensitivity. Among them, 13b exhibited the greatest anticancer activity in both MCF-7/Dx and MCF-7 cells, with IC50 values of 18.54±0.24 and 46.50±1.98 μmol/L, respectively. 13b altered cellular morphology and arrested the cell cycle at the G2/M phase. Additionally, 13b dose-dependently induced apoptosis, and inhibited cellular mitochondrial respiration in cells at rest and under stress. MDR presents a significant obstacle to the successful treatment of cancer clinically. These results demonstrate that thiosulfinate derivatives have potential as novel anticancer agents and may offer new therapeutic strategies for the treatment of chemoresistant cancers.

Roy Chowdhury, P, Scott, MJ & Djordjevic, SP 2017, 'Genomic islands 1 and 2 carry multiple antibiotic resistance genes in Pseudomonas aeruginosa ST235, ST253, ST111 and ST175 and are globally dispersed', Journal of Antimicrobial Chemotherapy, vol. 72, no. 2, pp. 620-622.
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Ruiz-Campillo, MT, Molina Hernandez, V, Escamilla, A, Stevenson, M, Perez, J, Martinez-Moreno, A, Donnelly, S, Dalton, JP & Cwiklinski, K 2017, 'Immune signatures of pathogenesis in the peritoneal compartment during early infection of sheep with Fasciola hepatica', Scientific Reports, vol. 7, no. 1, pp. 1-14.
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AbstractImmune signatures of sheep acutely-infected withFasciola hepatica, an important pathogen of livestock and humans were analysed within the peritoneal compartment to investigate early infection. Within the peritoneum,F. hepaticaantibodies coincided with an intense innate and adaptive cellular immune response, with infiltrating leukocytes and a marked eosinophilia (49%). However, while cytokine qPCR analysis revealed IL-10, IL-12, IL-13, IL-23 and TGFβ were elevated, these were not statistically different at 18 days post-infection compared to uninfected animals indicating that the immune response is muted and not yet skewed to a Th2 type response that is associated with chronic disease. Proteomic analysis of the peritoneal fluid identified infection-related proteins, including several structural proteins derived from the liver extracellular matrix, connective tissue and epithelium, and proteins related to the immune system. Periostin and vascular cell adhesion protein 1 (VCAM-1), molecules that mediate leukocyte infiltration and are associated with inflammatory disorders involving marked eosinophilia (e.g. asthma), were particularly elevated in the peritoneum. Immuno-histochemical studies indicated that the source of periostin and VCAM-1 was the inflamed sheep liver tissue. This study has revealed previously unknown aspects of the immunology and pathogenesis associated with acute fascioliasis in the peritoneum and liver.

Rumman, R, Cleverly, J, Nolan, RH, Tarin, T & Eamus, D 2017, 'Speculations on the application of foliar &lt;sup&gt;13&lt;/sup&gt;C discrimination to reveal groundwater dependency of vegetation, provide estimates of root depth and rates of groundwater use', Hydrology and Earth System Sciences Discussions, vol. 22, pp. 1-25.
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Abstract. Groundwater-dependent vegetation is globally distributed, having important ecological, social and economic value. Along with the groundwater resources upon which it depends, this vegetation is under increasing threat through excessive rates of groundwater extraction. In this study we examined one shallow-rooted and two deep-rooted tree species at multiple sites along a naturally occurring gradient in depth-to-groundwater. We measured (i) stable isotope ratios of leaves (δ13C), xylem and groundwater (δ2H and δ18O); and (ii) leaf vein density. We established that foliar discrimination of 13C (∆13C) is a reliable indicator of groundwater use by vegetation and can also be used to estimate rooting depth. Through comparison with a continental-scale assessment of foliar ∆13C, we also estimated the upper limits to annual rates of groundwater use. We conclude that maximum rooting depth for both deep-rooted species ranged between 9.4 m and 11.2 m and that annual rates of groundwater use ranged ca 1400–1700 mm for Eucalyptus camaldulensis and 600–900 mm for Corymbia opaca. Several predictions about hydraulic and leaf traits arising from the conclusion that these two species made extensive use of groundwater were supported by additional studies of these species in central Australia.

Rychener, L, In-Albon, S, Djordjevic, SP, Chowdhury, PR, Nicholson, P, Ziech, RE, de Vargas, AC, Frey, J & Falquet, L 2017, 'Clostridium chauvoei, an Evolutionary Dead-End Pathogen', Frontiers in Microbiology, vol. 8.
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Sadraeian, M, Guimarães, FEG, Araújo, APU, Worthylake, DK, LeCour, L & Pincus, SH 2017, 'Selective cytotoxicity of a novel immunotoxin based on pulchellin A chain for cells expressing HIV envelope', Scientific Reports, vol. 7, no. 1.
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AbstractImmunotoxins (ITs), which consist of antibodies conjugated to toxins, have been proposed as a treatment for cancer and chronic infections. To develop and improve the ITs, different toxins such as ricin, have been used, aiming for higher efficacy against target cells. The toxin pulchellin, isolated from theAbrus pulchellusplant, has similar structure and function as ricin. Here we have compared two plant toxins, recombinant A chains from ricin (RAC) and pulchellin (PAC) toxins, for their ability to kill HIV Env-expressing cells. In this study, RAC and PAC were produced inE. coli, and chromatographically purified, then chemically conjugated to two different anti-HIV monoclonal antibodies (MAbs), anti-gp120 MAb 924 or anti-gp41 MAb 7B2. These conjugates were characterized biochemically and immunologically. Cell internalization was studied by flow cytometry and confocal microscopy. Results showed that PAC can function within an effective IT. The ITs demonstrated specific binding against native antigens on persistently HIV-infected cells and recombinant antigens on Env-transfected cells. PAC cytotoxicity appears somewhat less than RAC, the standard for comparison. This is the first report that PAC may have utility for the design and construction of therapeutic ITs, highlighting the potential role for specific cell targeting.

Safadi, ME, Bhadbhade, M, Shimmon, R, Baker, AT & McDonagh, AM 2017, 'Cyclen-based chelators for the inhibition of Aβ aggregation: Synthesis, anti-oxidant and aggregation evaluation', Inorganica Chimica Acta, vol. 467, pp. 343-350.
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© 2017 Elsevier B.V. The aggregation of the protein amyloid-β in the brain has been associated with neurodegenerative diseases such as Alzheimer's disease. Such aggregation of amyloid-β can be induced by misregulated metal ions such as Cu2+ and Zn2+. Here we present four metal chelating compounds based on the cyclen macrocycle that each bear a pendant arm to provide additional anti-oxidant activity. The corresponding Cu2+, Zn2+ and Ni2+ complexes have been synthesized and characterized to examine the ability of the chelators to bind to the metal centres. Aβ40 de-aggregation by the cyclen compounds was assessed using turbidometry and the re-solubilization of the Aβ40 was also examined. Our results show that the cyclen compounds have the ability to effectively chelate Cu2+ and Zn2+ metal ions and thus de-aggregate Aβ40 that has been aggregated due to the presence of these ions. The antioxidant properties of the cyclen compounds were tested by using the DPPH scavenging assay and the results show that some of the compounds can decrease oxidative stress.

Samardzic, K & Rodgers, KJ 2017, 'Oxidised protein metabolism: recent insights', Biological Chemistry, vol. 398, no. 11, pp. 1165-1175.
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AbstractThe ‘oxygen paradox’ arises from the fact that oxygen, the molecule that aerobic life depends on, threatens its very existence. An oxygen-rich environment provided life on Earth with more efficient bioenergetics and, with it, the challenge of having to deal with a host of oxygen-derived reactive species capable of damaging proteins and other crucial cellular components. In this minireview, we explore recent insights into the metabolism of proteins that have been reversibly or irreversibly damaged by oxygen-derived species. We discuss recent data on the important roles played by the proteasomal and lysosomal systems in the proteolytic degradation of oxidatively damaged proteins and the effects of oxidative damage on the function of the proteolytic pathways themselves. Mitochondria are central to oxygen utilisation in the cell, and their ability to handle oxygen-derived radicals is an important and still emerging area of research. Current knowledge of the proteolytic machinery in the mitochondria, including the ATP-dependent AAA+ proteases and mitochondrial-derived vesicles, is also highlighted in the review. Significant progress is still being made in regard to understanding the mechanisms underlying the detection and degradation of oxidised proteins and how proteolytic pathways interact with each other. Finally, we highlight a few unanswered questions such as the possibility of oxidised amino acids released from oxidised proteins by proteolysis being re-utilised in protein synthesis thus establishing a vicious cycle of oxidation in cells.

Sandstrom, R, Ke, L, Martin, A, Wang, Z, Kianinia, M, Green, B, Gao, W & Aharonovich, I 2017, 'Optical properties of Xe color centers in diamond', Optics Communications, vol. 411, pp. 182-186.
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Optical properties of color centers in diamond have been the subject ofintense research due to their promising applications in quantum photonics. Inthis work we study the optical properties of Xe related color centers implantedinto nitrogen rich (type IIA) and an ultrapure, electronic grade diamond. TheXe defect has two zero phonon lines at ~ 794 and 811 nm, which can beeffectively excited using both green and red excitation, however, its emissionin the nitrogen rich diamond is brighter. Near resonant excitation is performedat cryogenic temperatures and luminescence is probed under strong magneticfield. Our results are important towards the understanding of the Xe relateddefect and other near infrared color centers in diamond.

Santos, J, Milthorpe, BK, Herbert, BR & Padula, MP 2017, 'Proteomic Analysis of Human Adipose Derived Stem Cells during Small Molecule Chemical Stimulated Pre-neuronal Differentiation', International Journal of Stem Cells, vol. 10, no. 2, pp. 193-217.
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© 2017 by the Korean Society for Stem Cells Research. Background: Adipose derived stem cells (ADSCs) are acquired from abdominal liposuction yielding a thousand fold more stem cells per millilitre than those from bone marrow. A large research void exists as to whether ADSCs are capable of transdermal differentiation toward neuronal phenotypes. Previous studies have investigated the use of chemical cocktails with varying inconclusive results. Methods: Human ADSCs were treated with a chemical stimulant, beta-mercaptoethanol, to direct them toward a neuronal- like lineage within 24 hours. Quantitative proteomics using iTRAQ was then performed to ascertain protein abundance differences between ADSCs, beta-mercaptoethanol treated ADSCs and a glioblastoma cell line. Results: The soluble proteome of ADSCs differentiated for 12 hours and 24 hours was significantly different from basal ADSCs and control cells, expressing a number of remodeling, neuroprotective and neuroproliferative proteins. However toward the later time point presented stress and shock related proteins were observed to be up regulated with a large down regulation of structural proteins. Cytokine profiles support a large cellular remodeling shift as well indicating cellular distress. Conclusion: The earlier time point indicates an initiation of differentiation. At the latter time point there is a vast loss of cell population during treatment. At 24 hours drastically decreased cytokine profiles and overexpression of stress proteins reveal that exposure to beta-mercaptoethanol beyond 24 hours may not be suitable for clinical application as our results indicate that the cells are in trauma whilst producing neuronal-like morphologies. The shorter treatment time is promising, indicating a reducing agent has fast acting potential to initiate neuronal differentiation of ADSCs.

Scanes, E, Parker, LM, O'Connor, WA, Stapp, LS & Ross, PM 2017, 'Intertidal oysters reach their physiological limit in a future high-CO2 world', Journal of Experimental Biology, vol. 220, no. 5, pp. 765-774.
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ABSTRACT Sessile marine molluscs living in the intertidal zone experience periods of internal acidosis when exposed to air (emersion) during low tide. Relative to other marine organisms, molluscs have been identified as vulnerable to future ocean acidification; however, paradoxically it has also been shown that molluscs exposed to high CO2 environments are more resilient compared with those molluscs naive to CO2 exposure. Two competing hypotheses were tested using a novel experimental design incorporating tidal simulations to predict the future intertidal limit of oysters in a high-CO2 world; either high-shore oysters will be more tolerant of elevated PCO2 because of their regular acidosis, or elevated PCO2 will cause high-shore oysters to reach their limit. Sydney rock oysters, Saccostrea glomerata, were collected from the high-intertidal and subtidal areas of the shore and exposed in an orthogonal design to either an intertidal or a subtidal treatment at ambient or elevated PCO2, and physiological variables were measured. The combined treatment of tidal emersion and elevated PCO2 interacted synergistically to reduce the haemolymph pH (pHe) of oysters, and increase the PCO2 in the haemolymph (Pe,CO2) and standard metabolic rate. Oysters in the intertidal treatment also had lower condition and growth. Oysters showed a high degree of plasticity, and little evidence was found that intertidal oysters were more resilient than subtidal oysters. It is concluded that in a high-CO2 world the upper vertical limit of oyster distribution on the shore may be reduced. These results suggest that previous studies on intertidal organisms that lacked tidal simulations may have underestimated the effects of elevated PCO2.

Schell, AW, Takashima, H, Tran, TT, Aharonovich, I & Takeuchi, S 2017, 'Coupling Quantum Emitters in 2D Materials with Tapered Fibers', ACS Photonics, vol. 4, no. 4, pp. 761-767.
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© 2017 American Chemical Society. Realization of integrated photonic circuits on a single chip requires controlled manipulation and integration of solid-state quantum emitters with nanophotonic components. Previous works focused on emitters embedded in a three-dimensional crystal, such as nanodiamonds or quantum dots. In contrast, in this work we demonstrate coupling of a single emitter in a two-dimensional (2D) material, namely, hexagonal boron nitride, with a tapered optical fiber and find a collection efficiency of the system of 10%. Furthermore, due to the single dipole character of the emitter, we were able to analyze the angular emission pattern of the coupled system via back focal plane imaging. The good coupling efficiency to the tapered fiber even allows excitation and detection in a fully fiber coupled way, yielding a true integrated system. Our results provide evidence of the feasibility to efficiently integrate quantum emitters in 2D materials with photonic structures.

Scott, PD, Coleman, HM, Colville, A, Lim, R, Matthews, B, McDonald, JA, Miranda, A, Neale, PA, Nugegoda, D, Tremblay, LA & Leusch, FDL 2017, 'Assessing the potential for trace organic contaminants commonly found in Australian rivers to induce vitellogenin in the native rainbowfish (Melanotaenia fluviatilis) and the introduced mosquitofish (Gambusia holbrooki)', Aquatic Toxicology, vol. 185, pp. 105-120.
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© 2017 Elsevier B.V. In Australia, trace organic contaminants (TrOCs) and endocrine active compounds (EACs) have been detected in rivers impacted by sewage effluent, urban stormwater, agricultural and industrial inputs. It is unclear whether these chemicals are at concentrations that can elicit endocrine disruption in Australian fish species. In this study, native rainbowfish (Melanotaenia fluviatilis) and introduced invasive (but prevalent) mosquitofish (Gambusia holbrooki) were exposed to the individual compounds atrazine, estrone, bisphenol A, propylparaben and pyrimethanil, and mixtures of compounds including hormones and personal care products, industrial compounds, and pesticides at environmentally relevant concentrations. Vitellogenin (Vtg) protein and liver Vtg mRNA induction were used to assess the estrogenic potential of these compounds. Vtg expression was significantly affected in both species exposed to estrone at concentrations that leave little margin for safety (p < 0.001). Propylparaben caused a small but statistically significant 3× increase in Vtg protein levels (p = 0.035) in rainbowfish but at a concentration 40× higher than that measured in the environment, therefore propylparaben poses a low risk of inducing endocrine disruption in fish. Mixtures of pesticides and a mixture of hormones, pharmaceuticals, industrial compounds and pesticides induced a small but statistically significant increase in plasma Vtg in rainbowfish, but did not affect mosquitofish Vtg protein or mRNA expression. These results suggest that estrogenic activity represents a low risk to fish in most Australian rivers monitored to-date except for some species of fish at the most polluted sites.

Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Dröge, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jørgensen, TS, Shapiro, N, Blood, PD, Gurevich, A, Bai, Y, Turaev, D, DeMaere, MZ, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvočiūtė, M, Hansen, LH, Sørensen, SJ, Chia, BKH, Denis, B, Froula, JL, Wang, Z, Egan, R, Don Kang, D, Cook, JJ, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, SW, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, MD, Lingner, T, Lin, H-H, Liao, Y-C, Silva, GGZ, Cuevas, DA, Edwards, RA, Saha, S, Piro, VC, Renard, BY, Pop, M, Klenk, H-P, Göker, M, Kyrpides, NC, Woyke, T, Vorholt, JA, Schulze-Lefert, P, Rubin, EM, Darling, AE, Rattei, T & McHardy, AC 2017, 'Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software', Nature Methods, vol. 14, no. 11, pp. 1063-1071.
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Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Segečová, A, Červený, J & Roitsch, T 2017, 'Stress Response Monitoring of Photoautotrophic Higher Plant Suspension Cultures by Fluorescence Imaging for High-Throughput Toxic Compound Screening', Journal of Environmental Protection, vol. 08, no. 06, pp. 678-692.
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Seymour, JR, Amin, SA, Raina, J-B & Stocker, R 2017, 'Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships', Nature Microbiology, vol. 2, no. 7, pp. 1-12.
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© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere, is the planktonic analogue of the rhizosphere in plants. The exchange of metabolites and infochemicals at this interface governs phytoplankton-bacteria relationships, which span mutualism, commensalism, antagonism, parasitism and competition. The importance of the phycosphere has been postulated for four decades, yet only recently have new technological and conceptual frameworks made it possible to start teasing apart the complex nature of this unique microbial habitat. It has subsequently become apparent that the chemical exchanges and ecological interactions between phytoplankton and bacteria are far more sophisticated than previously thought and often require close proximity of the two partners, which is facilitated by bacterial colonization of the phycosphere. It is also becoming increasingly clear that while interactions taking place within the phycosphere occur at the scale of individual microorganisms, they exert an ecosystem-scale influence on fundamental processes including nutrient provision and regeneration, primary production, toxin biosynthesis and biogeochemical cycling. Here we review the fundamental physical, chemical and ecological features of the phycosphere, with the goal of delivering a fresh perspective on the nature and importance of phytoplankton-bacteria interactions in aquatic ecosystems.

Sharma, P, Yi, R, Nayak, AP, Wang, N, Tang, F, Knight, MJ, Pan, S, Oliver, B & Deshpande, DA 2017, 'Bitter Taste Receptor Agonists Mitigate Features of Allergic Asthma in Mice.', Scientific reports, vol. 7, pp. 46166-14.
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Asthma is characterized by airway inflammation, mucus secretion, remodeling and hyperresponsiveness (AHR). Recent research has established the bronchodilatory effect of bitter taste receptor (TAS2R) agonists in various models. Comprehensive pre-clinical studies aimed at establishing effectiveness of TAS2R agonists in disease models are lacking. Here we aimed to determine the effect of TAS2R agonists on features of asthma. Further, we elucidated a mechanism by which TAS2R agonists mitigate features of asthma. Asthma was induced in mice using intranasal house dust mite or aerosol ova-albumin challenge, and chloroquine or quinine were tested in both prophylactic and treatment models. Allergen challenge resulted in airway inflammation as evidenced by increased immune cells infiltration and release of cytokines and chemokines in the lungs, which were significantly attenuated in TAS2R agonists treated mice. TAS2R agonists attenuated features of airway remodeling including smooth muscle mass, extracellular matrix deposition and pro-fibrotic signaling, and also prevented mucus accumulation and development of AHR in mice. Mechanistic studies using human neutrophils demonstrated that inhibition of immune cell chemotaxis is a key mechanism by which TAS2R agonists blocked allergic airway inflammation and exerted anti-asthma effects. Our comprehensive studies establish the effectiveness of TAS2R agonists in mitigating multiple features of allergic asthma.

Shi, B, Zheng, M, Tao, W, Chung, R, Jin, D, Ghaffari, D & Farokhzad, OC 2017, 'Challenges in DNA Delivery and Recent Advances in Multifunctional Polymeric DNA Delivery Systems', Biomacromolecules, vol. 18, no. 8, pp. 2231-2246.
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© 2017 American Chemical Society. After more than 20 years of intensive investigations, gene therapy has become one of the most promising strategies for treating genetic diseases. However, the lack of ideal delivery systems has limited the clinical realization of gene therapy's tremendous potential, especially for DNA-based gene therapy. Over the past decade, considerable advances have been made in the application of polymer-based DNA delivery systems for gene therapy, especially through multifunctional systems. The core concept behind multifunctional polymeric DNA delivery systems is to endow one single DNA carrier, via materials engineering and surface modification, with several active functions, e.g., good cargo DNA protection, excellent colloidal stability, high cellular uptake efficiency, efficient endo/lysosome escape, effective import into the nucleus, and DNA unpacking. Such specially developed vectors would be capable of overcoming multiple barriers to the successful delivery of DNA. In this review, we first provide a comprehensive overview of the interactions between the protein corona and DNA vectors, the mechanisms and challenges of nonviral DNA vectors, and important concepts in the design of DNA carriers identified via past reports on DNA delivery systems. Finally, we highlight and discuss recent advances in multifunctional polymeric DNA delivery systems based on 'off-the-shelf' polycations including polyethylenimine (PEI), poly-l-lysine (PLL), and chitosan and offer perspectives on future developments.

Shi, H, Li, L, Eamus, D, Huete, A, Cleverly, J, Tian, X, Yu, Q, Wang, S, Montagnani, L, Magliulo, V, Rotenberg, E, Pavelka, M & Carrara, A 2017, 'Assessing the ability of MODIS EVI to estimate terrestrial ecosystem gross primary production of multiple land cover types', Ecological Indicators, vol. 72, pp. 153-164.
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© 2016 Elsevier Ltd Terrestrial ecosystem gross primary production (GPP) is the largest component in the global carbon cycle. The enhanced vegetation index (EVI) has been proven to be strongly correlated with annual GPP within several biomes. However, the annual GPP-EVI relationship and associated environmental regulations have not yet been comprehensively investigated across biomes at the global scale. Here we explored relationships between annual integrated EVI (iEVI) and annual GPP observed at 155 flux sites, where GPP was predicted with a log-log model: ln(GPP)=a×ln(iEVI)+b. iEVI was computed from MODIS monthly EVI products following removal of values affected by snow or cold temperature and without calculating growing season duration. Through categorisation of flux sites into 12 land cover types, the ability of iEVI to estimate GPP was considerably improved (R2 from 0.62 to 0.74, RMSE from 454.7 to 368.2 g C m−2 yr−1). The biome-specific GPP-iEVI formulae generally showed a consistent performance in comparison to a global benchmarking dataset (R2 = 0.79, RMSE = 387.8 g C m−2 yr−1). Specifically, iEVI performed better in cropland regions with high productivity but poorer in forests. The ability of iEVI in estimating GPP was better in deciduous biomes (except deciduous broadleaf forest) than in evergreen due to the large seasonal signal in iEVI in deciduous biomes. Likewise, GPP estimated from iEVI was in a closer agreement to global benchmarks at mid and high-latitudes, where deciduous biomes are more common and cloud cover has a smaller effect on remote sensing retrievals. Across biomes, a significant and negative correlation (R2 = 0.37, p < 0.05) was observed between the strength (R2) of GPP-iEVI relationships and mean annual maximum leaf area index (LAImax), and the relationship between the strength and mean annual precipitation followed a similar trend. LAImax also revealed a scaling effect on GPP-iEVI relationships. Our results suggest that iEV...

Shilkin, DA, Lyubin, EV, Shcherbakov, MR, Lapine, M & Fedyanin, AA 2017, 'Directional Optical Sorting of Silicon Nanoparticles', ACS Photonics, vol. 4, no. 9, pp. 2312-2319.
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© 2017 American Chemical Society. Optical manipulation of nanoparticles is a topic of great practical importance, with applications in surface science, colloidal chemistry, microfluidics, biochemistry, and medicine. One of the major highlights of this topic is particle sorting, which serves to create monodisperse systems remotely and to separate particles of different composition and size. Here, we analyze optical forces acting on spherical silicon nanoparticles that exhibit high-quality Mie resonances and demonstrate the potential of optical sorting methods for these systems. In particular, we propose multidirectional static sorting of nanoparticles using noncollinear beams with different wavelengths, which results in all-optical separation into an angular spectrum of sizes. We also validate the proposed methods by considering the operation in the presence of Brownian motion and in the evanescent wave configuration.

Shukla, S, Hansbro, P & Walters, H 2017, 'Upregulated pneumococcal adhesion molecule (platelet-activating factor receptor) may predispose COPD patients to community-acquired pneumonia', International Journal of Chronic Obstructive Pulmonary Disease, vol. Volume 12, pp. 3111-3113.
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Shukla, SD, Budden, KF, Neal, R & Hansbro, PM 2017, 'Microbiome effects on immunity, health and disease in the lung', Clinical & Translational Immunology, vol. 6, no. 3, pp. e133-e133.
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Chronic respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF), are among the leading causes of mortality and morbidity worldwide. In the past decade, the interest in the role of microbiome in maintaining lung health and in respiratory diseases has grown exponentially. The advent of sophisticated multiomics techniques has enabled the identification and characterisation of microbiota and their roles in respiratory health and disease. Furthermore, associations between the microbiome of the lung and gut, as well as the immune cells and mediators that may link these two mucosal sites, appear to be important in the pathogenesis of lung conditions. Here we review the recent evidence of the role of normal gastrointestinal and respiratory microbiome in health and how dysbiosis affects chronic pulmonary diseases. The potential implications of host and environmental factors such as age, gender, diet and use of antibiotics on the composition and overall functionality of microbiome are also discussed. We summarise how microbiota may mediate the dynamic process of immune development and/or regulation focusing on recent data from both clinical human studies and translational animal studies. This furthers the understanding of the pathogenesis of chronic pulmonary diseases and may yield novel avenues for the utilisation of microbiota as potential therapeutic interventions.

Sierro, F, Evrard, M, Rizzetto, S, Melino, M, Mitchell, AJ, Florido, M, Beattie, L, Walters, SB, Tay, SS, Lu, B, Holz, LE, Roediger, B, Wong, YC, Warren, A, Ritchie, W, McGuffog, C, Weninger, W, Le Couteur, DG, Ginhoux, F, Britton, WJ, Heath, WR, Saunders, BM, McCaughan, GW, Luciani, F, MacDonald, KPA, Ng, LG, Bowen, DG & Bertolino, P 2017, 'A Liver Capsular Network of Monocyte-Derived Macrophages Restricts Hepatic Dissemination of Intraperitoneal Bacteria by Neutrophil Recruitment', Immunity, vol. 47, no. 2, pp. 374-388.e6.
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© 2017 Elsevier Inc. The liver is positioned at the interface between two routes traversed by pathogens in disseminating infection. Whereas blood-borne pathogens are efficiently cleared in hepatic sinusoids by Kupffer cells (KCs), it is unknown how the liver prevents dissemination of peritoneal pathogens accessing its outer membrane. We report here that the hepatic capsule harbors a contiguous cellular network of liver-resident macrophages phenotypically distinct from KCs. These liver capsular macrophages (LCMs) were replenished in the steady state from blood monocytes, unlike KCs that are embryonically derived and self-renewing. LCM numbers increased after weaning in a microbiota-dependent process. LCMs sensed peritoneal bacteria and promoted neutrophil recruitment to the capsule, and their specific ablation resulted in decreased neutrophil recruitment and increased intrahepatic bacterial burden. Thus, the liver contains two separate and non-overlapping niches occupied by distinct resident macrophage populations mediating immunosurveillance at these two pathogen entry points to the liver.

Smith, CA, Zaslawski, CJ, Cochrane, S, Zhu, X, Zheng, Z, Loyeung, B, Meier, PC, Walsh, S, Xue, CC, Zhang, AL, Fahey, PP & Bensoussan, A 2017, 'Reliability of the NICMAN Scale: An Instrument to Assess the Quality of Acupuncture Administered in Clinical Trials', Evidence-Based Complementary and Alternative Medicine, vol. 2017, pp. 1-8.
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Background. The aim of this study was to examine the reliability of a scale to assess the methodological quality of acupuncture administered in clinical research. Methods. We invited 36 acupuncture researchers and postgraduate students to participate in the study. Firstly, participants rated two articles using the scale. Following this initial stage, modifications were made to scale items and the exercise was repeated. Interrater reliability was assessed for individual items using the Fleiss kappa statistic, whilst the overall scale used the intraclass correlation coefficient statistic. A threshold agreement of ≥0.61 was acceptable. Results. We received 26 responses and a 72% response rate. The first phase of testing found moderate reliability with intraclass correlation coefficients of 0.46 and 0.55 for the articles. The interrater reliability of the scales varied between and within the researchers (0.35, 0.60) and was more consistent with the postgraduate students (0.54, 0.54). Five items on the scale scored below the threshold and were revised for further testing. In this phase the intraclass correlation coefficient demonstrated variability between articles but improved to achieve reliability above the agreed threshold. Conclusion. This study provides evidence of the reliability of the NICMAN scale although improvements to a small number of items remain.

Smith, G & Gentle, A 2017, 'Radiative cooling: Energy savings from the sky', Nature Energy, vol. 2, no. 9, pp. 1-2.
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Environmental heat sinks beyond local air are available for use with normal air conditioners to increase their efficiency. A study has exploited outer space and the atmosphere as remote sinks to demonstrate daytime sub-ambient fluid cooling and its application in reducing the energy needed to cool an interior

Smith, GB, Gentle, AR, Arnold, MD, Gali, MA & Cortie, MB 2017, 'The importance of surface finish to energy performance', Renewable Energy and Environmental Sustainability, vol. 2, pp. 13-13.
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Smith, KF, Kohli, GS, Murray, SA & Rhodes, LL 2017, 'Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities', New Zealand Journal of Marine and Freshwater Research, vol. 51, no. 4, pp. 555-576.
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© 2017 The Royal Society of New Zealand. In this study, we assessed the use of DNA metabarcoding as a method for biodiversity assessment of benthic-epiphytic dinoflagellate communities and for detecting rare, toxin-producing taxa. Mock communities and three primer pairs were used to establish the recovery of species signal and quantitative representation of species in the samples, as well as to determine primer biases, bioinformatic filtering steps, and threshold levels. Samples were analysed using high-throughput sequencing Illumina™ MiSeq technology. We did not find a relationship between read number and cell abundance for all treatments. However, the method was extremely sensitive, with two of the primer pairs detecting a single cell representing less than 0.001% of the cells in the sample. Benthic and epiphytic dinoflagellate communities were also collected from the Bay of Islands (Northland, New Zealand). Dinophyceae species richness was much higher when samples were analysed using metabarcoding than when analysed by microscopy, and we detected several new taxonomic records for New Zealand.

Smith, MJA, de Sterke, CM, Wolff, C, Lapine, M & Poulton, CG 2017, 'Enhanced acousto-optic properties in layered media', Physical Review B, vol. 96, no. 6, pp. 1-10.
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© 2017 American Physical Society. We present a rigorous procedure for evaluating the photoelastic coefficients of a layered medium in which the periodicity is smaller than the wavelengths of all optical and acoustic fields. Analytical expressions are given for the coefficients of a composite material comprising thin layers of optically isotropic materials. These photoelastic coefficients include artificial contributions that are unique to structured media and arise from the optical and mechanical contrast between the constituents. Using numerical examples, we demonstrate that the acousto-optic properties of layered structures can be enhanced beyond those of the constituent materials. Furthermore, we show that the acousto-optic response can be tuned as desired.

Söderström, B & Daley, DO 2017, 'The bacterial divisome: more than a ring?', Current Genetics, vol. 63, no. 2, pp. 161-164.
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Bacterial cells are critically dependent on their ability to divide. The process of division is carried out by a large and highly dynamic molecular machine, known as the divisome. An understanding of the divisomes' architecture is highly sought after, as it is essential for understanding molecular mechanisms and potentially designing antibiotic molecules that curb bacterial growth. Our current view, which is mainly based on high-resolution imaging of Escherichia coli, is that it is a patchy ring or toroid structure. However, recent super-resolution imaging has shown that the toroid structure contains at least three concentric rings, each containing a different set of proteins. Thus, the emerging picture is that the divisome has different functional modules that are spatially separated in concentric rings.

Sohal, SS, Hansbro, PM & Walters, EH 2017, 'Epithelial Mesenchymal Transition in Chronic Obstructive Pulmonary Disease, a Precursor for Epithelial Cancers: Understanding and Translation to Early Therapy', Annals of the American Thoracic Society, vol. 14, no. 9, pp. 1491-1492.
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Human epidemiological studies strongly suggest that patients receiving high-dose inhaled corticosteroids have an appreciable (50%) reduction in the risk for lung cancer (2). [...]in a proof-of-concept randomized controlled trial, we reported that inhaled fluticasone propionate delivered in high doses over the course of 6 months did suppress airway epithelial activation and EMT-related changes in large airways of patients with COPD (3). Inhaled corticosteroids and risk of lung cancer among patients with chronic obstructive pulmonary disease.

Sohal, SS, Hansbro, PM, Shukla, SD, Eapen, MS & Walters, EH 2017, 'Potential Mechanisms of Microbial Pathogens in Idiopathic Interstitial Lung Disease', Chest, vol. 152, no. 4, pp. 899-900.
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Soleymani, S, Aalders, J, Gahan, ME, Ireland, T & McNevin, D 2017, 'Fungal bioreceptivity of Japanese tissue papers treated with plant dyes, watercolours, and acrylic paints in paper conservation', Studies in Conservation, vol. 62, no. 2, pp. 104-113.
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© 2016, © The International Institute for Conservation of Historic and Artistic Works 2016. Despite substantial literature on the dyeing of textiles, there is a lack of research about colouring Japanese mending papers (tissue papers) used for paper conservation purposes. This study investigates the fungal bioreceptivity of Japanese tissue papers after they have been treated with various dyes and pigments. A variety of toning materials including plant dyes, watercolours, acrylic paints, inks, pastels, gouaches, and colour pencils are commonly used by conservators for paper toning purposes. In this study, two Japanese tissue papers (Yukyu-shi and Sekishu Mare) were treated with selected plant dyes, watercolours, and acrylic paints and then inoculated with fungal species. Quantitative real-time pol ymerase chain reaction (qPCR) was used to quantify the DNA from Aspergillus niger and Penicillium rubrum as a proxy for fungal species abundance before and after inoculation and artificial moist heat ageing. qPCR primers which were universal for fungi amplified DNA from papers inoculated with A. niger and P. rubrum and these species were found to grow less on treated Sekishu Mare and Yukyu-shi papers compared with untreated papers. Sekishu Mare papers treated with artists' acrylic paints were found to be more resistant to fungal growth than similarly treated Yukyu-shi papers. This study suggests that for the best long-term preservation outcomes for paper materials in archives, libraries, galleries, and museums, acrylic paints generally perform better in conservation terms than most plant dyes and watercolours, although most colourants displayed some bioinhibition.

Soleymani, S, Ireland, T & McNevin, D 2017, 'Influence of acidity on the mechanical stability of retouched Japanese tissue papers during the course of artificial ageing', AICCM Bulletin, vol. 38, no. 1, pp. 3-14.
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Solntsev, AS & Sukhorukov, AA 2017, 'Path-entangled photon sources on nonlinear chips', Reviews in Physics, vol. 2, pp. 19-31.
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© 2016 The Authors Photon entanglement has a range of applications from secure communication to the tests of quantum mechanics. Utilizing optical nonlinearity for the generation of entangled photons remains the most widely used approach due to its quality and simplicity. The on-chip integration of entangled light sources has enabled the increase of complexity and enhancement of stability compared to bulk optical implementations. Entanglement over different optical paths is uniquely suited for photonic chips, since waveguides are typically optimized for particular wavelength and polarization, making polarization- and frequency-entanglement less practical. In this review we focus on the latest developments in the field of on-chip nonlinear path-entangled photon sources. We provide a review of recent implementations and compare various approaches to tunability, including thermo-optical, electro-optical and all-optical tuning. We also discuss a range of important technical issues, in particular the on-chip separation of the pump and generated entangled photons. Finally, we review different quality control methods, including on-chip quantum tomography and recently discovered classical-quantum analogy that allows to characterize entangled photon sources by performing simple nonlinear measurements in the classical regime.

Solntsev, AS, Liu, T, Boes, A, Nguyen, TG, Wu, CW, Setzpfandt, F, Mitchell, A, Neshev, DN & Sukhorukov, AA 2017, 'Towards on-chip photon-pair bell tests: Spatial pump filtering in a LiNbO3 adiabatic coupler', Applied Physics Letters, vol. 111, no. 26, pp. 261108-261108.
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Nonlinear optical waveguides enable the integration of entangled photon sources and quantum logic gates on a quantum photonic chip. One of the major challenges in such systems is separating the generated entangled photons from the pump laser light. In this work, we experimentally characterize double-N-shaped nonlinear optical adiabatic couplers designed for the generation of spatially entangled photon pairs through spontaneous parametric down-conversion, while simultaneously providing spatial pump filtering and keeping photon-pair states pure. We observe that the pump photons at a wavelength of 671 nm mostly remain in the central waveguide, achieving a filtering ratio of over 20 dB at the outer waveguides. We also perform classical characterization at the photon-pair wavelength of 1342 nm and observe that light fully couples from an input central waveguide to the outer waveguides, showing on chip separation of the pump and the photon-pair wavelength.

Song, W, Lin, G, Ge, J, Fassbender, J & Makarov, D 2017, 'Encoding Microreactors with Droplet Chains in Microfluidics', ACS Sensors, vol. 2, no. 12, pp. 1839-1846.
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© 2017 American Chemical Society. Droplet-based high throughput biomolecular screening and combinatorial synthesis entail a viable indexing strategy to be developed for the identification of each microreactor. Here, we propose a novel indexing scheme based on the generation of droplet sequences on demand to form unique encoding droplet chains in fluidic networks. These codes are represented by multiunit and multilevel droplets packages, with each code unit possessing several distinct signal levels, potentially allowing large encoding capacity. For proof of concept, we use magnetic nanoparticles as the encoding material and a giant magnetoresistance (GMR) sensor-based active sorting system supplemented with an optical detector to generate and decode the sequence of one exemplar sample droplet reactor and a 4-unit quaternary magnetic code. The indexing capacity offered by 4-unit multilevel codes with this indexing strategy is estimated to exceed 104, which holds great promise for large-scale droplet-based screening and synthesis.

Soni, N, Tekade, M, Kesharwani, P, Bhattacharya, P, Maheshwari, R, Dua, K, Hansbro, PM & Tekade, RK 2017, 'Recent Advances in Oncological Submissions of Dendrimer', Current Pharmaceutical Design, vol. 23, no. 21, pp. 3084-3098.
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© 2017 Bentham Science Publishers. Background: Disseminated metastatic cancer requires insistent management owing to its reduced responsiveness for chemotherapeutic agents, toxicity to normal cells consequently lower survival rate and hampered quality of life of patients. Methods: Dendrimer mediated cancer therapy is advantageous over conventional chemotherapy, radiotherapy and surgical resection due to reduced systemic toxicity, and molecular level cell injury to cancerous mass, for an appreciable survival of the subject. Recently used dendrimer mediated nanotechnology for oncology aims to conquer these challenges. Dendrimers based nano-constructs are having architectures comparable to that of biological vesicles present in the human body. Results: Operating with dendrimer technology, proffers the exclusive and novel strategies with numerous applications in cancer management involving diagnostics, therapeutics, imaging, and prognostics by sub-molecular interactions. Dendrimers are designed to acquire the benefits of the malignant tumor morphology and characteristics, i.e. leaky vasculature of tumor, expression of specific cell surface antigen, and rapid proliferation. Conclusion: Dendrimers mediated targeted therapy recommends innovatory function equally in diagnostics (imaging, immune-detection) as well as chemotherapy. Currently, dendrimers as nanomedicine has offered a strong assurance and advancement in drastically varying approaches towards cancer imaging and treatment. The present review discusses different approaches for cancer diagnosis and treatment such as, targeted and control therapy, photodynamic therapy, photo-thermal therapy, gene therapy, antiangiogenics therapy, radiotherapy etc.

Sontheimer, B, Braun, M, Nikolay, N, Sadzak, N, Aharonovich, I & Benson, O 2017, 'Photodynamics of quantum emitters in hexagonal boron nitride revealed by low temperature spectroscopy', Phys. Rev. B, vol. 96, no. 12, pp. 121202-5.
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Quantum emitters in hexagonal boron nitride (hBN) have recently emerged aspromising bright single photon sources. In this letter we investigate indetails their optical properties at cryogenic temperatures. In particular, weperform temperature resolved photoluminescence studies and measure photoncoherence times from the hBN emitters. The obtained value of 81(1) pstranslates to a width of $\sim$12 GHz which is higher than the Fouriertransform limited value of $\sim$32 MHz. To account for the photodynamics ofthe emitter, we perform ultrafast spectral diffusion measurements thatpartially account for the coherence times. Our results provide importantinsight into the relaxation processes in quantum emitters in hBN which ismandatory to evaluate their applicability for quantum information processing.

Srivastava, A, Sahoo, B, Raghuwanshi, NS & Singh, R 2017, 'Evaluation of Variable-Infiltration Capacity Model and MODIS-Terra Satellite-Derived Grid-Scale Evapotranspiration Estimates in a River Basin with Tropical Monsoon-Type Climatology', Journal of Irrigation and Drainage Engineering, vol. 143, no. 8, pp. 1-16.
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With the limited availability of meteorological variables in many remote areas, estimation of evapotranspiration (ET) at different spatiotemporal scales for efficient irrigation water management and hydrometeorological studies is becoming a challenging task. Hence, in this study, indirect ET estimation methods, such as moderate resolution imaging spectroradiometer (MODIS) satellite-based remote-sensing techniques and the water-budget approach built into the semidistributed variable infiltration capacity (VIC-3L) land-surface model are evaluated using the Penman-Monteith (PM) equation approach suggested in the literature together with a crop coefficient approach. To answer the research question of whether regional or local controls of a river basin with tropical monsoon-type climatology affect the accuracy of the VIC and MODIS-based ET estimates, these methodologies are applied in the Kangsabati River Basin in eastern India at 25 × 25 km resolutions attributed with dominant paddy land uses. The results reveal that the VIC-estimated ET values are reasonably matched with the PM-based ET estimates with the Nash-Sutcliffe efficiency (NSE) of 54.14-71.94%; however, the corresponding MODIS-ET values are highly underestimated with a periodic shift that may be attributed to the cloud cover and leaf shadowing effects. To enhance the field applicability of the satellite-based MODIS-ET products, these estimates are standardized by using a genetic-algorithm-based transformation that improves the NSE from -390.83 to 99.57%. Hence, this study reveals that there is the need of a regional-scale standardization of the MODIS-ET products using the PM or lysimeter data or possible modification of the MOD16A2 algorithm built-into the MODIS for generalization. Conversely, the satisfactory grid-scale ET estimates by the VIC model show that this model could be reliably used for the world's river basins; however, at smaller temporal scales, the estimates could be slightly inconsistent.

Stalder, O, Asher, A, Liang, L, Carroll, RJ, Ma, Y & Chatterjee, N 2017, 'Semiparametric analysis of complex polygenic gene-environment interactions in case-control studies', Biometrika, vol. 104, no. 4, pp. 801-812.
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Many methods have recently been proposed for efficient analysis of case-control studies of gene-environment interactions using a retrospective likelihood framework that exploits the natural assumption of gene-environment independence in the underlying population. However, for polygenic modelling of gene-environment interactions, which is a topic of increasing scientific interest, applications of retrospective methods have been limited due to a requirement in the literature for parametric modelling of the distribution of the genetic factors. We propose a general, computationally simple, semiparametric method for analysis of case-control studies that allows exploitation of the assumption of gene-environment independence without any further parametric modelling assumptions about the marginal distributions of any of the two sets of factors. The method relies on the key observation that an underlying efficient profile likelihood depends on the distribution of genetic factors only through certain expectation terms that can be evaluated empirically. We develop asymptotic inferential theory for the estimator and evaluate its numerical performance via simulation studies. An application of the method is presented.

Startsev, MA, Ostrowski, M, Goldys, EM & Inglis, DW 2017, 'A mobility shift assay for DNA detection using nanochannel gradient electrophoresis', ELECTROPHORESIS, vol. 38, no. 2, pp. 335-341.
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Conventional detection of pathogenic or other biological contamination relies on amplification of DNA using sequence‐specific primers. Recent work in nanofluidics has shown very high concentration enhancement of biomolecules with some degree of simultaneous separation. This work demonstrates the combination of these two approaches by selectively concentrating a mobility‐shifted hybridization product, potentially enabling rapid detection of rare DNA fragments such as highly specific 16S ribosomal DNA. We have performed conductivity gradient electrofocusing within nanofluidic channels and have shown concentration of hybridized peptide nucleic acids and DNA oligomers. We also show selectivity to single base‐pair mismatch on 18‐mer oligos. This approach may enable sensitive optical detection of small amounts of DNA.

Stelzer‐Braid, S, Liu, N, Doumit, M, D'Cunha, R, Belessis, Y, Jaffe, A & Rawlinson, WD 2017, 'Association of rhinovirus with exacerbations in young children affected by cystic fibrosis: Preliminary data', Journal of Medical Virology, vol. 89, no. 8, pp. 1494-1497.
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Rhinovirus (RV) is a common respiratory viral infection linked to worsening of chronic respiratory diseases including cystic fibrosis (CF) and asthma. RV was tested by RT‐PCR in samples (n = 465) collected from the upper (nasal swab, oropharyngeal suction, and sputum) and lower (bronchoalveolar washings) respiratory tract of 110 children with CF. Air samples (n = 52) collected from the operating theatres and outpatient clinics were tested for RV. RV was found in 43% of children <5 years suffering an exacerbation, and 12% of older children (5‐17 years). RV particles were detected in the air of clinic rooms. Detection of RV is important in better understanding viral infections in patients with CF.

Stevens, BJ, Hare, DJ, Volitakis, I, Cherny, RA & Roberts, BR 2017, 'Direct determination of zinc in plasma by graphite furnace atomic absorption spectrometry using palladium/magnesium and EDTA matrix modification with high temperature pyrolysis', Journal of Analytical Atomic Spectrometry, vol. 32, no. 4, pp. 843-847.
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A new graphite furnace atomic absorption spectrometry method is presented for the analysis of zinc in small volume biological samples.

Stevens, RL, McNeil, HP, Wensing, LA, Shin, K, Wong, GW, Hansbro, PM & Krilis, SA 2017, 'Experimental Arthritis Is Dependent on Mouse Mast Cell Protease-5', Journal of Biological Chemistry, vol. 292, no. 13, pp. 5392-5404.
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© 2017 by The American Society for Biochemistry and Molecular Biology, Inc. The constitutive heparin+ (HP) mast cells (MCs) in mice express mouseMCprotease (mMCP)-5 and carboxypeptidaseA (mMC-CPA). The amino acid sequence ofmMCP-5is most similar to that of human chymase-1, as are the nucleotide sequences of their genes and transcripts. Using a homologous recombination approach, a C57BL/6 mouse line was created that possessed a disrupted mMCP-5 gene. The resulting mice were fertile and had no obvious developmental abnormality. Lack of mMCP-5 protein did not alter the granulation of the IL-3/IL-9-dependent mMCP-2+ MCs in the jejunal mucosa of Trichinella spiralisinfected mice. In contrast, the constitutive HP+ MCs in the tongues of mMCP-5-null mice were poorly granulated and lacked mMC-CPA protein. Bone marrow-derived MCs were readily developed from the transgenic mice using IL-3. Although these MCs contained high levels of mMC-CPA mRNA, they also lacked the latter exopeptidase. mMCP-5 protein is therefore needed to target translated mMC-CPA to the secretory granule along with HP-containing serglycin proteoglycans. Alternately, mMCP-5 is needed to protect mMC-CPA from autolysis in the cell's granules. Fibronectin was identified as a target of mMCP-5, and the exocytosis ofmMCP-5from theMCs in the mouse's peritoneal cavity resulted in the expression of metalloproteinase protease-9, which has been implicated in arthritis. In support of the latter finding, experimental arthritis was markedly reduced in mMCP-5-null mice relative to wildtype mice in two disease models.

Stroud, LJ, Šlapeta, J, Padula, MP, Druery, D, Tsiotsioras, G, Coorssen, JR & Stack, CM 2017, 'Comparative proteomic analysis of two pathogenic Tritrichomonas foetus genotypes: there is more to the proteome than meets the eye', International Journal for Parasitology, vol. 47, no. 4, pp. 203-213.
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© 2017 Australian Society for Parasitology Certain clinical isolates of Tritrichomonas foetus infect the urogenital tract of cattle while others infect the gastrointestinal tract of cats. Previous studies have identified subtle genetic differences between these isolates with the term “genotype” adopted to reflect host origin. The aim of this work was to seek evidence of host-specific adaptation and to clarify the relationship between T. foetus genotypes. To do this we characterised the proteomes of both genotypes using two-dimensional gel electrophoresis (2DE) coupled with LC-MS/MS. Our comparative analysis of the data revealed that both genotypes exhibited largely similar proteoform profiles; however differentiation was possible with 24 spots identified as having a four-fold or greater change. Deeper analysis using 2DE zymography and protease-specific fluorogenic substrates revealed marked differences in cysteine protease (CP) expression profiles between the two genotypes. These variances in CP activities could also account for the pathogenic and histopathological differences previously observed between T. foetus genotypes in cross-infection studies. Our findings highlight the importance of CPs as major determinants of parasite virulence and provide a foundation for future host-parasite interaction studies, with direct implications for the development of vaccines or drugs targeting T. foetus.

Stützer, S, Solntsev, AS, Nolte, S, Sukhorukov, AA & Szameit, A 2017, 'Observation of Bloch oscillations with a threshold', APL Photonics, vol. 2, no. 5, pp. 1-7.
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We demonstrate experimentally Bloch oscillations, which occur above a certain threshold value of the effective potential gradient in lattices with specially modulated coupling between the neighboring sites. We formulate the general conditions for this phenomenon, arising due to the competition between the tilting and broadening of the transmission band, and explain why no threshold was present in any previous observations. Our experiments are performed in inhomogeneous photonic lattices, which represent the process of quantum two-mode squeezing in Fock space, underpinning a fundamental quantum-classical correspondence.

Su, D, Cortie, M & Wang, G 2017, 'Fabrication of N‐doped Graphene–Carbon Nanotube Hybrids from Prussian Blue for Lithium–Sulfur Batteries', Advanced Energy Materials, vol. 7, no. 8, pp. 1602014-1602014.
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Hybrid nanostructures containing 1D carbon nanotubes and 2D graphene sheets have many promising applications due to their unique physical and chemical properties. In this study, the authors find Prussian blue (dehydrated sodium ferrocyanide) can be converted to N‐doped graphene–carbon nanotube hybrid materials through a simple one‐step pyrolysis process. Through field emission scanning electron microscopy, transmission electron microscopy, X‐ray diffraction, Raman spectra, atomic force microscopy, and isothermal analyses, the authors identify that 2D graphene and 1D carbon nanotubes are bonded seamlessly during the growth stage. When used as the sulfur scaffold for lithium–sulfur batteries, it demonstrates outstanding electrochemical performance, including a high reversible capacity (1221 mA h g−1 at 0.2 C rate), excellent rate capability (458 and 220 mA h g−1 at 5 and 10 C rates, respectively), and excellent cycling stability (321 and 164 mA h g−1 at 5 and 10 C (1 C = 1673 mA g−1) after 1000 cycles). The enhancement of electrochemical performance can be attributed to the 3D architecture of the hybrid material, in which, additionally, the nitrogen doping generates defects and active sites for improved interfacial adsorption. Furthermore, the nitrogen doping enables the effective trapping of lithium polysulfides on electroactive sites within the cathode, leading to a much‐improved cycling performance. Therefore, the hybrid material functions as a redox shuttle to catenate and bind polysulfides, and convert them to insoluble lithium sulfide during reduction. The strategy reported in this paper could open a new avenue for low cost synthesis of N‐doped graphene–carbon nanotube hybrid materials for high performance lithium–sulfur batteries.

Su, D, Cortie, M, Fan, H & Wang, G 2017, 'Prussian Blue Nanocubes with an Open Framework Structure Coated with PEDOT as High‐Capacity Cathodes for Lithium–Sulfur Batteries', Advanced Materials, vol. 29, no. 48, pp. 1700587-1700587.
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AbstractIt is shown that Prussian blue analogues (PBAs) can be a very competitive sulfur host for lithium–sulfur (Li–S) batteries. Sulfur stored in the large interstitial sites of a PBA host can take advantage of reversible and efficient insertion/extraction of both Li+ and electrons, due to the well‐trapped mobile dielectron redox centers in the well‐defined host. It is demonstrated that Na2Fe[Fe(CN)6] has a large open framework, and as a cathode, it both stores sulfur and acts as a polysulfide diffusion inhibitor based on the Lewis acid–base bonding effect. The electrochemical testing shows that the S@Na2Fe[Fe(CN)6]@poly(3,4‐ethylenedioxythiophene) composite achieves excellent reversibility, good stability, and fast kinetics. Its outstanding electrochemical properties should be ascribed to the internal transport of Li+/e−, maximizing the utilization of sulfur. Moreover, the open metal centers serve as the Lewis acid sites with high affinity to the negatively charged polysulfide anions, reducing the diffusion of polysulfides out of the cathode and minimizing the shuttling effect. The fundamental basis of these exceptional performance characteristics is explored through a detailed analysis of the structural and electrochemical behavior of the material. It is believed that the PBAs will have a useful role in ensuring more effective and stable Li–S batteries.

Su, D, McDonagh, A, Qiao, S & Wang, G 2017, 'High‐Capacity Aqueous Potassium‐Ion Batteries for Large‐Scale Energy Storage', Advanced Materials, vol. 29, no. 1, pp. 1604007-1604007.
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The synthesis of high-potassium-ion-content potassium iron (II) hexacyanoferrate dehydrate nanocubes and their performance as electrodes in aqueous electrolyte potassium-ion batteries were reported. To maintain a uniform size distribution, surfactants such as poly(vinylpyrrolidone) have been used. Here, we found that changing the solvent from water to ethylene glycol, which is also a mild reducing agent, gave uniform particle size and maintained the iron in the divalent state. Uniform potassium iron hexacyanoferrate dehydrate nanocubes with an edge length of =200 nm were obtained using a solvothermal method at 80°C. For comparison, when water was used as a solvent, potassium iron hexacyanoferrate dihydrate with a large particle size distribution was obtained. Rietveld-refined XRD was used to identify the crystal structure of the as-prepared potassium iron hexacyanoferrate. The results show that the particles have an orthorhombic symmetry structure with the Pmn21 space group.

Suggett, DJ, Warner, ME & Leggat, W 2017, 'Symbiotic Dinoflagellate Functional Diversity Mediates Coral Survival under Ecological Crisis', Trends in Ecology & Evolution, vol. 32, no. 10, pp. 735-745.
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© 2017 Elsevier Ltd Coral reefs have entered an era of ‘ecological crisis’ as climate change drives catastrophic reef loss worldwide. Coral growth and stress susceptibility are regulated by their endosymbiotic dinoflagellates (genus Symbiodinium). The phylogenetic diversity of Symbiodinium frequently corresponds to patterns of coral health and survival, but knowledge of functional diversity is ultimately necessary to reconcile broader ecological success over space and time. We explore here functional traits underpinning the complex biology of Symbiodinium that spans free-living algae to coral endosymbionts. In doing so we propose a mechanistic framework integrating the primary traits of resource acquisition and utilisation as a means to explain Symbiodinium functional diversity and to resolve the role of Symbiodinium in driving the stability of coral reefs under an uncertain future. Coral ecosystem health is strongly influenced by Symbiodinium diversity. The ecological success of Symbiodinium cannot be resolved from phylogenetic diversity alone. Traits describing resource acquisition and incorporation capture the functional diversity of Symbiodinium. Symbiodinium species shifts reflect the changing metabolic requirements of the host. Functional diversity will determine the resilience of coral reefs to environmental change.

Sukačová, K & Červený, J 2017, 'Can algal biotechnology bring effective solution for closing the phosphorus cycle? Use of algae for nutrient removal: Review of past trends and future perspectives in the context of nutrient recovery', EUROPEAN JOURNAL OF ENVIRONMENTAL SCIENCES, vol. 7, no. 1, pp. 63-72.
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© 2017 The Author. Eutrophication of water by nutrient pollution is a global environmental issue. Biological methods for removing nutrients are environmentally friendly and sustainable. Therefore, this article summarizes main trends in the use of algae for removing nutrients from wastewater using both suspended and attached algal-based systems. A wide variety of algal species and experimental approaches has been tested to date. Researchers report that algae are able to effectively remove a variety of pollutants and nutrients. This review also discusses the potential of algal-based technology for nutrient, especially phosphorus, recovery. Despite the fact that effective nutrient removal has been demonstrated, there are still many challenges to be overcome in the development of succesfull technologies.

Sukjamnong, S, Chan, YL, Zakarya, R, Saad, S, Sharma, P, Santiyanont, R, Chen, H & Oliver, BG 2017, 'Effect of long-term maternal smoking on the offspring’s lung health', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 313, no. 2, pp. L416-L423.
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Maternal smoking during pregnancy contributes to long-term health problems in offspring, especially respiratory disorders that can manifest in either childhood or adulthood. Receptors for advanced glycation end products (RAGE) are multiligand receptors abundantly localized in the lung, capable of responding to by-products of reactive oxygen species and proinflammatory responses. RAGE signaling is a key regulator of inflammation in cigarette smoking-related pulmonary diseases. However, the impact of maternal cigarette smoke exposure on lung RAGE signaling in the offspring is unclear. This study aims to investigate the effect of maternal cigarette smoke exposure (SE), as well as mitochondria-targeted antioxidant [mitoquinone mesylate (MitoQ)] treatment, during pregnancy on the RAGE-mediated signaling pathway in the lung of male offspring. Female Balb/c mice (8 wk) were divided into a sham group (exposed to air), an SE group (exposed to cigarette smoke), and an SE + MQ group (exposed to cigarette smoke with MitoQ supplement from mating). The lungs from male offspring were collected at 13 wk. RAGE and its downstream signaling, including nuclear factor-κB and mitogen-activated protein kinase family consisting of extracellular signal-regulated kinase 1, ERK2, c-JUN NH2-terminal kinase (JNK), and phosphorylated JNK, in the lung were significantly increased in the SE offspring. Mitochondrial antioxidant manganese superoxide dismutase was reduced, whereas IL-1β and oxidative stress response nuclear factor (erythroid-derived 2)-like 2 were significantly increased in the SE offspring. Maternal MitoQ treatment normalized RAGE, IL-1β, and Nrf-2 levels in the SE + MQ offspring. Maternal SE increased RAGE and its signaling elements associated with increased oxidative stress and inflammatory cytokines in offspring lungs, whereas maternal MitoQ treatment can partially normalize these changes.

Sun, B, Kretschmer, K, Xie, X, Munroe, P, Peng, Z & Wang, G 2017, 'Hierarchical Porous Carbon Spheres for High‐Performance Na–O₂ Batteries', Advanced Materials, vol. 29, no. 48, pp. 1606816-1606816.
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AbstractAs a new family member of room‐temperature aprotic metal–O2 batteries, Na–O2 batteries, are attracting growing attention because of their relatively high theoretical specific energy and particularly their uncompromised round‐trip efficiency. Here, a hierarchical porous carbon sphere (PCS) electrode that has outstanding properties to realize Na–O2 batteries with excellent electrochemical performances is reported. The controlled porosity of the PCS electrode, with macropores formed between PCSs and nanopores inside each PCS, enables effective formation/decomposition of NaO2 by facilitating the electrolyte impregnation and oxygen diffusion to the inner part of the oxygen electrode. In addition, the discharge product of NaO2 is deposited on the surface of individual PCSs with an unusual conformal film‐like morphology, which can be more easily decomposed than the commonly observed microsized NaO2 cubes in Na–O2 batteries. A combination of coulometry, X‐ray diffraction, and in situ differential electrochemical mass spectrometry provides compelling evidence that the operation of the PCS‐based Na–O2 battery is underpinned by the formation and decomposition of NaO2. This work demonstrates that employing nanostructured carbon materials to control the porosity, pore‐size distribution of the oxygen electrodes, and the morphology of the discharged NaO2 is a promising strategy to develop high‐performance Na–O2 batteries.

Sundaraneedi, MK, Ammit, AJ, Tedla, BA, Pearson, MS, Loukas, A, Keene, FR & Collins, JG 2017, 'Tetranuclear Polypyridylruthenium(II) Complexes as Inhibitors and Down‐Regulators of Phosphatase Enzymes', ChemistrySelect, vol. 2, no. 33, pp. 10668-10672.
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AbstractMitogen‐activated protein kinase phosphatases (MKPs) are over‐expressed in many cancers. The increased levels of MKP enzymes protect cells from apoptosis induced by anticancer drugs, and thereby decrease the efficacy of the drug. Consequently, there is considerable interest in the development of agents that can down‐regulate the production of the MKP enzymes or inhibit their catalytic activities. We have examined the ability of a series of oligonuclear polypyridylruthenium(II) complexes to inhibit the activity of MKP‐1 and MKP‐3. The results demonstrated that two tetranuclear complexes inhibit the activity of MKP‐1 and MKP‐3 at 10‐20 μM concentrations. The ability of the ruthenium complexes to inhibit the production of MKP‐1 in live cancer cells was demonstrated through Western blotting assays, while real‐time reverse transcription polymerase chain reaction assays demonstrated the tetranuclear complexes decreased the amount of mkp‐1 mRNA produced in cancer cells. The results of this study suggest that tetranuclear ruthenium complexes could be used to enhance the antiproliferative effect of anticancer drugs.

Sutherland, TC, Mathews, KJ, Mao, Y, Nguyen, T & Gorrie, CA 2017, 'Differences in the Cellular Response to Acute Spinal Cord Injury between Developing and Mature Rats Highlights the Potential Significance of the Inflammatory Response', Frontiers in Cellular Neuroscience, vol. 10, pp. 1-18.
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© 2017 Sutherland, Mathews, Mao, Nguyen and Gorrie. There exists a trend for a better functional recovery from spinal cord injury (SCI) in younger patients compared to adults, which is also reported for animal studies; however, the reasons for this are yet to be elucidated. The post injury tissue microenvironment is a complex milieu of cells and signals that interact on multiple levels. Inflammation has been shown to play a significant role in this post injury microenvironment. Endogenous neural progenitor cells (NPC), in the ependymal layer of the central canal, have also been shown to respond and migrate to the lesion site. This study used a mild contusion injury model to compare adult (9 week), juvenile (5 week) and infant (P7) Sprague-Dawley rats at 24 h, 1, 2, and 6 weeks post-injury (n = 108). The innate cells of the inflammatory response were examined using counts of ED1/IBA1 labeled cells. This found a decreased inflammatory response in the infants, compared to the adult and juvenile animals, demonstrated by a decreased neutrophil infiltration and macrophage and microglial activation at all 4 time points. Two other prominent cellular contributors to the post-injury microenvironment, the reactive astrocytes, which eventually form the glial scar, and the NPC were quantitated using GFAP and Nestin immunohistochemistry. After SCI in all 3 ages there was an obvious increase in Nestin staining in the ependymal layer, with long basal processes extending into the parenchyma. This was consistent between age groups early post injury then deviated at 2 weeks. The GFAP results also showed stark differences between the mature and infant animals. These results point to significant differences in the inflammatory response between infants and adults that may contribute to the better recovery indicated by other researchers, as well as differences in the overall injury progression and cellular responses. This may have important consequences if we are able to mirr...

Szabó, M, Larkum, AWD, Suggett, DJ, Vass, I, Sass, L, Osmond, B, Zavafer, A, Ralph, PJ & Chow, WS 2017, 'Non-intrusive Assessment of Photosystem II and Photosystem I in Whole Coral Tissues', Frontiers in Marine Science, vol. 4, no. AUG, pp. 1-12.
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© 2017 Szabó, Larkum, Suggett, Vass, Sass, Osmond, Zavafer, Ralph and Chow. Reef building corals (phylum Cnidaria) harbor endosymbiotic dinoflagellate algae (genus Symbiodinium) that generate photosynthetic products to fuel their host's metabolism. Non-invasive techniques such as chlorophyll (Chl) fluorescence analyses of Photosystem II (PSII) have been widely used to estimate the photosynthetic performance of Symbiodinium in hospite. However, since the spatial origin of PSII chlorophyll fluorescence in coral tissues is uncertain, such signals give limited information on depth-integrated photosynthetic performance of the whole tissue. In contrast, detection of absorbance changes in the near infrared (NIR) region integrates signals from deeper tissue layers due to weak absorption and multiple scattering of NIR light. While extensively utilized in higher plants, NIR bio-optical techniques are seldom applied to corals. We have developed a non-intrusive measurement method to examine photochemistry of intact corals, based on redox kinetics of the primary electron donor in Photosystem I (P700) and chlorophyll fluorescence kinetics (Fast-Repetition Rate fluorometry, FRRf). Since the redox state of P700 depends on the operation of both PSI and PSII, important information can be obtained on the PSII-PSI intersystem electron transfer kinetics. Under moderate, sub-lethal heat stress treatments (33◦ C for~20 min), the coral Pavona decussata exhibited down-regulation of PSII electron transfer kinetics, indicated by slower rates of electron transport from QA to plastoquinone (PQ) pool, and smaller relative size of oxidized PQ with concomitant decrease of a specifically-defined P700 kinetics area, which represents the active pool of PSII. The maximum quantum efficiency of PSII (Fv /Fm ) and functional absorption cross-section of PSII (σPSII ) remained unchanged. Based on the coordinated response of P700 parameters and PSII-PSI electron transport properties, we propose...

Szychlinska, M, Yamakado, K, Castorina, A & Ljubisavljevic, M 2017, 'The “Journal of Functional Morphology and Kinesiology” Journal Club Series: Highlights on Recent Papers in Musculoskeletal Disorders', Journal of Functional Morphology and Kinesiology, vol. 2, no. 2, pp. 10-10.
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Tabassum, H, Guo, W, Meng, W, Mahmood, A, Zhao, R, Wang, Q & Zou, R 2017, 'Hydrogen Evolution: Metal–Organic Frameworks Derived Cobalt Phosphide Architecture Encapsulated into B/N Co‐Doped Graphene Nanotubes for All pH Value Electrochemical Hydrogen Evolution (Adv. Energy Mater. 9/2017)', Advanced Energy Materials, vol. 7, no. 9.
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Tabassum, H, Guo, W, Meng, W, Mahmood, A, Zhao, R, Wang, Q & Zou, R 2017, 'Metal–Organic Frameworks Derived Cobalt Phosphide Architecture Encapsulated into B/N Co‐Doped Graphene Nanotubes for All pH Value Electrochemical Hydrogen Evolution', Advanced Energy Materials, vol. 7, no. 9, pp. 1601671-1601671.
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Tabassum, H, Mahmood, A, Wang, Q, Xia, W, Liang, Z, Qiu, B, zhao, R & Zou, R 2017, 'Hierarchical Cobalt Hydroxide and B/N Co-Doped Graphene Nanohybrids Derived from Metal-Organic Frameworks for High Energy Density Asymmetric Supercapacitors', Scientific Reports, vol. 7, no. 1.
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AbstractTo cater for the demands of electrochemical energy storage system, the development of cost effective, durable and highly efficient electrode materials is desired. Here, a novel electrode material based on redox active β-Co(OH)2 and B, N co-doped graphene nanohybrid is presented for electrochemical supercapacitor by employing a facile metal-organic frameworks (MOFs) route through pyrolysis and hydrothermal treatment. The Co(OH)2 could be firmly stabilized by dual protection of N-doped carbon polyhedron (CP) and B/N co-doped graphene (BCN) nanosheets. Interestingly, the porous carbon and BCN nanosheets greatly improve the charge storage, wettability, and redox activity of electrodes. Thus the hybrid delivers specific capacitance of 1263 F g−1 at a current density of 1A g−1 with 90% capacitance retention over 5000 cycles. Furthermore, the new aqueous asymmetric supercapacitor (ASC) was also designed by using Co(OH)2@CP@BCN nanohybrid and BCN nanosheets as positive and negative electrodes respectively, which leads to high energy density of 20.25 Whkg−1. This device also exhibits excellent rate capability with energy density of 15.55 Whkg−1 at power density of 9331 Wkg−1 coupled long termed stability up to 6000 cycles.

Tachapermpon, Y, Maniam, S, Wanichacheva, N & Langford, SJ 2017, 'New Di‐, Tri‐, and Tetra‐Core‐Functionalized Naphthalene Diimides from Reactions of Allyl Ethers with Lewis Acids', Asian Journal of Organic Chemistry, vol. 6, no. 1, pp. 47-53.
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AbstractCore‐substituted NDIs bearing aryl allyl ethers have a predisposition to deallylation in the presence of Lewis Acids (LA). However, under certain conditions, with appropriate choice of LA, the reaction can be controlled to yield unexpected and highly functionalized dinaphthol systems through a [3,3]‐sigmatropic (Claisen) rearrangement. The major products of the rearrangement study have been characterized by X‐ray crystallographic analysis and the per‐substituted products are shown to undergo ring‐closing metathesis to form heterocyclic core‐extended NDIs. This study highlights a simple method to construct a series of important donor–acceptor building blocks for the preparation of new conjugated materials.

Tam, R, Heather, E, Shimmon, R, Lam, B & McDonagh, AM 2017, 'Synthesis and organic impurity profiling of 4-methoxymethamphetamine hydrochloride and its precursors', Forensic Science International, vol. 272, pp. 184-189.
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© 2016 Elsevier Ireland Ltd 4-Methoxymethamphetamine (PMMA) was synthesised from star anise and from 4-methoxytoluene and the organic impurity profiles examined. These two starting materials are unrestricted chemicals in many jurisdictions and contain the requisite functional groups and are thus well suited for clandestine manufacturers. trans-Anethole was extracted from star anise and oxidised to 4-methoxyphenyl-2-propanone (PMP2P). 4-Methoxytoluene was oxidised to anisaldehyde, converted to 4-methoxyphenyl-2-nitropropene, and then reduced to PMP2P. The PMP2P obtained by both methods was then converted to PMMA via the Leuckart reaction. 4-Methoxymethamphetamine hydrochloride (PMMA·HCl) was synthesised from PMMA using hydrogen chloride gas. Both of the examined synthetic methods were found to be feasible routes into PMMA·HCl. The products of each step were analysed by gas chromatography–mass spectrometry (GC–MS) and proton nuclear magnetic resonance spectroscopy (1H NMR). Impurities were examined in an attempt to identify route specific compounds, which may provide valuable information about the synthetic pathway and precursors.

Tan, CH, Lee, KWK, Burmølle, M, Kjelleberg, S & Rice, SA 2017, 'All together now: experimental multispecies biofilm model systems', Environmental Microbiology, vol. 19, no. 1, pp. 42-53.
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SummaryStudies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta‐omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community‐based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.

Tan, Y, Kim, J, Cheng, J, Ong, M, Lao, W-G, Jin, X-L, Lin, Y-G, Xiao, L, Zhu, X-Q & Qu, X-Q 2017, 'Green tea polyphenols ameliorate non-alcoholic fatty liver disease through upregulating AMPK activation in high fat fed Zucker fatty rats', World Journal of Gastroenterology, vol. 23, no. 21, pp. 3805-3805.
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AIM To investigate protective effects and molecular mechanisms of green tea polyphenols (GTP) on non-alcoholic fatty liver disease (NAFLD) in Zucker fatty (ZF) rats. METHODS Male ZF rats were fed a high-fat diet (HFD) for 2 wk then treated with GTP (200 mg/kg) or saline (5 mL/kg) for 8 wk, with Zucker lean rat as their control. At the end of experiment, serum and liver tissue were collected for measurement of metabolic parameters, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), inflammatory cytokines and hepatic triglyceride and liver histology. Immunoblotting was used to detect phosphorylation of AMP-activated protein kinase (AMPK) acetyl-CoA carboxylase (ACC), and sterol regulatory element-binding protein 1c (SREBP1c). RESULTS Genetically obese ZF rats on a HFD presented with metabolic features of hepatic pathological changes comparable to human with NAFLD. GTP intervention decreased weight gain (10.1%, P = 0.052) and significantly lowered visceral fat (31.0%, P < 0.01). Compared with ZF-controls, GTP treatment significantly reduced fasting serum insulin, glucose and lipids levels. Reduction in serum ALT and AST levels (both P < 0.01) were observed in GTP-treated ZF rats. GTP treatment also attenuated the elevated TNFα and IL-6 in the circulation. The increased hepatic TG accumulation and cytoplasmic lipid droplet were attenuated by GTP treatment, associated with significantly increased expression of AMPK-Thr172 (P < 0.05) and phosphorylated ACC and SREBP1c (both P < 0.05), indicating diminished hepatic lipogenesis and triglycerides out flux from liver in GTP treated rats. CONCLUSION The protective effects of GTP against HFD-induced NAFLD in genetically obese ZF rats are positively correlated to reduction in hepatic lipogenesis through upregulating the AMPK pathway.

Tanaka, A, To, J, O’Brien, B, Donnelly, S & Lund, M 2017, 'Selection of reliable reference genes for the normalisation of gene expression levels following time course LPS stimulation of murine bone marrow derived macrophages', BMC Immunology, vol. 18, no. 1, pp. 1-12.
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© 2017 The Author(s). Background: Macrophages are key players in the initiation, perpetuation and regulation of both innate and adaptive immune responses. They largely perform these roles through modulation of the expression of genes, especially those encoding cytokines. Murine bone marrow derived macrophages (BMDMs) are commonly used as a model macrophage population for the study of immune responses to pro-inflammatory stimuli, notably lipopolysaccharide (LPS), which may be pertinent to the human situation. Evaluation of the temporal responses of LPS stimulated macrophages is widely conducted via the measurement of gene expression levels by RT-qPCR. While providing a robust and sensitive measure of gene expression levels, RT-qPCR relies on the normalisation of gene expression data to a stably expressed reference gene. Generally, a normalisation gene(s) is selected from a list of 'traditional' reference genes without validation of expression stability under the specific experimental conditions of the study. In the absence of such validation, and given that many studies use only a single reference gene, the reliability of data is questionable. Results: The stability of expression levels of eight commonly used reference genes was assessed during the peak (6 h) and resolution (24 h) phases of the BMDM response to LPS. Further, this study identified two additional genes, which have not previously been described as reference genes, and the stability of their expression levels during the same phases of the inflammatory response were validated. Importantly, this study demonstrates that certain 'traditional' reference genes are in fact regulated by LPS exposure, and, therefore, are not reliable candidates as their inclusion may compromise the accuracy of data interpretation. Testament to this, this study shows that the normalisation of gene expression data using an unstable reference gene greatly affects the experimental data obtained, and, therefore, the ultim...

Tang, AT, Choi, JP, Kotzin, JJ, Yang, Y, Hong, CC, Hobson, N, Girard, R, Zeineddine, HA, Lightle, R, Moore, T, Cao, Y, Shenkar, R, Chen, M, Mericko, P, Yang, J, Li, L, Tanes, C, Kobuley, D, Võsa, U, Whitehead, KJ, Li, DY, Franke, L, Hart, B, Schwaninger, M, Henao-Mejia, J, Morrison, L, Kim, H, Awad, IA, Zheng, X & Kahn, ML 2017, 'Endothelial TLR4 and the microbiome drive cerebral cavernous malformations', Nature, vol. 545, no. 7654, pp. 305-310.
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Cerebral cavernous malformations (CCMs) are a cause of stroke and seizure for which no effective medical therapies yet exist. CCMs arise from the loss of an adaptor complex that negatively regulates MEKK3-KLF2/4 signalling in brain endothelial cells, but upstream activators of this disease pathway have yet to be identified. Here we identify endothelial Toll-like receptor 4 (TLR4) and the gut microbiome as critical stimulants of CCM formation. Activation of TLR4 by Gram-negative bacteria or lipopolysaccharide accelerates CCM formation, and genetic or pharmacologic blockade of TLR4 signalling prevents CCM formation in mice. Polymorphisms that increase expression of the TLR4 gene or the gene encoding its co-receptor CD14 are associated with higher CCM lesion burden in humans. Germ-free mice are protected from CCM formation, and a single course of antibiotics permanently alters CCM susceptibility in mice. These studies identify unexpected roles for the microbiome and innate immune signalling in the pathogenesis of a cerebrovascular disease, as well as strategies for its treatment.

Taspinar, S, Mohanty, M & Memon, N 2017, 'PRNU-Based Camera Attribution From Multiple Seam-Carved Images', IEEE Transactions on Information Forensics and Security, vol. 12, no. 12, pp. 3065-3080.
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Taudte, RV, Roux, C & Beavis, A 2017, 'Stability of smokeless powder compounds on collection devices', Forensic Science International, vol. 270, pp. 55-60.
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© 2016 Elsevier Ireland Ltd The current trend towards the implementation of organic gunshot residue (OGSR) analysis into gunshot residue (GSR) investigation protocols typically involves the sequential analysis of inorganic and organic GSR. However, to allow for the consecutive analysis of inorganic and organic GSR, specimens will often be stored for different lengths of time which may result in compounds of interest degrading. In order to optimise storage conditions, it is important to consider compound degradation on collection devices during storage. This study investigated the degradation over time of compounds potentially present in smokeless powders and OGSR on two collection devices, alcohol swabs and GSR stubs. Over a period of 63 days, the highest degree of degradation was found in the first four days. Interestingly, energetic compounds were generally found to be more stable than smokeless powder additives such as stabilisers including diphenylamine and ethyl centralite, which might be problematic considering that these compounds are common targets for OGSR. The findings can provide valuable information to operational forensic laboratories to optimise their storage durations.

Tawfik, SA, Ali, S, Fronzi, M, Kianinia, M, Tran, TT, Stampfl, C, Aharonovich, I, Toth, M & Ford, MJ 2017, 'First principles investigation of quantum emission from hBN defects', Nanoscale, vol. 9, no. 36, pp. 13575-13582.
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Hexagonal boron nitride (hBN) has recently emerged as a fascinating platformfor room-temperature quantum photonics due to the discovery of robust visiblelight single-photon emitters. In order to utilize these emitters, it isnecessary to have a clear understanding of their atomic structure and theassociated excitation processes that give rise to this single photon emission.Here we perform density-functional theory (DFT) and constrained DFTcalculations for a range of hBN point defects in order to identify potentialemission candidates. By applying a number of criteria on the electronicstructure of the ground state and the atomic structure of the excited states ofthe considered defects, and then calculating the Huang-Rhys (HR) factor, wefind that the CBVN defect, in which a carbon atom substitutes a boron atom andthe opposite nitrogen atom is removed, is a potential emission source with a HRfactor of 1.66, in good agreement with the experimental HR factor. We calculatethe photoluminescence (PL) line shape for this defect and find that itreproduces a number of key features in the the experimental PL lineshape.

Tayeb, HH, Piantavigna, S, Howard, CB, Nouwens, A, Mahler, SM, Middelberg, APJ, He, L, Holt, SA & Sainsbury, F 2017, 'Insights into the interfacial structure–function of poly(ethylene glycol)-decorated peptide-stabilised nanoscale emulsions', Soft Matter, vol. 13, no. 43, pp. 7953-7961.
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This work provides describes the presentation and accessibility of functional moieties, such as targeting ligands, on peptide-stabilised nanocarrier emulsions.

Teng, B, Ma, P, Yu, C, Zhang, X, Feng, Q, Wen, L, Li, C, Cheng, Z, Jin, D & Lin, J 2017, 'Upconversion nanoparticles loaded with eIF4E siRNA and platinum(iv) prodrug to sensitize platinum based chemotherapy for laryngeal cancer and bioimaging', Journal of Materials Chemistry B, vol. 5, no. 2, pp. 307-317.
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Eukaryotic translation initiation factor (eIF) 4E is a valuable marker in cancer prognostics in many human cancers.

Teng, B, Peng, J, Ong, M & Qu, X 2017, 'Successful Pregnancy after Treatment with Chinese Herbal Medicine in a 43‐Year‐Old Woman with Diminished Ovarian Reserve and Multiple Uterus Fibrosis: A Case Report', Medicines, vol. 4, no. 1, pp. 7-7.
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To highlight a natural approach to coexisting oligomenorrhea, subfertility, luteal phase insufficiency and multiple fibroids cohesively when in vitro fertilisation (IVF) has failed.A 43-year-old woman with diminished ovarian reserve and multiple uterine fibroids had previously been advised to discontinue IVF treatment. According to Chinese Medicine diagnosis, herbal formulae were prescribed for improving age-related ovarian insufficiency as well as to control the growth of fibroids. After 4 months of treatment, the patient's menstrual cycle became regula r and plasma progesterone one week after ovulation increased from 10.9 nmol/L to 44.9 nmol/L. After 6 months, she achieved a natural conception, resulting in a live birth of a healthy infant at an estimated gestational age of 40 weeks.The successful treatment with Chinese Herbal Medicine for this case highlights a natural therapy to manage infertility due to ovarian insufficiency and multiple fibroids after unsuccessful IVF outcome.

Tian, H, Liu, H, Yang, T, Veder, J-P, Wang, G, Hu, M, Wang, S, Jaroniec, M & Liu, J 2017, 'Fabrication of core–shell, yolk–shell and hollow Fe₃O₄@carbon microboxes for high-performance lithium-ion batteries', Materials Chemistry Frontiers, vol. 1, no. 5, pp. 823-830.
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Fe₃O₄@C microboxes with core–shell, yolk–shell and hollow structures were synthesized, the core–shell microboxes exhibited high specific capacity, good rate performance, and exceptional cycling stability.

Tian, H, Wang, S, Zhang, C, Veder, J-P, Pan, J, Jaroniec, M, Wang, L & Liu, J 2017, 'Design and synthesis of porous ZnTiO₃/TiO₂ nanocages with heterojunctions for enhanced photocatalytic H₂ production', Journal of Materials Chemistry A, vol. 5, no. 23, pp. 11615-11622.
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Unique mesoporous ZnTiO₃/TiO₂ hollow polyhedra with selectively located Pt nanoparticles have been designed and constructed for photocatalytic hydrogen production.

Tjin, G, White, ES, Faiz, A, Sicard, D, Tschumperlin, DJ, Mahar, A, Kable, EPW & Burgess, JK 2017, 'Correction: Lysyl oxidases regulate fibrillar collagen remodelling in idiopathic pulmonary fibrosis (doi: 10.1242/dmm.030114)', Disease Models & Mechanisms, vol. 10, no. 12, pp. 1545-1545.
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Tjin, G, White, ES, Faiz, A, Sicard, D, Tschumperlin, DJ, Mahar, A, Kable, EPW & Burgess, JK 2017, 'Lysyl oxidases regulate fibrillar collagen remodelling in idiopathic pulmonary fibrosis', Disease Models & Mechanisms, vol. 10, no. 11, pp. 1301-1312.
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ABSTRACT Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease of the lung with few effective therapeutic options. Structural remodelling of the extracellular matrix [i.e. collagen cross-linking mediated by the lysyl oxidase (LO) family of enzymes (LOX, LOXL1-4)] might contribute to disease pathogenesis and represent a therapeutic target. This study aimed to further our understanding of the mechanisms by which LO inhibitors might improve lung fibrosis. Lung tissues from IPF and non-IPF subjects were examined for collagen structure (second harmonic generation imaging) and LO gene (microarray analysis) and protein (immunohistochemistry and western blotting) levels. Functional effects (collagen structure and tissue stiffness using atomic force microscopy) of LO inhibitors on collagen remodelling were examined in two models, collagen hydrogels and decellularized human lung matrices. LOXL1/LOXL2 gene expression and protein levels were increased in IPF versus non-IPF. Increased collagen fibril thickness in IPF versus non-IPF lung tissues correlated with increased LOXL1/LOXL2, and decreased LOX, protein expression. β-Aminoproprionitrile (β-APN; pan-LO inhibitor) but not Compound A (LOXL2-specific inhibitor) interfered with transforming growth factor-β-induced collagen remodelling in both models. The β-APN treatment group was tested further, and β-APN was found to interfere with stiffening in the decellularized matrix model. LOXL1 activity might drive collagen remodelling in IPF lungs. The interrelationship between collagen structural remodelling and LOs is disrupted in IPF lungs. Inhibition of LO activity alleviates fibrosis by limiting fibrillar collagen cross-linking, thereby potentially impeding the formation of a pathological microenvironment in IPF.

Tkacheva, A, McDonagh, A, Sun, B & Wang, G 2017, 'TEMPO-Substituted Ionic Liquids As Redox Mediators for High Performance Lithium-Oxygen Batteries', ECS Meeting Abstracts, vol. MA2017-02, no. 5, pp. 456-456.
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The performance of lithium-oxygen (Li-O2) batteries can be improved using redox mediators (RMs) to promote the decomposition of the insoluble, electronically insulating discharge product Li2O2 during the charging process. Homogenous RMs are expected to have a better performance in Li-O2 batteries than heterogeneous catalysts due to a larger contact area.1 Several redox mediators have been tested, including TEMPO and its derivatives.2 However, the use of Li-O2 batteries in many applications such as electric vehicles is still restricted due to electrolyte decomposition, flammability and volatility. In order to overcome these issues, ionic liquids have been successfully used as solvents for Li-O2 batteries.3, 4 In this project, we present TEMPO-substituted imidazolium ionic liquids that can perform the dual roles of solvent and redox mediator for Li-O2batteries (Figure 1). Figure 1. Structure and cyclic voltammograms of TEMPO-substituted imidazolium ionic liquids. Ionic liquids were prepared using modified literature procedures.5-7 Cyclic voltammetry of the ionic liquids in dimethylacetamide with 0.1 M lithium bis(trifluoromethane)sulfonimide was performed using a CHI660D electrochemical workstation in combination with a conventional three-electrode cell. Figure 1 shows cyclic voltammograms for compounds with 4, 5, and 8 carbon atoms in the chains linking the TEMPO and imidazolium moieties. The ionic liquids undergo a reversible electrochemical oxidation reaction at ~0.5 V vs Ag/AgCl (~3.8 V vs Li/Li+) which means that they should be capable of oxidizing the discharge product Li2

Tobias, SHA, Jacques, GS, Morgan, RM & Meakin, GE 2017, 'The effect of pressure on DNA deposition by touch', Forensic Science International: Genetics Supplement Series, vol. 6, pp. e12-e14.
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Casework exhibits are routinely examined for DNA that might have been deposited by touch, although the success of downstream profiling can vary. Many variables affect DNA deposition by touch, such as ‘shedder status’ surface type, and nature of contact. This may include pressure, which has been shown to increase the transfer of DNA between two surfaces, although whether pressure can impact DNA deposition directly from skin has yet to be examined. Therefore, this study uses a novel method to investigate whether pressure can affect the amount and quality of DNA directly deposited by touch. With the fingertips of one hand, volunteers exerted pressure for one minute onto a DNA-free polycarbonate board placed on top of a balance; all five fingermarks were then swabbed and combined as one sample for DNA extraction, quantification and profiling. For each hand, the area of the combined fingertips was used to determine the weight value to which to push the balance to give pressures of 4, 21 or 37 kPa. Volunteers used both their right and left hands at each pressure in a randomised order on each day of three non-consecutive days. Increasing the pressure between skin and surface significantly increased the amount of DNA deposited, which resulted in the detection of more alleles, from both the donor and unknown sources. No significant differences were observed in the amounts of DNA deposited between hands and among different days for each volunteer. DNA amounts significantly varied between individuals at 21 and 37 kPa, but not at 4 kPa. These findings provide insights into the impact of pressure on touch DNA deposition, and suggest that pressure is a key variable for crime scene investigators and forensic examiners to consider when prioritising items/surfaces that are likely to produce successful touch DNA results during a criminal investigation.

Torpy, FR, Zavattaro, M & Irga, PJ 2017, 'Green wall technology for the phytoremediation of indoor air: a system for the reduction of high CO2 concentrations', Air Quality, Atmosphere & Health, vol. 10, no. 5, pp. 575-585.
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© 2016, Springer Science+Business Media Dordrecht. Along with the growing requirement to reduce building carbon emissions, a need has arisen to find energy efficient means of improving the quality of indoor air. Indoor plants have been shown to be capable of reducing most air pollutants; however, practical numbers of potted plants will not have the capacity to control many forms of air pollution, especially CO2. Green walls are space-efficient means of increasing the density of indoor plants. We assessed an active green wall for its potential to reduce CO2 in chambers and a test room. Chlorophytum comosum and Epipremnum aureum were both effective cultivars for CO2 removal at light densities greater than 50 μmol m−2 s−1. Substrate ventilation increased the rate of CO2 draw down from chambers, possibly due to increased leaf gas exchange rates. Green walls were then tested in a 15.65-m3 sealed simulation room, allowing the calculation of clean air delivery rate (CADR) and air changes per hour (ACH) equivalents based on CO2 draw down. Rates of CO2 draw down were modest under typical brightly lit indoor conditions (50 μmol m−2 s−1); however, when light intensity was increased to relatively bright levels, similar to indoor conditions next to a window or with the addition of supplementary lighting (250 μmol m−2 s−1), a 1-m2 green wall was capable of significant quantifiable reductions of high CO2 concentrations within a sealed room environment. Extrapolating these findings indicates that a 5-m2 green wall containing C. comosum could balance the respiratory emissions of a full-time occupant.

Tout, J, Astudillo‐García, C, Taylor, MW, Tyson, GW, Stocker, R, Ralph, PJ, Seymour, JR & Webster, NS 2017, 'Redefining the sponge‐symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host‐derived compounds', Environmental Microbiology Reports, vol. 9, no. 6, pp. 750-755.
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SummaryMarine sponges host stable and species‐specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of ‘sponge‐specific’ microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.

Tran, N-AT, Seymour, JR, Siboni, N, Evenhuis, CR & Tamburic, B 2017, 'Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata', Algal Research, vol. 26, pp. 302-311.
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© 2017 Elsevier B.V. Microalgal biomass has been used to produce biofuels, aquaculture feed, high-value chemicals such as pigments and antioxidants, and even human food. This study addresses one of the key bottlenecks to the commercialisation of microalgal bioproducts: the high energy and environmental cost of harvesting microalgal cells out of suspension. An innovative and sustainable autoflocculation procedure was developed to pre-concentrate microalgal biomass for easier harvesting. Microalgal cell agglomeration by autoflocculation at high pH was induced for the first time, without the addition of a chemical flocculant, in the commercially-relevant microalga Nannochloropsis oculata. Photosynthetic inorganic carbon uptake, in the absence of carbon dioxide supply by mass transfer, was used to raise the culture pH. Autoflocculation started at pH 9.5 and reached a maximum flocculation efficiency of 90% at pH 10.4. Microalgal surface charge-neutralisation by calcium cations, and sweep flocculation by calcium carbonate and calcium phosphate precipitates were identified as the dominant flocculation mechanisms. This was also the first study to measure changes in bacterial community composition under autoflocculation. There was a clear shift from free-living bacteria in suspension to attached bacteria during autoflocculation, with Flavobacteriales becoming the dominant order of bacteria. This highlights the influential role of attached bacteria and bacteria-produced extracellular polymeric substances in microalgal flocculation. This study shows that regulating carbon dioxide supply is a promising green alternative to traditional microalgal flocculation processes as it alleviates the requirement for costly and harmful chemical flocculants and brings us closer to sustainable microalgal bioproducts.

Tran, TT, Choi, S, Scott, JA, Xu, Z, Zheng, C, Seniutinas, G, Bendavid, A, Fuhrer, MS, Toth, M & Aharonovich, I 2017, 'Room‐Temperature Single‐Photon Emission from Oxidized Tungsten Disulfide Multilayers', Advanced Optical Materials, vol. 5, no. 5, pp. 1600939-1600939.
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Robust quantum emitters fabricated by thermal oxidation of tungsten disulfide multilayers are reported. The emitters show robust, optically stable, linearly polarized luminescence at room temperature, can be modeled using a three‐level system, and exhibit moderate bunching. Overall, the results provide important insights into understanding of defect formation and quantum emitter activation in two‐dimensional materials.

Tran, TT, Kianinia, M, Bray, K, Kim, S, Xu, Z-Q, Gentle, A, Sontheimer, B, Bradac, C & Aharonovich, I 2017, 'Nanodiamonds with photostable, sub-gigahertz linewidths quantum emitters', APL Photonics, vol. 2, no. 11, pp. 116103-116103.
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Single photon emitters with narrow linewidths are highly sought after forapplications in quantum information processing and quantum communications. Inthis letter, we report on a bright, highly polarized near infrared singlephoton emitter embedded in diamond nanocrystals with a narrow, sub GHz opticallinewidths at 10K. The observed zero phonon line at ~ 780 nm is opticallystable under low power resonant excitation and blue shifts as the excitationpower increases. Our results highlight the prospect for using new near infraredcolor centers in nanodiamonds for quantum applications.

Tran, TT, Kianinia, M, Nguyen, M, Kim, S, Xu, Z-Q, Kubanek, A, Toth, M & Aharonovich, I 2017, 'Resonant Excitation of Quantum Emitters in Hexagonal Boron Nitride', ACS Photonics, vol. 5, no. 2, pp. 295-300.
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Quantum emitters in layered hexagonal boron nitride (hBN) have recentlyattracted a great attention as promising single photon sources. In this work,we demonstrate resonant excitation of a single defect center in hBN, one of themost important prerequisites for employment of optical sources in quantuminformation application. We observe spectral linewidths of hBN emitter narrowerthan 1 GHz while the emitter experiences spectral diffusion. Temporalphotoluminescence measurements reveals an average spectral diffusion time ofaround 100 ms. On-resonance photon antibunching measurement is also realized.Our results shed light on the potential use of quantum emitters from hBN innanophotonics and quantum information.

Tran, TT, Wang, D, Xu, Z-Q, Yang, A, Toth, M, Odom, TW & Aharonovich, I 2017, 'Deterministic Coupling of Quantum Emitters in 2D Materials to Plasmonic Nanocavity Arrays', Nano Letters, vol. 17, no. 4, pp. 2634-2639.
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© 2017 American Chemical Society. Quantum emitters in two-dimensional materials are promising candidates for studies of light-matter interaction and next generation, integrated on-chip quantum nanophotonics. However, the realization of integrated nanophotonic systems requires the coupling of emitters to optical cavities and resonators. In this work, we demonstrate hybrid systems in which quantum emitters in 2D hexagonal boron nitride (hBN) are deterministically coupled to high-quality plasmonic nanocavity arrays. The plasmonic nanoparticle arrays offer a high-quality, low-loss cavity in the same spectral range as the quantum emitters in hBN. The coupled emitters exhibit enhanced emission rates and reduced fluorescence lifetimes, consistent with Purcell enhancement in the weak coupling regime. Our results provide the foundation for a versatile approach for achieving scalable, integrated hybrid systems based on low-loss plasmonic nanoparticle arrays and 2D materials.

Tran, VS, Ngo, HH, Guo, W, Ton-That, C, Li, J, Li, J & Liu, Y 2017, 'Removal of antibiotics (sulfamethazine, tetracycline and chloramphenicol) from aqueous solution by raw and nitrogen plasma modified steel shavings', Science of The Total Environment, vol. 601-602, pp. 845-856.
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© 2017 Elsevier B.V. The removal of sulfamethazine (SMT), tetracycline (TC) and chloramphenicol (CP) from synthetic wastewater by raw (M3) and nitrogen plasma modified steel shavings (M3-plN2) was investigated using batch experiments. The adsorption kinetics could be expressed by both pseudo-first-order kinetic (PFO) and pseudo-second-order kinetic (PSO) models, where correlation coefficient r2 values were high. The values of PFO rate constant k1p and PSO rate constant k2p decreased as SMT-M3 > SMT-M3-plN2 > TC-M3-plN2 > TC-M3 > CP-M3 > CP-M3-plN2 and SMT-M3 > SMT-M3-plN2 > TC-M3 > TC-M3-plN2 > CP-M3 > CP-M3-plN2, respectively. Solution pH, adsorbent dose and temperature exerted great influences on the adsorption process. The plasma modification with nitrogen gas cleaned and enhanced 1.7-fold the surface area and 1.4-fold the pore volume of steel shavings. Consequently, the removal capacity of SMT, TC, CP on the adsorbent rose from 2519.98 to 2702.55, 1720.20 to 2158.36, and 2772.81 to 2920.11 μg/g, respectively. Typical chemical states of iron (XPS in Fe2p3 region) in the adsorbents which are mainly responsible for removing antibiotics through hydrogen bonding, electrostatic and non- electrostatic interactions and redox reaction were as follows: Fe3O4/Fe2 +, Fe3O4/Fe3 +, FeO/Fe2 + and Fe2O3/Fe3 +.

Trevathan-Tackett, SM, Macreadie, PI, Sanderman, J, Baldock, J, Howes, JM & Ralph, PJ 2017, 'A Global Assessment of the Chemical Recalcitrance of Seagrass Tissues: Implications for Long-Term Carbon Sequestration', Frontiers in Plant Science, vol. 8.
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© 2017 Trevathan-Tackett, Macreadie, Sanderman, Baldock, Howes and Ralph. Seagrass ecosystems have recently been identified for their role in climate change mitigation due to their globally-significant carbon sinks; yet, the capacity of seagrasses to sequester carbon has been shown to vary greatly among seagrass ecosystems. The recalcitrant nature of seagrass tissues, or the resistance to degradation back into carbon dioxide, is one aspect thought to influence sediment carbon stocks. In this study, a global survey investigated how the macromolecular chemistry of seagrass leaves, sheaths/stems, rhizomes and roots varied across 23 species from 16 countries. The goal was to understand how this seagrass chemistry might influence the capacity of seagrasses to contribute to sediment carbon stocks. Three non-destructive analytical chemical analyses were used to investigate seagrass chemistry: thermogravimetric analysis (TGA) and solid state13 C-NMR and infrared spectroscopy. A strong latitudinal influence on carbon quality was found, whereby temperate seagrasses contained 5% relatively more labile carbon, and tropical seagrasses contained 3% relatively more refractory carbon. Sheath/stem tissues significantly varied across taxa, with larger morphologies typically containing more refractory carbon than smaller morphologies. Rhizomes were characterized by a higher proportion of labile carbon (16%of total organic matter compared to 8–10%in other tissues); however, high rhizome biomass production and slower remineralization in anoxic sediments will likely enhance these below-ground tissues’ contributions to long-termcarbon stocks. Our study provides a standardized and global dataset on seagrass carbon quality across tissue types, taxa and geography that can be incorporated in carbon sequestration and storage models as well as ecosystem valuation and management strategies.

Trevathan-Tackett, SM, Seymour, JR, Nielsen, DA, Macreadie, PI, Jeffries, TC, Sanderman, J, Baldock, J, Howes, JM, Steven, ADL & Ralph, PJ 2017, 'Sediment anoxia limits microbial-driven seagrass carbon remineralization under warming conditions', FEMS Microbiology Ecology, vol. 93, no. 6.
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© FEMS 2017. All rights reserved. Seagrass ecosystems are significant carbon sinks, and their resident microbial communities ultimately determine the quantity and quality of carbon sequestered. However, environmental perturbations have been predicted to affect microbial-driven seagrass decomposition and subsequent carbon sequestration. Utilizing techniques including 16S-rDNA sequencing, solid-state NMR and microsensor profiling, we tested the hypothesis that elevated seawater temperatures and eutrophication enhance the microbial decomposition of seagrass leaf detritus and rhizome/root tissues. Nutrient additions had a negligible effect on seagrass decomposition, indicating an absence of nutrient limitation. Elevated temperatures caused a 19% higher biomass loss for aerobically decaying leaf detritus, coinciding with changes in bacterial community structure and enhanced lignocellulose degradation. Although, community shifts and lignocellulose degradation were also observed for rhizome/root decomposition, anaerobic decay was unaffected by temperature. These observations suggest that oxygen availability constrains the stimulatory effects of temperature increases on bacterial carbon remineralization, possibly through differential temperature effects on bacterial functional groups, including putative aerobic heterotrophs (e.g. Erythrobacteraceae, Hyphomicrobiaceae) and sulfate reducers (e.g. Desulfobacteraceae). Consequently, under elevated seawater temperatures, carbon accumulation rates may diminish due to higher remineralization rates at the sediment surface. Nonetheless, the anoxic conditions ubiquitous to seagrass sediments can provide a degree of carbon protection under warming seawater temperatures.

Trist, BG, Davies, KM, Cottam, V, Genoud, S, Ortega, R, Roudeau, S, Carmona, A, De Silva, K, Wasinger, V, Lewis, SJG, Sachdev, P, Smith, B, Troakes, C, Vance, C, Shaw, C, Al-Sarraj, S, Ball, HJ, Halliday, GM, Hare, DJ & Double, KL 2017, 'Amyotrophic lateral sclerosis-like superoxide dismutase 1 proteinopathy is associated with neuronal loss in Parkinson’s disease brain', Acta Neuropathologica, vol. 134, no. 1, pp. 113-127.
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© 2017, Springer-Verlag Berlin Heidelberg. Neuronal loss in numerous neurodegenerative disorders has been linked to protein aggregation and oxidative stress. Emerging data regarding overlapping proteinopathy in traditionally distinct neurodegenerative diseases suggest that disease-modifying treatments targeting these pathological features may exhibit efficacy across multiple disorders. Here, we describe proteinopathy distinct from classic synucleinopathy, predominantly comprised of the anti-oxidant enzyme superoxide dismutase-1 (SOD1), in the Parkinson’s disease brain. Significant expression of this pathology closely reflected the regional pattern of neuronal loss. The protein composition and non-amyloid macrostructure of these novel aggregates closely resembles that of neurotoxic SOD1 deposits in SOD1-associated familial amyotrophic lateral sclerosis (fALS). Consistent with the hypothesis that deposition of protein aggregates in neurodegenerative disorders reflects upstream dysfunction, we demonstrated that SOD1 in the Parkinson’s disease brain exhibits evidence of misfolding and metal deficiency, similar to that seen in mutant SOD1 in fALS. Our data suggest common mechanisms of toxic SOD1 aggregation in both disorders and a potential role for SOD1 dysfunction in neuronal loss in the Parkinson’s disease brain. This shared restricted proteinopathy highlights the potential translation of therapeutic approaches targeting SOD1 toxicity, already in clinical trials for ALS, into disease-modifying treatments for Parkinson’s disease.

Trussart, M, Yus, E, Martinez, S, Baù, D, Tahara, YO, Pengo, T, Widjaja, M, Kretschmer, S, Swoger, J, Djordjevic, S, Turnbull, L, Whitchurch, C, Miyata, M, Marti-Renom, MA, Lluch-Senar, M & Serrano, L 2017, 'Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae', Nature Communications, vol. 8, no. 1.
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AbstractDNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.

Turturice, BA, McGee, HS, Oliver, B, Baraket, M, Nguyen, BT, Ascoli, C, Ranjan, R, Rani, A, Perkins, DL & Finn, PW 2017, 'Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction', PLOS ONE, vol. 12, no. 10, pp. e0184566-e0184566.
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© 2017 Turturice 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. Background: Differences in asthma severity may be related to inflammation in the airways. The lower airway microbiota has been associated with clinical features such as airway obstruction, symptom control, and response to corticosteroids. Objective: To assess the relationship between local airway inflammation, severity of disease, and the lower airway microbiota in atopic asthmatics. Methods: A cohort of young adult, atopic asthmatics with intermittent or mild/moderate persistent symptoms (n = 13) were assessed via bronchoscopy, lavage, and spirometry. These individuals were compared to age matched non-asthmatic controls (n = 6) and to themselves after six weeks of treatment with fluticasone propionate (FP). Inflammation of the airways was assessed via a cytokine and chemokine panel. Lower airway microbiota composition was determined by metagenomic shotgun sequencing. Results: Unsupervised clustering of cytokines and chemokines prior to treatment with FP identified two asthmatic phenotypes (AP), termed AP1 and AP2, with distinct bronchoalveolar lavage inflammatory profiles. AP2 was associated with more obstruction, compared to AP1. After treatment with FP reduced MIP-1β and TNF-α and increased IL-2 was observed. A module of highly correlated cytokines that include MIP-1β and TNF-α was identified that negatively correlated with pulmonary function. Independently, IL-2 was positively correlated with pulmonary function. The airway microbiome composition correlated with asthmatic phenotypes. AP2, prior to FP treatment, was enriched with Streptococcus pneumoniae. Unique associations between IL-2 or the cytokine module and the microbiota composition of the airways were observed in asthmatics subjects prio...

Ueland, M, Howes, JM, Forbes, SL & Stuart, BH 2017, 'Degradation patterns of natural and synthetic textiles on a soil surface during summer and winter seasons studied using ATR-FTIR spectroscopy', Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 185, pp. 69-76.
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© 2017 Elsevier B.V. Textiles are a valuable source of forensic evidence and the nature and condition of textiles collected from a crime scene can assist investigators in determining the nature of the death and aid in the identification of the victim. Until now, much of the knowledge of textile degradation in forensic contexts has been based on the visual inspection of material collected from soil environments. The purpose of the current study was to investigate the potential of a more quantitative approach to the understanding of forensic textile degradation through the application of infrared spectroscopy. Degradation patterns of natural and synthetic textile materials as they were subjected to a natural outdoor environment in Australia were investigated. Cotton, polyester and polyester – cotton blend textiles were placed on a soil surface during the summer and winter seasons and were analysed over periods 1 and 1.5 years, respectively, and examined using attenuated total reflectance (ATR) spectroscopy. Statistical analysis of the spectral data obtained for the cotton material correlated with visual degradation and a difference in the onset of degradation between the summer and winter season was revealed. The synthetic material did not show any signs of degradation either visually or statistically throughout the experimental period and highlighted the importance of material type in terms of preservation. The cotton section from the polyester – cotton blend samples was found to behave in a similar manner to that of the 100% cotton samples, however principal component analysis (PCA) demonstrated that the degradation patterns were less distinct in both the summer and winter trial for the blend samples. These findings indicated that the presence of the synthetic material may have inhibited the degradation of the natural material. The use of statistics to analyse the spectral data obtained for textiles of forensic interest provides a better foundation for ...

Unnikrishnan, A, Papaemmanuil, E, Beck, D, Deshpande, NP, Verma, A, Kumari, A, Woll, PS, Richards, LA, Knezevic, K, Chandrakanthan, V, Thoms, JAI, Tursky, ML, Huang, Y, Ali, Z, Olivier, J, Galbraith, S, Kulasekararaj, AG, Tobiasson, M, Karimi, M, Pellagatti, A, Wilson, SR, Lindeman, R, Young, B, Ramakrishna, R, Arthur, C, Stark, R, Crispin, P, Curnow, J, Warburton, P, Roncolato, F, Boultwood, J, Lynch, K, Jacobsen, SEW, Mufti, GJ, Hellstrom-Lindberg, E, Wilkins, MR, MacKenzie, KL, Wong, JWH, Campbell, PJ & Pimanda, JE 2017, 'Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes', Cell Reports, vol. 20, no. 3, pp. 572-585.
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© 2017 The Author(s) Myelodysplastic syndromes and chronic myelomonocytic leukemia are blood disorders characterized by ineffective hematopoiesis and progressive marrow failure that can transform into acute leukemia. The DNA methyltransferase inhibitor 5-azacytidine (AZA) is the most effective pharmacological option, but only ∼50% of patients respond. A response only manifests after many months of treatment and is transient. The reasons underlying AZA resistance are unknown, and few alternatives exist for non-responders. Here, we show that AZA responders have more hematopoietic progenitor cells (HPCs) in the cell cycle. Non-responder HPC quiescence is mediated by integrin α5 (ITGA5) signaling and their hematopoietic potential improved by combining AZA with an ITGA5 inhibitor. AZA response is associated with the induction of an inflammatory response in HPCs in vivo. By molecular bar coding and tracking individual clones, we found that, although AZA alters the sub-clonal contribution to different lineages, founder clones are not eliminated and continue to drive hematopoiesis even in complete responders.

Vallotton, P, van Oijen, AM, Whitchurch, CB, Gelfand, V, Yeo, L, Tsiavaliaris, G, Heinrich, S, Dultz, E, Weis, K & Grünwald, D 2017, 'Diatrack particle tracking software: Review of applications and performance evaluation', Traffic, vol. 18, no. 12, pp. 840-852.
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Object tracking is an instrumental tool supporting studies of cellular trafficking. There are three challenges in object tracking: the identification of targets; the precise determination of their position and boundaries; and the assembly of correct trajectories. This last challenge is particularly relevant when dealing with densely populated images with low signal‐to‐noise ratios—conditions that are often encountered in applications such as organelle tracking, virus particle tracking or single‐molecule imaging. We have developed a set of methods that can handle a wide variety of signal complexities. They are compiled into a free software package called Diatrack. Here we review its main features and utility in a range of applications, providing a survey of the dynamic imaging field together with recommendations for effective use. The performance of our framework is shown to compare favorably to a wide selection of custom‐developed algorithms, whether in terms of localization precision, processing speed or correctness of tracks.

van den Engh, GJ, Doggett, JK, Thompson, AW, Doblin, MA, Gimpel, CNG & Karl, DM 2017, 'Dynamics of Prochlorococcus and Synechococcus at Station ALOHA Revealed through Flow Cytometry and High-Resolution Vertical Sampling', Frontiers in Marine Science, vol. 4, no. NOV.
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© 2017 van den Engh, Doggett, Thompson, Doblin, Gimpel and Karl. The fluorescence and scattering properties of Prochlorococcus and Synechococcus at Station ALOHA as measured by flow cytometry (termed the FCM phenotype) vary with depth and over a variety of time scales. The variation in FCM phenotypes may reflect population selection or physiological acclimation to local conditions. Observations before, during, and after a storm with deep water mixing show a short-term homogenization of the FCM phenotypes with depth, followed by a return to the stable pattern over the time span of a few days. These dynamics indicate that, within the upper mixed-layer, the FCM phenotype distribution represents acclimation to ambient light. The populations in the pycnocline (around 100 m and below), remain stable and are invariant with light conditions. In samples where both cyanobacteria coexist, fluorescence properties of Prochlorococcus and Synechococcus are tightly correlated providing further evidence that FCM phenotype variability is caused by a common environmental factor or factors. Measurements of the dynamics of FCM phenotypes provide insights into phytoplankton physiology and adaptation. Alternatively, FCM phenotype census of a water mass may provide information about its origin and illumination history.

van der Plaat, DA, de Jong, K, Lahousse, L, Faiz, A, Vonk, JM, van Diemen, CC, Nedeljkovic, I, Amin, N, Brusselle, GG, Hofman, A, Brandsma, C-A, Bossé, Y, Sin, DD, Nickle, DC, van Duijn, CM, Postma, DS & Boezen, HM 2017, 'Genome-wide association study on the FEV 1 /FVC ratio in never-smokers identifies HHIP and FAM13A', Journal of Allergy and Clinical Immunology, vol. 139, no. 2, pp. 533-540.
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Van Dolah, FM, Kohli, GS, Morey, JS & Murray, SA 2017, 'Both modular and single‐domain Type I polyketide synthases are expressed in the brevetoxin‐producing dinoflagellate, Karenia brevis (Dinophyceae)', Journal of Phycology, vol. 53, no. 6, pp. 1325-1339.
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Dinoflagellates are prolific producers of polyketide compounds, many of which are potent toxins with adverse impacts on human and marine animal health. To identify polyketide synthase (PKS) genes in the brevetoxin‐producing dinoflagellate, Karenia brevis, we assembled a transcriptome from 595 million Illumina reads, sampled under different growth conditions. The assembly included 125,687 transcripts greater than 300 nt in length, with over half having >100× coverage. We found 121 transcripts encoding Type I ketosynthase (KS) domains, of which 99 encoded single KS domains, while 22 contained multiple KS domains arranged in 1–3 protein modules. Phylogenetic analysis placed all single domain and a majority of multidomain KSs within a monophyletic clade of protist PKSs. In contrast with the highly amplified single‐domain KSs, only eight single‐domain ketoreductase transcripts were found in the assembly, suggesting that they are more evolutionarily conserved. The multidomain PKSs were dominated by trans‐acyltransferase architectures, which were recently shown to be prevalent in other algal protists. Karenia brevis also expressed several hybrid nonribosomal peptide synthetase (NRPS)/PKS sequences, including a burA‐like sequence previo...

Vodstrcil, LA, Rupasinghe, TWT, Kong, FYS, Tull, D, Worthington, K, Chen, MY, Huston, WM, Timms, P, McConville, MJ, Fairley, CK, Bradshaw, CS, Tabrizi, SN & Hocking, JS 2017, 'Measurement of tissue azithromycin levels in self-collected vaginal swabs post treatment using liquid chromatography and tandem mass spectrometry (LC-MS/MS)', PLOS ONE, vol. 12, no. 5, pp. e0177615-e0177615.
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© 2017 Vodstrcil 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. Background Azithromycin is recommended for the treatment of uncomplicated urogenital chlamydia infection although the standard 1gram dose sometimes fails to eradicate the infection (treatment failure). One hypothesis proposed for treatment failure has been insufficient levels of the antibiotic at the site of infection. We developed an assay using liquid chromatography and tandem mass spectrometry (LC-MS/MS) to measure azithromycin concentration in high-vaginal swabs and monitor how concentration changes over time following routine azithromycin treatment. Methods Azithromycin concentrations were measured in two groups of women either within the first 24h of taking a 1g dose (N = 11) or over 9 days (N = 10). Azithromycin concentrations were normalised to an internal standard (leucine enkephalin), and the bulk lipid species phosphatidylcholine [PC(34:1)], using an Agilent 6490 triple quadrupole instrument in positive ionisation mode. The abundances of azithromycin, PC(34:1), and leu-enkephalin were determined by multiple reaction monitoring and absolute levels of azithromycin estimated using standard curves prepared on vaginal specimens. Results Vaginal azithromycin concentrations of women were rapidly obtained after 5h post-treatment (mean concentration = 1031mcg/mg of lipid, range = 173-2693mcg/mg). In women followed for 9 days, peak concentrations were highest after day 2 (mean concentration = 2206mcg/mg, range = 721-5791mcg/mg), and remained high for at least 9 days with a mean concentration of 384mcg/mg (range = 139-1024mcg/mg) on day 9. Conclusion Our study confirmed that a single 1g dose of azithromycin is rapidly absorbed and remains in the vagina at relatively high levels for at least a week,...

Voerman, SE, Glasby, TM, Gladstone, W & Gribben, PE 2017, 'Habitat associations of an expanding native alga', Marine Environmental Research, vol. 131, pp. 205-214.
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© 2017 Elsevier Ltd There are many examples of native macrophytes becoming locally dominant and spreading outside their traditional distributions, but the causes and impacts are often not understood. In New South Wales, Australia, the green alga Caulerpa filiformis is undergoing a range expansion and has transitioned from a subdominant to a dominant alga on several rocky shores around the Sydney coastline. Here we investigated relationships between established patches of C. filiformis, the habitat it occupies and associated algal communities at multiple subtidal sites over the green alga's 700 km range. We tested the following predictions: 1) C. filiformis cover differs among substrata, being greatest on turf-forming algae; 2) C. filiformis cover is positively related to environmental variables linked to increased sedimentation (e.g. reduced reef width, surface slope, increased rugosity and distance from shore); 3) occurrence of C. filiformis is associated with a change in macrophyte community structure and a reduction of macrophyte richness; 4) intact native algal canopies inhibit C. filiformis spread, but turf-forming algae and bare sand are susceptible to invasion. Substratum associations were highly consistent among sites, but contrary to our prediction, C. filiformis was most commonly associated with rock or rock + sand substratum and less frequently associated with turf-forming algae substratum. C. filiformis cover was negatively correlated with reef width, which explained most of the variation observed, although local scale variables distance from shore, reef slope, and water depth were also correlated with C. filiformis cover. Algal diversity and community composition typically differed in the presence of C. filiformis, often with a reduction of algal abundances, in particular Sargassum spp., although results varied among substrata and sites. However, monitoring of borders suggested that C. filiformis does not invade and outcompete undisturbed adjacent ca...

Voyer, M & Gladstone, W 2017, 'Human considerations in the use of marine protected areas for biodiversity conservation', Australian Zoologist, vol. 39, no. 2, pp. 173-180.
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Marine protected areas (MPAs) are one approach, amongst many, for the protection of marine biodiversity. Although proven to be effective at protecting biodiversity and to be supported by local and wider communities, the implementation of some MPAs has been very contentious especially with fishing stakeholders. We researched the causes of these issues by examining the experience of implementation of the Batemans Marine Park in New South Wales, Australia. While MPA selection and management need to be based on rigorous science, a commensurate level of attention needs to be applied to understanding the social systems that also play a role in determining the protection measures and approaches. The most pressing issue that needs to be resolved early on in a planning process is the MPA's objectives, and whether these objectives are well understood and accepted by the local community. Building community support for MPAs also involves taking into account the different systems of knowledge and views of the natural world that exist within the community. Science alone is not sufficient to convince communities of the need for MPAs or their value in achieving conservation outcomes. Incorporating 'bottom-up' approaches into communication and engagement strategies will allow for a greater diversity of voices to be heard and acknowledged, protecting the planning processes against polarisation. Engaging local communities needs to go beyond large-scale consultation processes to include more rigorous, integrated social, economic and ecological assessment exercises, involving a collaborative participatory approach. Context is important and planning processes need to recognise the individual and unique needs of each affected community. Rigid ideas around the best means of achieving biodiversity protection combined with 'a one size fits all' approach to planning and community engagement are likely to exacerbate conflict and division and stimulate opposition.

Vu, LT, Long, NT, Brito, B, Stenfeldt, C, Phuong, NT, Hoang, BH, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, PP, Quang, LTV, Hung, VV, Tho, ND, Dong, PV, Minh, PQ, Bertram, M, Fish, IH, Rodriguez, LL, Dung, DH & Arzt, J 2017, 'First detection of foot-and-mouth disease virus O/Ind-2001d in Vietnam', PLOS ONE, vol. 12, no. 6, pp. e0177361-e0177361.
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In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam in May, 2015 in Đắk Nông province. Three subsequent outbreaks caused by genetically related viruses occurred between May–October, 2015 after which the virus was not detected in clinical outbreaks for at least 15 subsequent months. The observed outbreaks affected (in chronological order): cattle in Đắk Nông province, pigs in Đắk Lắk province and Đắk Nông province, and cattle in Ninh Thuận province. The clinical syndromes associated with these outbreaks were consistent with typical FMD in the affected species. Overall attack rate on affected premises was 0.85 in pigs and 0.93 in cattle over the course of the outbreak. Amongst 378 pigs at risk on affected premises, 85 pigs died during the outbreaks; there were no deaths among cattle. The manner in which FMDV/O/ME-SA/Ind-2001d was introduced into Vietnam remains undetermined; however, movement of live cattle is the suspected route. This incursion has substantial implications for epidemiology and control of FMD in Southeast Asia.

Walia, S, Balendhran, S, Ahmed, T, Singh, M, El‐Badawi, C, Brennan, MD, Weerathunge, P, Karim, MN, Rahman, F, Rassell, A, Duckworth, J, Ramanathan, R, Collis, GE, Lobo, CJ, Toth, M, Kotsakidis, JC, Weber, B, Fuhrer, M, Dominguez‐Vera, JM, Spencer, MJS, Aharonovich, I, Sriram, S, Bhaskaran, M & Bansal, V 2017, 'Ambient Protection of Few‐Layer Black Phosphorus via Sequestration of Reactive Oxygen Species', Advanced Materials, vol. 29, no. 27, pp. 1700152-1700152.
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Few‐layer black phosphorous (BP) has emerged as a promising candidate for next‐generation nanophotonic and nanoelectronic devices. However, rapid ambient degradation of mechanically exfoliated BP poses challenges in its practical deployment in scalable devices. To date, the strategies employed to protect BP have relied upon preventing its exposure to atmospheric conditions. Here, an approach that allows this sensitive material to remain stable without requiring its isolation from the ambient environment is reported. The method draws inspiration from the unique ability of biological systems to avoid photo‐oxidative damage caused by reactive oxygen species. Since BP undergoes similar photo‐oxidative degradation, imidazolium‐based ionic liquids are employed as quenchers of these damaging species on the BP surface. This chemical sequestration strategy allows BP to remain stable for over 13 weeks, while retaining its key electronic characteristics. This study opens opportunities to practically implement BP and other environmentally sensitive 2D materials for electronic applications.

Walia, S, Balendhran, S, Ahmed, T, Singh, M, El‐Badawi, C, Brennan, MD, Weerathunge, P, Karim, MN, Rahman, F, Rassell, A, Duckworth, J, Ramanathan, R, Collis, GE, Lobo, CJ, Toth, M, Kotsakidis, JC, Weber, B, Fuhrer, M, Dominguez‐Vera, JM, Spencer, MJS, Aharonovich, I, Sriram, S, Bhaskaran, M & Bansal, V 2017, 'Black Phosphorus: Ambient Protection of Few‐Layer Black Phosphorus via Sequestration of Reactive Oxygen Species (Adv. Mater. 27/2017)', Advanced Materials, vol. 29, no. 27.
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Walsh, JC, Angstmann, CN, Duggin, IG & Curmi, PMG 2017, 'Non-linear Min protein interactions generate harmonics that signal mid-cell division in Escherichia coli', PLOS ONE, vol. 12, no. 10, pp. e0185947-e0185947.
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The Min protein system creates a dynamic spatial pattern in Escherichia coli cells where the proteins MinD and MinE oscillate from pole to pole. MinD positions MinC, an inhibitor of FtsZ ring formation, contributing to the mid-cell localization of cell division. In this paper, Fourier analysis is used to decompose experimental and model MinD spatial distributions into time-dependent harmonic components. In both experiment and model, the second harmonic component is responsible for producing a mid-cell minimum in MinD concentration. The features of this harmonic are robust in both experiment and model. Fourier analysis reveals a close correspondence between the time-dependent behaviour of the harmonic components in the experimental data and model. Given this, each molecular species in the model was analysed individually. This analysis revealed that membrane-bound MinD dimer shows the mid-cell minimum with the highest contrast when averaged over time, carrying the strongest signal for positioning the cell division ring. This concurs with previous data showing that the MinD dimer binds to MinC inhibiting FtsZ ring formation. These results show that non-linear interactions of Min proteins are essential for producing the mid-cell positioning signal via the generation of second-order harmonic components in the time-dependent spatial protein distribution.

Wand, MP 2017, 'Rejoinder', Journal of the American Statistical Association, vol. 112, no. 517, pp. 166-168.
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Wang, B, Liu, DL, Asseng, S, Macadam, I, Yang, X & Yu, Q 2017, 'Spatiotemporal changes in wheat phenology, yield and water use efficiency under the CMIP5 multimodel ensemble projections in eastern Australia', Climate Research, vol. 72, no. 2, pp. 83-99.
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© Inter-Research 2017. The New South Wales (NSW) wheat belt is one of the most important regions for winter crops in Australia; however, its agricultural system is significantly affected by water stress and ongoing climate change. Statistically downscaled scenarios from 13 selected global climate models with RCP4.5 and RCP8.5 scenarios were combined with crop simulation models to simulate wheat productivity and water use. We projected that multi-model median yields could increase by 0.2% for RCP4.5 and 9.0% for RCP8.5 by 2061-2100. Although RCP4.5 showed a small decrease in median yield in the dry southwestern parts of the wheat belt, the higher CO2 concentration in RCP8.5 compensated some of the negative effects, resulting in 12.6% yield increase. Our results show that drier areas would benefit more from elevated CO2 than would the wetter areas. Without the increase in CO2 concentration, wheat yields decrease rapidly under RCP4.5 by 2061-2100 and much more so under RCP8.5 compared to the present. A decline in growing season length and a decrease in rainfall resulted in reduced crop water consumption. As a consequence, simulated evapotranspiration decreased by 10.2% for RCP4.5 and 16.9% for RCP8.5 across the NSW wheat belt. Increasing yields combined with decreasing evapotranspiration resulted in a simulated increase in water use efficiency by 9.9% for RCP4.5 and 29.7% for RCP8.5. Wheat production in water-limited, low-yielding environments appears to be less negatively impacted or in some cases even positively affected under future climate and CO2 changes, compared to other growing environments in the world.

Wang, JJJ, Bartlett, M & Ryan, L 2017, 'Non‐ignorable missingness in logistic regression', Statistics in Medicine, vol. 36, no. 19, pp. 3005-3021.
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Nonresponses and missing data are common in observational studies. Ignoring or inadequately handling missing data may lead to biased parameter estimation, incorrect standard errors and, as a consequence, incorrect statistical inference and conclusions. We present a strategy for modelling non‐ignorable missingness where the probability of nonresponse depends on the outcome. Using a simple case of logistic regression, we quantify the bias in regression estimates and show the observed likelihood is non‐identifiable under non‐ignorable missing data mechanism. We then adopt a selection model factorisation of the joint distribution as the basis for a sensitivity analysis to study changes in estimated parameters and the robustness of study conclusions against different assumptions. A Bayesian framework for model estimation is used as it provides a flexible approach for incorporating different missing data assumptions and conducting sensitivity analysis.Using simulated data, we explore the performance of the Bayesian selection model in correcting for bias in a logistic regression. We then implement our strategy using survey data from the 45 and Up Study to investigate factors associated with worsening health from the baseline to follow‐up survey. Our findings have practical implications for the use of the 45 and Up Study data to answer important research questions relating to health and quality‐of‐life. Copyright © 2017 John Wiley & Sons, Ltd.

Wang, JJJ, Bartlett, M & Ryan, L 2017, 'On the impact of nonresponse in logistic regression: application to the 45 and Up study', BMC Medical Research Methodology, vol. 17, no. 1, pp. 1-13.
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© 2017 The Author(s). Background: In longitudinal studies, nonresponse to follow-up surveys poses a major threat to validity, interpretability and generalisation of results. The problem of nonresponse is further complicated by the possibility that nonresponse may depend on the outcome of interest. We identified sociodemographic, general health and wellbeing characteristics associated with nonresponse to the follow-up questionnaire and assessed the extent and effect of nonresponse on statistical inference in a large-scale population cohort study. Methods: We obtained the data from the baseline and first wave of the follow-up survey of the 45 and Up Study. Of those who were invited to participate in the follow-up survey, 65.2% responded. Logistic regression model was used to identify baseline characteristics associated with follow-up response. A Bayesian selection model approach with sensitivity analysis was implemented to model nonignorable nonresponse. Results: Characteristics associated with a higher likelihood of responding to the follow-up survey include female gender, age categories 55-74, high educational qualification, married/de facto, worked part or partially or fully retired and higher household income. Parameter estimates and conclusions are generally consistent across different assumptions on the missing data mechanism. However, we observed some sensitivity for variables that are strong predictors for both the outcome and nonresponse. Conclusions: Results indicated in the context of the binary outcome under study, nonresponse did not result in substantial bias and did not alter the interpretation of results in general. Conclusions were still largely robust under nonignorable missing data mechanism. Use of a Bayesian selection model is recommended as a useful strategy for assessing potential sensitivity of results to missing data.

Wang, K, Chen, Y-Q, Salido, MM, Kohli, GS, Kong, J-L, Liang, H-J, Yao, Z-T, Xie, Y-T, Wu, H-Y, Cai, S-Q, Drautz-Moses, DI, Darling, AE, Schuster, SC, Yang, L & Ding, Y 2017, 'The rapid in vivo evolution of Pseudomonas aeruginosa in ventilator-associated pneumonia patients leads to attenuated virulence', Open Biology, vol. 7, no. 9, pp. 170029-170029.
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Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients. Pacbio and Illumina sequencing were used to analyse the in vivo evolutionary trajectories of these isolates. Our analysis showed that positive selection dominantly shaped P. aeruginosa genomes during VAP infections and led to three convergent evolution events, including loss-of-function mutations of lasR and mpl , and a pyoverdine-deficient phenotype. Specifically, lasR encodes one of the major transcriptional regulators in quorum sensing, whereas mpl encodes an enzyme responsible for recycling cell wall peptidoglycan. We also found that P. aeruginosa isolated at late stages of VAP infections produce less elastase and are less virulent in vivo than their earlier isolated counterparts, suggesting the short-term

Wang, K, Shi, Y, Solntsev, AS, Fan, S, Sukhorukov, AA & Neshev, DN 2017, 'Non-reciprocal geometric phase in nonlinear frequency conversion', Optics Letters, vol. 42, no. 10, pp. 1990-1990.
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We describe analytically and numerically the geometric phase arising from nonlinear frequency conversion and show that such a phase can be made non-reciprocal by momentum-dependent photonic transition. Such non-reciprocity is immune to the shortcomings imposed by dynamic reciprocity in Kerr and Kerr-like devices. We propose a simple and practical implementation, requiring only a single waveguide and one pump, while the geometric phase is controllable by the pump and promises robustness against fabrication errors.

Wang, L, Kruk, S, Xu, L, Rahmani, M, Smirnova, D, Solntsev, A, Kravchenko, I, Neshev, D & Kivshar, Y 2017, 'Shaping the third-harmonic radiation from silicon nanodimers', Nanoscale, vol. 9, no. 6, pp. 2201-2206.
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© The Royal Society of Chemistry. Recent progress in the study of resonant light confinement in high-index dielectric nanostructures suggests a new route for achieving efficient control of both electric and magnetic components of light. It also leads to the enhancement of nonlinear effects near electric and magnetic Mie resonances with an engineered radiation directionality. Here we study the third-harmonic generation from dimers composed of pairs of two identical silicon nanoparticles and demonstrate, both numerically and experimentally, that the multipolar harmonic modes generated by the dimers near the Mie resonances allow the shaping of the directionality of nonlinear radiation.

Wang, L, Ren, L, Mitchell, D, Casillas-Garcia, G, Ren, W, Ma, C, Xu, XX, Wen, S, Wang, F, Zhou, J, Xu, X, Hao, W, Dou, SX & Du, Y 2017, 'Enhanced energy transfer in heterogeneous nanocrystals for near infrared upconversion photocurrent generation', Nanoscale, vol. 9, no. 47, pp. 18661-18667.
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A heterogeneous NaYF₄:Yb,Tm@ZnO nanoparticle with an epitaxial interface is prepared, and it possesses an enhanced upconversion emission intensity and an excellent photocurrent response.

Wang, L, Wu, LM, Greaves, IK, Zhu, A, Dennis, ES & Peacock, WJ 2017, 'PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana', Proceedings of the National Academy of Sciences, vol. 114, no. 17, pp. E3555-E3562.
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Significance Hybrids are of high value in agriculture. Hybrid vigor applies only to the F1 generation. Pure breeding lines, which maintain the hybrid phenotype, hybrid mimics, together with the small phenotype line have proven to be powerful in identifying genes and pathways critical for hybrid vigor. PHYTOCHROME-INTERACTING FACTOR (PIF4), regulating auxin biosynthesis and action, features in the development of the hybrid vigor phenotype. The homozygous hybrid mimic lines all have the same particular 12 chromosomal segments, 4 from the C24 parent and 8 from L er . The small phenotype line has each of these segments derived from the genome of the alternative parent, so one or more loci needed for the large hybrid mimic phenotype are likely to be on each segment.

Wang, S, Clapper, A, Chen, P, Wang, L, Aharonovich, I, Jin, D & Li, Q 2017, 'Tuning Enhancement Efficiency of Multiple Emissive Centers in Graphene Quantum Dots by Core–Shell Plasmonic Nanoparticles', The Journal of Physical Chemistry Letters, vol. 8, no. 22, pp. 5673-5679.
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© 2017 American Chemical Society. Graphene quantum dots (GQDs) are emerging luminescent nanomaterials for energy, bioimaging, and optoelectronic applications. However, unlike conventional fluorophores, GQDs contain multiple emissive centers that result in a complex interaction with external electromagnetic fields. Here we utilize core-shell plasmonic nanoparticles to simultaneously enhance and modulate the photoluminescence (PL) intensities and spectral profiles of GQDs. By analyzing the spectral profiles, we show that the emissive centers are highly influenced by the proximity to the metal particles. Under optimal spacer thickness of 25 nm, the overall PL displays a four-fold enhancement compared with a pristine GQD. However, detailed lifetime measurements indicate the presence of midgap states that act as the bottleneck for further enhancement. Our results offer new perspectives for fundamental understanding and new design of functional luminescent materials (e.g., GQDs, graphene oxide, carbon dots) for imaging, sensing, and light harvesting.

Wangpraseurt, D, Holm, JB, Larkum, AWD, Pernice, M, Ralph, PJ, Suggett, DJ & Kühl, M 2017, 'In vivo Microscale Measurements of Light and Photosynthesis during Coral Bleaching: Evidence for the Optical Feedback Loop?', Frontiers in Microbiology, vol. 8, no. JAN, pp. 1-12.
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© 2017 Wangpraseurt, Holm, Larkum, Pernice, Ralph, Suggett and Kühl. Climate change-related coral bleaching, i.e., the visible loss of zooxanthellae from the coral host, is increasing in frequency and extent and presents a major threat to coral reefs globally. Coral bleaching has been proposed to involve accelerating light stress of their microalgal endosymbionts via a positive feedback loop of photodamage, symbiont expulsion and excess in vivo light exposure. To test this hypothesis, we used light and O2 microsensors to characterize in vivo light exposure and photosynthesis of Symbiodinium during a thermal stress experiment. We created tissue areas with different densities of Symbiodinium cells in order to understand the optical properties and light microenvironment of corals during bleaching. Our results showed that in bleached Pocillopora damicornis corals, Symbiodinium light exposure was up to fivefold enhanced relative to healthy corals, and the relationship between symbiont loss and light enhancement was well-described by a power-law function. Cell-specific rates of Symbiodinium gross photosynthesis and light respiration were enhanced in bleached P. damicornis compared to healthy corals, while areal rates of net photosynthesis decreased. Symbiodinium light exposure in Favites sp. revealed the presence of low light microniches in bleached coral tissues, suggesting that light scattering in thick coral tissues can enable photoprotection of cryptic symbionts. Our study provides evidence for the acceleration of in vivo light exposure during coral bleaching but this optical feedback mechanism differs between coral hosts. Enhanced photosynthesis in relation to accelerating light exposure shows that coral microscale optics exerts a key role on coral photophysiology and the subsequent degree of radiative stress during coral bleaching.

Ward, J 2017, 'Best practice recommendations for the establishment of a national DNA identification program for missing persons: A global perspective', Forensic Science International: Genetics Supplement Series, vol. 6, pp. e43-e45.
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© 2017 I was awarded a 2015 Churchill Fellowship to visit international laboratories which have specialisation in the DNA identification of unidentified human remains (UHR), applied new technologies to DNA identification casework including the massively parallel sequencing (MPS) of mitochondrial DNA (mtDNA) and forensic DNA phenotyping markers, and established successful DNA-led identification programs for missing persons (MP) casework or disaster victim identification. The goal of the Fellowship was to improve the DNA profiling outcomes for the 500+ cases of UHR in Australia, explore new technologies or DNA markers which could aid the identification effort in the absence of other investigative leads, and devise recommendations for the establishment of a DNA identification program for the 2000+ long-term MP in Australia. Despite DNA being used worldwide to successfully identify large numbers of MP resulting from armed conflicts, human rights abuses and natural or man-made disasters, the cost, labour and success rate of using DNA for routinely identifying compromised UHR has historically been prohibitive for many countries, resulting in current backlogs of identification casework. The introduction of a nationally coordinated DNA testing program, and adoption of DNA technological advancements, will facilitate the effective and efficient identification of a country's unknown and missing citizens thus bringing closure to potentially large numbers of missing person and criminal cold cases. I will translate key Fellowship findings into practical recommendations for the establishment of a national DNA identification program based on international best practice that will be applicable for any country considering implementing a DNA-led MP program.

Ward, TJ, Booth, DJ, Fairweather, PG, Ford, JR, Jenkins, GI, Keough, MJ, Prince, JD & Smyth, C 2017, 'Australia's coastal fisheries and farmed seafood: an ecological basis for determining sustainability', Australian Zoologist, vol. 39, no. 1, pp. 3-16.
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In response to consumer concerns about the sustainability of Australian-sourced seafood we derive a set of criteria within an explicit decision-process that can be used to determine whether locally farmed and wild-caught Australian seafood products meet standards of ecological sustainability and Ecologically Sustainable Development. These criteria substantially address the ecological deficiencies we identified in other systems commonly used for assessing seafood sustainability. The criteria address the issues that are relevant to local seafood production, and are populated with indicators (metrics) and benchmarks relevant to the Australian context. The indicators establish performance thresholds drawn from public domain data about the products, including observed empirical data and proxies, and include default decisions to be applied in the absence of adequate information. This decision structure is set within a peer-reviewed expert jury decision-making process. The criteria, decision process and decision outcomes from assessment of a number of pilot products were tested in a real seafood market (Melbourne), where we found a high level of producer, reseller and consumer acceptance of the judgements and ratings. The use of ecologically-derived standards results in several outcomes that differ from those of other seafood assessment systems, especially those assessments more focused on production standards, such as government, industry and NGO-supported programs, popularly used in Australia and worldwide. We conclude that despite high levels of uncertainty surrounding many of the population parameters, ecological patterns and processes, empirical cost-effective proxies can be used to reasonably estimate a form of sustainability that matches consumer interests/expectations for production of fresh local seafood. Despite the plethora of industry and government programs, there remains a significant but presently unmet consumer demand for ecologically-based, te...

Watanabe, S, Kuzhiumparambil, U, Nguyen, MA, Cameron, J & Fu, S 2017, 'Metabolic Profile of Synthetic Cannabinoids 5F-PB-22, PB-22, XLR-11 and UR-144 by Cunninghamella elegans', The AAPS Journal, vol. 19, no. 4, pp. 1148-1162.
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© 2017, American Association of Pharmaceutical Scientists. The knowledge of metabolic profile of synthetic cannabinoids is important for the detection of drugs in urinalysis due to the typical absence or low abundance of parent cannabinoids in human urine. The fungus Cunninghamella elegans has been reported to be a useful tool for metabolism study and thus applicability to synthetic cannabinoid metabolism was examined. In this study, 8-quinolinyl 1-(5-fluoropentyl)-1H–indole-3-carboxylate (5F-PB-22), 8-quinolinyl 1-pentyl-1H-indole-3-carboxylate (PB-22), [1-(5-fluoropentyl)-1H-indol-3-yl](2,2,3,3-tetramethylcyclopropyl)methanone (XLR-11) and (1-pentyl-1H-indol-3-yl)(2,2,3,3-tetramethylcyclopropyl)methanone (UR-144) were incubated with C. elegans and the metabolites were identified using liquid chromatography-quadrupole time-of-flight mass spectrometry. The obtained metabolites were compared with reported human metabolites to assess the suitability of the fungus to extrapolate human metabolism. 5F-PB-22 underwent dihydroxylation, dihydrodiol formation, oxidative defluorination, oxidative defluorination to carboxylic acid, ester hydrolysis and glucosidation, alone and/or in combination. The metabolites of PB-22 were generated by hydroxylation, dihydroxylation, trihydroxylation, dihydrodiol formation, ketone formation, carboxylation, ester hydrolysis and glucosidation, alone and/or in combination. XLR-11 was transformed through hydroxylation, dihydroxylation, aldehyde formation, carboxylation, oxidative defluorination, oxidative defluorination to carboxylic acid and glucosidation, alone and/or in combination. UR-144 was metabolised by hydroxylation, dihydroxylation, trihydroxylation, aldehyde formation, ketone formation, carboxylation, N-dealkylation and combinations. These findings were consistent with previously reported human metabolism except for the small extent of ester hydrolysis observed and the absence of glucuronidation. Despite the limitations, ...

Waters, L, Padula, MP, Marks, DC & Johnson, L 2017, 'Cryopreserved platelets demonstrate reduced activation responses and impaired signaling after agonist stimulation', Transfusion, vol. 57, no. 12, pp. 2845-2857.
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BACKGROUNDRoom temperature–stored (20‐24°C) platelets (PLTs) have a shelf life of 5 days, making it logistically challenging to supply remote medical centers with PLT products. Cryopreservation of PLTs in dimethyl sulfoxide (DMSO) and storage at –80°C enables an extended shelf life up to 2 years. Although cryopreserved PLTs have been widely characterized under resting conditions, their ability to undergo agonist‐induced activation is yet to be fully explored.STUDY DESIGN AND METHODSBuffy coat PLTs were cryopreserved at –80°C with 5% to 6% DMSO and sampled before freezing and after thawing. PLTs were analyzed under resting conditions and after agonist stimulation with adenosine diphosphate, collagen, or thrombin receptor–activating peptide‐6. The expression of activation markers, microparticle formation, and calcium mobilization were analyzed by flow cytometry. Soluble PLT proteins present in the PLT supernatant were examined by enzyme‐linked immunosorbent assay. Protein phosphorylation was investigated with Western blotting.RESULTSAfter cryopreservation, PLTs displayed increased surface activation markers and higher basal calcium levels. Cryopreserved PLTs demonstrated diminished aggregation responses. Additionally, cryopreserved PLTs showed a limited ability to become activated (as measured by CD62P and phosphatidylserine exposure and cytokine release) after agonist stimulation. A reduction in the abundance and phosphorylation of key signaling proteins (Akt, Src, Lyn, ERK, and p38) was seen in cryopreserved PLTs.CONCLUSIONSCryopreservation of PLTs induces dramatic changes to the basal PLT phenotype and renders them largely nonresponsive to agonist stimulation, likely due to the alterations in signal transduction. Therefore, ...

Watson, DM, Milner, KV & Leigh, A 2017, 'Novel application of species richness estimators to predict the host range of parasites', International Journal for Parasitology, vol. 47, no. 1, pp. 31-39.
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© 2016 Australian Society for Parasitology Host range is a critical life history trait of parasites, influencing prevalence, virulence and ultimately determining their distributional extent. Current approaches to measure host range are sensitive to sampling effort, the number of known hosts increasing with more records. Here, we develop a novel application of results-based stopping rules to determine how many hosts should be sampled to yield stable estimates of the number of primary hosts within regions, then use species richness estimation to predict host ranges of parasites across their distributional ranges. We selected three mistletoe species (hemiparasitic plants in the Loranthaceae) to evaluate our approach: a strict host specialist (Amyema lucasii, dependent on a single host species), an intermediate species (Amyema quandang, dependent on hosts in one genus) and a generalist (Lysiana exocarpi, dependent on many genera across multiple families), comparing results from geographically-stratified surveys against known host lists derived from herbarium specimens. The results-based stopping rule (stop sampling bioregion once observed host richness exceeds 80% of the host richness predicted using the Abundance-based Coverage Estimator) worked well for most bioregions studied, being satisfied after three to six sampling plots (each representing 25 host trees) but was unreliable in those bioregions with high host richness or high proportions of rare hosts. Although generating stable predictions of host range with minimal variation among six estimators trialled, distribution-wide estimates fell well short of the number of hosts known from herbarium records. This mismatch, coupled with the discovery of nine previously unrecorded mistletoe-host combinations, further demonstrates the limited ecological relevance of simple host-parasite lists. By collecting estimates of host range of constrained completeness, our approach maximises sampling efficiency while ge...

Webb, JR, Martin, AA, Johnson, RP, Joseph, MB, Newton, ME, Aharonovich, I, Toth, M & Macpherson, JV 2017, 'Fabrication of a single sub-micron pore spanning a single crystal (100) diamond membrane and impact on particle translocation', Carbon, vol. 122, pp. 319-328.
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© 2017 Elsevier Ltd The fabrication of sub-micron pores in single crystal diamond membranes, which span the entirety of the membrane, is described for the first time, and the translocation properties of polymeric particles through the pore investigated. The pores are produced using a combination of laser micromachining to form the membrane and electron beam induced etching to form the pore. Single crystal diamond as the membrane material, has the advantages of chemical stability and durability, does not hydrate and swell, has outstanding electrical properties that facilitate fast, low noise current-time measurements and is optically transparent for combined optical-conductance sensing. The resulting pores are characterized individually using both conductance measurements, employing a microcapillary electrochemical setup, and electron microscopy. Proof-of-concept experiments to sense charged polystyrene particles as they are electrophoretically driven through a single diamond pore are performed, and the impact of this new pore material on particle translocation is explored. These findings reveal the potential of diamond as a platform for pore-based sensing technologies and pave the way for the fabrication of single nanopores which span the entirety of a diamond membrane.

Weidner, J, Jarenbäck, L, de Jong, K, Vonk, JM, van den Berge, M, Brandsma, C-A, Boezen, HM, Sin, D, Bossé, Y, Nickle, D, Ankerst, J, Bjermer, L, Postma, DS, Faiz, A & Tufvesson, E 2017, 'Sulfatase modifying factor 1 (SUMF1) is associated with Chronic Obstructive Pulmonary Disease', Respiratory Research, vol. 18, no. 1.
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© 2017 The Author(s). Background: It has been observed that mice lacking the sulfatase modifying factor (Sumf1) developed an emphysema-like phenotype. However, it is unknown if SUMF1 may play a role in Chronic Obstructive Pulmonary Disease (COPD) in humans. The aim was to investigate if the expression and genetic regulation of SUMF1 differs between smokers with and without COPD. Methods: SUMF1 mRNA was investigated in sputum cells and whole blood from controls and COPD patients (all current or former smokers). Expression quantitative trait loci (eQTL) analysis was used to investigate if single nucleotide polymorphisms (SNPs) in SUMF1 were significantly associated with SUMF1 expression. The association of SUMF1 SNPs with COPD was examined in a population based cohort, Lifelines. SUMF1 mRNA from sputum cells, lung tissue, and lung fibroblasts, as well as lung function parameters, were investigated in relation to genotype. Results: Certain splice variants of SUMF1 showed a relatively high expression in lung tissue compared to many other tissues. SUMF1 Splice variant 2 and 3 showed lower levels in sputum cells from COPD patients as compared to controls. Twelve SNPs were found significant by eQTL analysis and overlapped with the array used for genotyping of Lifelines. We found alterations in mRNA expression in sputum cells and lung fibroblasts associated with SNP rs11915920 (top hit in eQTL), which validated the results of the lung tissue eQTL analysis. Of the twelve SNPs, two SNPs, rs793391 and rs308739, were found to be associated with COPD in Lifelines. The SNP rs793391 was also confirmed to be associated with lung function changes. Conclusions: We show that SUMF1 expression is affected in COPD patients compared to controls, and that SNPs in SUMF1 are associated with an increased risk of COPD. Certain COPD-associated SNPs have effects on either SUMF1 gene expression or on lung function. Collectively, this study shows that SUMF1 is associated with an incre...

Wen, S, Zhao, L, Zhao, Q, Li, D, Liu, C, Yu, Z, Shen, M, Majoral, J-P, Mignani, S, Zhao, J & Shi, X 2017, 'A promising dual mode SPECT/CT imaging platform based on^99mTc-labeled multifunctional dendrimer-entrapped gold nanoparticles', Journal of Materials Chemistry B, vol. 5, no. 21, pp. 3810-3815.
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Multifunctional^99mTc-labeled dendrimer-entrapped gold nanoparticles modified with different surface groups can be used for preferential SPECT/CT imaging of different organs.

Whyte, T, Gibson, T, Eager, D & Milthorpe, B 2017, 'Full-face motorcycle helmet protection from facial impacts: an investigation using THOR dummy impacts and SIMon finite element head model', Injury Prevention, vol. 23, no. 3, pp. 205-210.
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© 2017, BMJ Publishing Group. All rights reserved. Objective Facial impacts are both common and injurious for helmeted motorcyclists who crash; however, there is no facial impact requirement in major motorcycle helmet standards. This study examined the effect of fullface motorcycle helmet protection on brain injury risk in facial impacts using a test device with biofidelic head and neck motion. A preliminary investigation of energy absorbing foam in the helmet chin bar was carried out. Method Flat-faced rigid pendulum impacts were performed on a THOR dummy in an unprotected (no helmet) and protected mode (two full-face helmet conditions). The head responses of the dummy were input into the simulated injury monitor finite element head model to analyse the risk of brain injury in these impacts. Results Full-face helmet protection provides a significant reduction in brain injury risk in facial impacts at increasing impact speeds compared with an unprotected rider (p<0.05). The effect of low-density crushable foam added to the chin bar could not be distinguished from an unpadded chin bar impact. Conclusions Despite the lack of an impact attenuation requirement for the face, full-face helmets do provide a reduction in head injury risk to the wearer in facial impacts. The specific helmet design factors that influence head injury risk in facial impacts need further investigation if improved protection for helmeted motorcyclists is to be achieved.

Widjaja, M, Harvey, KL, Hagemann, L, Berry, IJ, Jarocki, VM, Raymond, BBA, Tacchi, JL, Gründel, A, Steele, JR, Padula, MP, Charles, IG, Dumke, R & Djordjevic, SP 2017, 'Elongation factor Tu is a multifunctional and processed moonlighting protein', Scientific Reports, vol. 7, no. 1, pp. 1-17.
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AbstractMany bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline. Recombinant MpnEf-Tu bound strongly to a diverse range of host molecules, and when bound to plasminogen, was able to convert plasminogen to plasmin in the presence of plasminogen activators. Fragments of Ef-Tu retain binding capabilities to host proteins. Bioinformatics and structural modelling studies indicate that the accumulation of positively charged amino acids in short linear motifs (SLiMs), and protein processing promote multifunctional behaviour. Codon bias engendered by an A + T rich genome may influence how positively-charged residues accumulate in SLiMs.

Wilkinson, AD, Collier, CJ, Flores, F, Langlois, L, Ralph, PJ & Negri, AP 2017, 'Combined effects of temperature and the herbicide diuron on Photosystem II activity of the tropical seagrass Halophila ovalis', Scientific Reports, vol. 7, no. 1, pp. 1-11.
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AbstractTropical seagrasses are at their highest risk of exposure to photosystem II (PSII) herbicides when elevated rainfall and runoff from farms transports these toxicants into coastal habitats during summer, coinciding with periods of elevated temperature. PSII herbicides, such as diuron, can increase the sensitivity of corals to thermal stress, but little is known of the potential for herbicides to impact the thermal optima of tropical seagrass. Here we employed a well-plate approach to experimentally assess the effects of diuron on the photosynthetic performance of Halophila ovalis leaves across a 25 °C temperature range (36 combinations of these stressors across 15–40 °C). The thermal optimum for photosynthetic efficiency (▵'Equation missing') in H. ovalis was 31 °C while lower and higher temperatures reduced ▵'Equation missing' as did all elevated concentrations of diuron. There were significant interactions between the effects of temperature and diuron, with a majority of the combined stresses causing sub-additive (antagonistic) effects. However, both stressors caused negative responses and the sum of the responses was greater than that caused by temperature or diuron alone. These results indicate that improving water quality (reducing herbicide in runoff) is likely to maximise seagrass health during extreme temperature events that will become more common as the climate changes.

Wilkinson, S, Stoller, P, Ralph, P, Hamdorf, B, Catana, LN & Kuzava, GS 2017, 'Exploring the Feasibility of Algae Building Technology in NSW', Procedia Engineering, vol. 180, pp. 1121-1130.
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© 2017 The Authors. Published by Elsevier Ltd. For some time, Biochemists have been exploring the potential to produce biofuels as an alternative to fossil fuel energy. Biofuels can be derived from crops such as corn, soybean and sugarcane however these crops can contribute to water scarcity and deforestation. Furthermore, large areas of land are used that could otherwise be used for food production. Another possibility is to use microalgae, which does not have the disadvantages associated with crop-based biofuels. Depending on conditions, microalgae can produce bio compounds that are converted into biofuels. The built environment is responsible for around 40 to 50% of total greenhouse gas emissions through fossil fuel consumption. Not only is it necessary to design and to retrofit our built environment to be more energy efficient, but it is also necessary to consider alternative fuel sources. To date, this has mostly focused on solar, wind and geothermal sources, however one residential building in Hamburg Germany has adopted algae building technology in the form of façade panels which act as a source of energy for heating the apartments and for hot water. The climate in northern Germany is very different to Australia, and the question arises; what is the feasibility to adopt algae building technology in New South Wales? There are issues around the physical and technical aspects of the technology, the social and environmental aspects, the regulatory and planning aspects, as well as the economic considerations. This paper reports on a study with key stakeholders in New South Wales to explore barriers and drivers associated with the adoption of algae building technology.

Williams, KA, Wallman, JF, Lessard, BD, Kavazos, CRJ, Mazungula, DN & Villet, MH 2017, 'Nocturnal oviposition behavior of blowflies (Diptera: Calliphoridae) in the southern hemisphere (South Africa and Australia) and its forensic implications', Forensic Science, Medicine, and Pathology, vol. 13, no. 2, pp. 123-134.
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Williams, SG, Bhadbhade, M, Bishop, R & Ung, AT 2017, 'An alkaloid-like 3-azabicyclo[3.3.1]non-3-ene library obtained from the bridged Ritter reaction', Tetrahedron, vol. 73, no. 2, pp. 116-128.
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Williams, SG, Bhadbhade, M, Bishop, R & Ung, AT 2017, 'Synthesis and Crystal Structure of Unexpected (1S,4R,5R,6S)-4-Cyano-2,2,6-trimethyl-3-azabicyclo[3.3.1]nonan-6-yl Acetate', Australian Journal of Chemistry, vol. 70, no. 12, pp. 1269-1269.
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The reaction of (–)-β-pinene with KCN under a mild bridged Ritter reaction gave (1S,5R,6S)-2,2,6-trimethyl-3-aza-bicyclo[3.3.1]non-3-en-6-yl acetate that subsequently reacted to provide an unexpected (1S,4R,5R,6S)-4-cyano-2,2,6-trimethyl-3-azabicyclo[3.3.1]nonane-6-yl acetate. The structure of the compound was determined by high-resolution mass spectrometry, and IR and NMR spectroscopy and confirmed by single crystal X-ray crystallography. The compound crystallises in the monoclinic P21 space group, with unit cell parameters a 8.6120 (17), b 7.4570 (15), c 11.189 (2) Å, and β 110.16 (3)°.

Williams, TJ, Liao, Y, Ye, J, Kuchel, RP, Poljak, A, Raftery, MJ & Cavicchioli, R 2017, 'Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi', Environmental Microbiology, vol. 19, no. 6, pp. 2210-2227.
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SummaryHalohasta litchfieldiae represents ∼ 44% and Halorubrum lacusprofundi ∼ 10% of the hypersaline, perennially cold (≥ −20°C) Deep Lake community in Antarctica. We used proteomics and microscopy to define physiological responses of these haloarchaea to growth at high (30°C) and low (10 and 4°C) temperatures. The proteomic data indicate that both species responded to low temperature by modifying their cell envelope including protein N‐glycosylation, maintaining osmotic balance and translation initiation, and modifying RNA turnover and tRNA modification. Distinctions between the two species included DNA protection and repair strategies (e.g. roles of UspA and Rad50), and metabolism of glycerol and pyruvate. For Hrr. lacusprofundi, low temperature led to the formation of polyhydroxyalkanoate‐like granules, with granule formation occurring by an unknown mechanism. Hrr. lacusprofundi also formed biofilms and synthesized high levels of Hsp20 chaperones. Hht. litchfieldiae was characterized by an active CRISPR system, and elevated levels of the core gene expression machinery, which contrasted markedly to the decreased levels of Hrr. lacusprofundi. These findings greatly expand the understanding of cellular mechanisms of cold adaptation in psychrophilic archaea, and provide insight into how Hht. litchfieldiae gains dominance in Deep Lake.

Winata, P, Williams, M, McGowan, E, Nassif, N, van Zandwijk, N & Reid, G 2017, 'The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection', BMC Research Notes, vol. 10, no. 1, pp. 1-7.
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© 2017 The Author(s). Objective: MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. Results: The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

Wolff, C, Stiller, B, Eggleton, BJ, Steel, MJ & Poulton, CG 2017, 'Cascaded forward Brillouin scattering to all Stokes orders', New Journal of Physics, vol. 19, no. 2, pp. 023021-023021.
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© 2017 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. Inelastic scattering processes such as Brillouin scattering can often function in cascaded regimes and this is likely to occur in certain integrated opto-acoustic devices. We develop a Hamiltonian formalism for cascaded Brillouin scattering valid for both quantum and classical regimes. By regarding Brillouin scattering as the interaction of a single acoustic envelope and a single optical envelope that covers all Stokes and anti-Stokes orders, we obtain a compact model that is well suited for numerical implementation, extension to include other optical nonlinearities or short pulses, and application in the quantum-optics domain. We then theoretically analyze intra-mode forward Brillouin scattering (FBS) for arbitrary waveguides with and without optical dispersion. In the absence of optical dispersion, we find an exact analytical solution. With a perturbative approach, we furthermore solve the case of weak optical dispersion. Our work leads to several key results on intra-mode FBS. For negligible dispersion, we show that cascaded intra-mode FBS results in a pure phase modulation and discuss how this necessitates specific experimental methods for the observation of fiber-based and integrated FBS. Further, we discuss how the descriptions that have been established in these two classes of waveguides connect to each other and to the broader context of cavity opto-mechanics and Raman scattering. Finally, we draw an unexpected striking similarity between FBS and discrete diffraction phenomena in waveguide arrays, which makes FBS an interesting candidate for future research in quantum-optics.

Wongsai, N, Wongsai, S & Huete, A 2017, 'Annual Seasonality Extraction Using the Cubic Spline Function and Decadal Trend in Temporal Daytime MODIS LST Data', Remote Sensing, vol. 9, no. 12, pp. 1254-1254.
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© 2017 by the author. Examining climate-related satellite data that strongly relate to seasonal phenomena requires appropriate methods for detecting the seasonality to accommodate different temporal resolutions, high signal variability and consecutive missing values in the data series. Detection of satellite-based Land Surface Temperature (LST) seasonality is essential and challenging due to missing data and noise in time series data, particularly in tropical regions with heavy cloud cover and rainy seasons. We used a semi-parametric approach, involving the cubic spline function with the annual periodic boundary condition and weighted least square (WLS) regression, to extract annual LST seasonal pattern without attempting to estimate the missing values. The time series from daytime Aqua eight-day MODIS LST located on Phuket Island, southern Thailand, was selected for seasonal extraction modelling across three different land cover types. The spline-based technique with appropriate number and placement of knots produces an acceptable seasonal pattern of surface temperature time series that reflects the actual local season and weather. Finally, the approach was applied to the morning and afternoon MODIS LST datasets (MOD11A2 and MYD11A2) to demonstrate its application on seasonally-adjusted long-term LST time series. The surface temperature trend in both space and time was examined to reveal the overall 10-year period trend of LST in the study area. The result of decadal trend analysis shows that various Land Use and Land Cover (LULC) types have increasing, but variable surface temperature trends.

Wood, I, Park, S, Tooke, J, Smith, O, Morgan, RM & Meakin, GE 2017, 'Efficiencies of recovery and extraction of trace DNA from non-porous surfaces', Forensic Science International: Genetics Supplement Series, vol. 6, pp. e153-e155.
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DNA recovery and extraction efficiencies are key considerations for trace DNA interpretation in casework, but prior studies have tended to focus on assessing these for body fluids rather than trace DNA. This study therefore examined the recovery and extraction of trace DNA using different collection methods from a range of non-porous surfaces relevant to crimes including homicides, terror attacks, and wildlife poaching. Direct extraction of DNA from solutions of a known concentration revealed absolute extraction efficiencies of ∼82%. When DNA was extracted from swabs seeded with the DNA solution, a similarly high efficiency of ∼85% was achieved from nylon-flocked swabs, with a lower efficiency of ∼55% from cotton swabs. However, when DNA was recovered from non-porous surfaces with swabs, ∼55% of DNA was still recovered from plastic knife handles, but lower efficiencies were achieved from the other substrates, particularly metal cable. Varied and poor recovery was observed using mini-tapes and requires further investigation. These results demonstrate that >50% recovery efficiency of trace DNA is achievable with both swab types, although recovery rates may be affected by surface type and/or practitioner experience.

Wood, RJ, Mitrovic, SM, Lim, RP & Kefford, BJ 2017, 'Chronic effects of atrazine exposure and recovery in freshwater benthic diatoms from two communities with different pollution histories', Aquatic Toxicology, vol. 189, pp. 200-208.
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Woodcock, S & Sloan, WT 2017, 'Biofilm community succession: a neutral perspective', Microbiology, vol. 163, no. 5, pp. 664-668.
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© 2017 The Authors. Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

Wu, G, Jiang, Y, Zhu, X, Jin, D, Han, Y, Han, J, Wu, Z & Wu, Z 2017, 'Prevalence and risk factors for complications in adult patients with short bowel syndrome receiving long-term home parenteral nutrition.', Asia Pac J Clin Nutr, vol. 26, no. 4, pp. 591-597.
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BACKGROUND AND OBJECTIVES: Short bowel syndrome (SBS) is a complicated and challenging disease where home parenteral nutrition (HPN) is widely used. The complications of long-term HPN-dependent in adult patients with SBS are poorly documented. This study was mainly aimed to assess the prevalence and risk factors of HPNassociated complications in adult patients with SBS, especially the catheter-related sepsis and HPN-associated liver/biliary disorders. METHODS AND STUDY DESIGN: 47 non-malignant adult patients with SBS who received HPN for more than 2 years in our clinical nutrition center were included. Patients were divided into two groups according to whether HPN-associated complications were present or not. Student's t-test and χ2 test were applied to compare the differences between the two groups. RESULTS: The mean frequency of catheter-related sepsis was 0.31±0.05 per catheter year of HPN. An higher incidence of catheter-related infections (p<0.001) and shorter delay between HPN onset and first infection (p<0.001) were identified as risk factors for catheter-related sepsis. A total of 25 patients (53.2%) developed HPN-associated liver/biliary diseases. The identified risk factors for HPNassociated liver/biliary disorders were higher rate of catheter-related infections (p=0.009), shorter delay between HPN onset and first infection (p=0.017), higher energy content of HPN (p=0.014), higher glucose rate of HPN (p=0.009), and lower lipid rate of HPN (p=0.022). CONCLUSION: Our study revealed that adult patients with SBS receiving long-term HPN treatment developed a low prevalence of catheter-related sepsis but a rather high prevalence of HPN-associated liver/biliary disorders. We also identified several risk factors for HPN-associated complications which should be taken notice of in clinical practice.

Wu, J, Guan, K, Hayek, M, Restrepo‐Coupe, N, Wiedemann, KT, Xu, X, Wehr, R, Christoffersen, BO, Miao, G, da Silva, R, de Araujo, AC, Oliviera, RC, Camargo, PB, Monson, RK, Huete, AR & Saleska, SR 2017, 'Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales', Global Change Biology, vol. 23, no. 3, pp. 1240-1257.
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AbstractGross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance‐derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light‐use efficiency associated with changes in the parameters themselves. Our fitted model was able to explain most of the variability in GEP at hourly (R2 = 0.77) to interannual (R2 = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light‐use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing bio...

Wu, R, Zhou, J, Lei, L, Zhang, S, Xiao, Z, Zhang, J & Xu, S 2017, 'α-NaYF4:Yb3+-Tm3+@CaF2 nanocrystals for NIR-to-NIR temperature sensing', Chemical Physics Letters, vol. 667, pp. 206-210.
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© 2016 The approach of lanthanides doping upconversion temperature sensing exhibits high superiority in bioscience. However, most of the upconversion nanothermometers show their fluorescences temperature sensing beyond biological transparent window (650–950 nm) while suffering from the interference of surrounding environment. Here we report a nanoprobe with ultrasmall size, i.e. α-NaYF4:Yb-Tm@CaF2 nanocrystal, which has a sensitive capability to realize NIR-to-NIR temperature sensing. Temperature sensing sensitivities through 3H4 → 3H6 and 1G4 → 3H6 transitions of Tm3+ ions are evaluated in temperature region of 313–373 K. The results indicate that α-NaYF4:Yb-Tm@CaF2 nanocrystal is a promising candidate for biological temperature sensing.

Xie, F, Zhang, L, Su, D, Jaroniec, M & Qiao, S 2017, 'Na₂Ti₃O₇@N‐Doped Carbon Hollow Spheres for Sodium‐Ion Batteries with Excellent Rate Performance', Advanced Materials, vol. 29, no. 24, pp. 1700989-1700989.
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Uniform Na2Ti3O7 hollow spheres assembled from N‐doped carbon‐coated ultrathin nanosheets are synthesized. A unique multilayer structure of nanosheets is presumed to significantly reduce energy consumption during the diffusion process of sodium ions, while the carbon‐coated structure can increase the overall conductivity. The as‐prepared sample used as an anode in sodium‐ion batteries exhibits the best rate performance ever reported for Na2Ti3O7, delivering more than 60 mAh g−1 after 1000 continuous cycles at the high rate of 50 C, which was achieved due to its unique structure.

Xie, J, Xie, X, Mi, C, Gao, Z, Pan, Y, Fan, Q, Su, H, Jin, D, Huang, L & Huang, W 2017, 'Controlled Synthesis, Evolution Mechanisms, and Luminescent Properties of ScF_x:Ln (x = 2.76, 3) Nanocrystals', Chemistry of Materials, vol. 29, no. 22, pp. 9758-9766.
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© 2017 American Chemical Society. Kinetic or thermodynamic control has been employed to guide the selective synthesis of conventional organic compounds, and it should be a powerful tool as well for accessing unusual inorganic nanocrystals, particularly when a series of members with similar chemical compositions and phase structures exist. Indeed, a comprehensive mapping of the energy barrier distribution of each nanocrystal in a predefined reaction system will enable not only the precise synthesis of nanocrystals with expected sizes, morphologies, phase structures, and ultimately functionalities, but also disclosure of the evolution details of nanocrystals from one structure to another. Using ScFx:Ln (x = 2.76, 3) series as a proof-of-concept, we have successfully mapped out the energy barriers that correspond to each of the ScFx:Ln nanocrystals, unraveled suitable temperatures for each type of nanocrystal formation, recorded their phase transition procedures, and also discovered the relationships of the products at each reaction stage. To testify how this approach allows one to tailor the structure-related optical properties, different lanthanide-doped ScFx nanocrystals were synthesized and a wide-range of luminescence fine-tuning was achieved, which not only showcases high quality of the nanocrystals, but also provides more candidates for various luminescence applications, especially when single-particle upconversion emission is required.

Xu, X, Clarke, C, Ma, C, Casillas, G, Das, M, Guan, M, Liu, D, Wang, L, Tadich, A, Du, Y, Ton-That, C & Jin, D 2017, 'Depth-profiling of Yb³⁺ sensitizer ions in NaYF₄ upconversion nanoparticles', Nanoscale, vol. 9, no. 23, pp. 7719-7726.
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© 2017 The Royal Society of Chemistry. Enhancing the efficiency of upconversion nanoparticles (UCNPs) and therefore their brightness is the critical goal for this emerging material to meet growing demands in many potential applications including sensing, imaging, solar energy conversion and photonics. The distribution of the photon sensitizer and activator ions that form a network of energy transfer systems within each single UCNP is vital for understanding and optimizing their optical properties. Here we employ synchrotron-based X-ray Photoelectron Spectroscopy (XPS) to characterize the depth distribution of Yb3+ sensitizer ions in host NaYF4 nanoparticles and systematically correlate the structure with the optical properties for a range of UCNPs with different sizes and doping concentrations. We find a radial gradient distribution of Yb3+ from the core to the surface of the NaYF4 nanoparticles, regardless of their size or the sensitizer's concentration. Energy dispersive X-ray Spectroscopy (EDX) was also used to further confirm the distribution of the sensitizer ions in the host matrix. These results have profound implications for the upconversion optical property variations.

Xu, X, Rawling, T, Roseblade, A, Bishop, R & Ung, AT 2017, 'Antiproliferative activities of alkaloid-like compounds', MedChemComm, vol. 8, no. 11, pp. 2105-2114.
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Tricyclic alkaloid-like compounds were synthesised in a few steps, via the bridging Ritter reaction.

Xu, Z-Q, Elbadawi, C, Tran, TT, Kianinia, M, Li, X, Liu, D, Hoffman, TB, Nguyen, M, Kim, S, Edgar, JH, Wu, X, Song, L, Ali, S, Ford, M, Toth, M & Aharonovich, I 2017, 'Single Photon Emission from Plasma Treated 2D Hexagonal Boron Nitride', Nanoscale, vol. 10, no. 17, pp. 7957-7965.
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Artificial atomic systems in solids are becoming increasingly importantbuilding blocks in quantum information processing and scalable quantumnanophotonic networks. Yet, synthesis of color centers that act as singlephoton emitters which are suitable for on-chip applications is still beyondreach. Here, we report a number of plasma and thermal annealing methods for thefabrication of emitters in tape-exfoliated hexagonal boron nitride (hBN)crystals. A two-step process comprised of Ar plasma etching and subsequentannealing in Ar is highly robust, and yields a seven-fold increase in theconcentration of emitters in hBN. The initial plasma etching step generatesemitters that suffer from blinking and bleaching, whereas the two-step processyields emitters that are photostable at room temperature and have an emissionenergy distribution that is red-shifted relative to that of pristine hBN. Ananalysis of emitters fabricated by a range of plasma and annealing treatments,combined with a theoretical investigation of point defects in hBN indicatesthat single photon emitters characterized by a high degree of photostabilityand emission wavelengths greater than ~700 nm are associated with defectcomplexes that contain oxygen. This is further confirmed by generating theemitters by annealing hBN in an oxidative atmosphere. Our findings advancepresent understanding of the structure of quantum emitter in hBN and enhancethe nanofabrication toolkit that is needed to realize integrated quantumnanophotonics based on 2D materials.

Yan, J, Kuzhiumparambil, U, Bandodkar, S, Solowij, N & Fu, S 2017, 'Development and validation of a simple, rapid and sensitive LC-MS/MS method for the measurement of urinary neurotransmitters and their metabolites', Analytical and Bioanalytical Chemistry, vol. 409, no. 30, pp. 7191-7199.
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Yang, Y, Zhu, Y, Zhou, J, Wang, F & Qiu, J 2017, 'Integrated Strategy for High Luminescence Intensity of Upconversion Nanocrystals', ACS Photonics, vol. 4, no. 8, pp. 1930-1936.
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© 2017 American Chemical Society. The growing applications of upconversion nanocrystals in bioimaging, therapeutics, and photonics have given rise to a demand of high quality nanocrystals with desirable luminescence intensity. Although the design of optimal nanocrystals such as core-shell nanostructures has improved the intensity, the internal links between dopant concentration balance, epitaxial growth protection, and shell thickness effect encounter a compromised situation that lacks of integrated consideration and comprehensive assessment. Here we propose an integrated strategy based on a core-shell design for the enhancement of upconversion luminescence intensity. Epitaxial protection can enable higher activator accommodation capacity in limited spatial scale, which leads to an Er3+ concentration threshold improvement in β-NaYF4 core-shell nanocrystals from 2 to 6 mol %. We further perform a comprehensive assessment of the nanocrystals with convincing performance improvement in ensemble spectroscopic intensity, upconversion quantum yield, and single nanocrystal intensity. Our findings provide improved understanding of electronic behaviors in multiphoton upconversion and opportunities for diverse applications requiring high quality upconversion nanocrystals.

Young, NA, Drew, SC, Maniam, S & Langford, SJ 2017, 'Systematically Studying the Effect of Fluoride on the Properties of Cyclophanes Bearing Naphthalene Diimide and Dialkoxyaryl Groups', Chemistry – An Asian Journal, vol. 12, no. 13, pp. 1668-1675.
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AbstractAnion–π interactions between the Lewis basic anion fluoride and π‐acidic naphthalene diimide was systematically studied in a series of cyclophanes in which the properties are modulated through the influence of a second, electron‐rich aromatic unit. The systems and subsequently generated radical anions, upon addition of fluoride, were studied by absorption spectroscopic and EPR techniques. The results infer a modulation as a result of the nature and strength of the π–π interaction in the macrocyclic structure.

Yu, TT, Nizalapur, S, Ho, KKK, Yee, E, Berry, T, Cranfield, CG, Willcox, M, Black, DS & Kumar, N 2017, 'Design, Synthesis and Biological Evaluation of N‐Sulfonylphenyl glyoxamide‐Based Antimicrobial Peptide Mimics as Novel Antimicrobial Agents', ChemistrySelect, vol. 2, no. 12, pp. 3452-3461.
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AbstractAntibiotic resistance is a major global health concern. There is an urgent need for the development of novel antimicrobials. Recently, phenylglyoxamide‐based small molecular antimicrobial peptide mimics have been identified as potential new leads to treat bacterial infections. Here, we describe the synthesis of novel phenylglyoxamide derivatives via the ring‐opening reaction of N‐sulfonylisatins with primary amines, followed by conversion into hydrochloride, quaternary ammonium iodide or gunidinium salts. The antibacterial activity of the compounds against Staphylococcus aureus was evaluated by in vitro assays. Structure‐activity relationship studies revealed that 5‐bromo‐substituent at the phenyl ring, octyl group appended to the ortho sulfonamide group or guanidine hydrochloride salt as the terminal group significantly contributed to potency. The most potent compound, the gunidinium salt 35 d, exhibited a minimum inhibitory concentration value of 12 μM and a therapeutic index of 15. It also demonstrated its potential to act as antimicrobial pore‐forming agent. Overall, the results identified 35 d as a new lead antimicrobial compound.

Zachreson, C, Wolff, C, Whitchurch, CB & Toth, M 2017, 'Emergent pattern formation in an interstitial biofilm', Physical Review E, vol. 95, no. 1, pp. 1-14.
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© 2017 American Physical Society. Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns. By systematically varying this property (which we quantify with a stiffness coefficient γ), we show that subtle changes in the substratum stiffness can give rise to a stable state characterized by a high degree of local order and long-range pattern formation. The ordered state exhibits characteristics typically associated with bacterial fitness advantages, even though it is induced by changes in environmental conditions rather than changes in biological parameters. Our findings are applicable to a broad range of biofilms and provide insights into the relationship between bacterial movement and their environment, and basic mechanisms behind self-organization of biophysical systems.

Zachreson, C, Yap, X, Gloag, ES, Shimoni, R, Whitchurch, CB & Toth, M 2017, 'Network patterns in exponentially growing 2D biofilms', Phys. Rev. E, vol. 96, no. 4, pp. 042401-042401.
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Anisotropic collective patterns occur frequently in the morphogenesis of 2Dbiofilms. These patterns are often attributed to growth regulation mechanismsand differentiation based on gradients of diffusing nutrients and signallingmolecules. Here, we employ a model of bacterial growth dynamics to show thateven in the absence of growth regulation or differentiation, confinement by anenclosing medium such as agar can itself lead to stable pattern formation overtime scales that are employed in experiments. The underlying mechanism relieson path formation through physical deformation of the enclosing environment.

Zavřel, T, Očenášová, P & Červený, J 2017, 'Phenotypic characterization of Synechocystis sp. PCC 6803 substrains reveals differences in sensitivity to abiotic stress', PLOS ONE, vol. 12, no. 12, pp. e0189130-e0189130.
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© 2017 Zavřel 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. Synechocystis sp. PCC 6803 is a widely used model cyanobacterium, whose substrains can vary on both genotype and phenotype levels. Previously described phenotypic variations include ability of mixotrophic growth, ability of movement on agar plates and variations in pigments composition or cell size. In this study, we report for the first time significant variation among Synechocystis substrains in complex cellular traits such as growth rate, photosynthesis efficiency, cellular dry weight and cellular composition (including protein or carbohydrates content). We also confirmed previously reported differences in cell size. Synechocystis cultures were cultivated in controlled environment of flat panel photobioreactors under red, blue and white light of intensities up to 790 μmol(photons) m-2 s-1, temperatures 23C–60C, input CO2 concentrations ranging from 400 to 15 000 ppm and in BG11 cultivation medium with and without addition of NaCl. Three Synechocystis substrains were used for the comparative experiments: GT-L, GT-B (Brno, CZ) and PCC-B (Brno, CZ). Growth rates of Synechocystis GT-B were inhibited under high intensities of red light (585–670 nm), and growth rates of both substrains GT-B and PCC-B were inhibited under photons of wavelengths 485–585 nm and 670–700 nm. Synechocystis GT-B was more sensitive to low temperatures than the other two tested substrains, and Synechocystis GT-L was sensitive to the presence of NaCl in the cultivation media. The results suggest that stress sensitivity of commonly used Synechocystis substrains can strongly vary, similarly as glucose tolerance or motility as reported previously. Our study further supports the previous statement that emphasizes importance of proper ...

Zhang, J, Sun, B, McDonagh, AM, Zhao, Y, Kretschmer, K, Guo, X & Wang, G 2017, 'A multi-functional gel co-polymer bridging liquid electrolyte and solid cathode nanoparticles: An efficient route to Li–O 2 batteries with improved performance', Energy Storage Materials, vol. 7, pp. 1-7.
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© 2016 Lithium-oxygen (Li–O2) batteries have the highest theoretical energy density amongst all rechargeable batteries and have attracted significant attention. However, large over-potentials originating from sluggish reaction kinetics often lead to low round-trip energy efficiency and short cycle life. We report here a novel multi-functional gel co-polymer that efficiently enhances the discharge and charge performances in Li–O2 batteries by intimately connecting the liquid electrolyte and solid cathode nanoparticles. On one hand, the co-polymer material, poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate-co-methyl methacrylate) (P(TMA-MMA)), functions as a binder during the fabrication of the cathode and forms a gel polymer membrane to retain liquid electrolyte and to increase ionic conductivity. On the other hand, the TMA units, containing N–O radical groups that catalyse Li2O2 formation and decomposition during charge and discharge cycles, are distributed throughout the polymer membrane. This allows more effective formation and decomposition of Li2O2 than surface bound catalytic units. The combination of gelable MMA and catalytic TMA moieties enhances the interface between liquid electrolyte and solid cathode by functioning as a medium both to transport Li+ (enhancing discharge process) and to carry electrons (reducing charge over-potential). Consequently, the optimized P(TMA-MMA) co-polymers provide exceptional electrochemical performance in Li–O2 batteries.

Zhang, J, Sun, B, Zhao, Y, Kretschmer, K & Wang, G 2017, 'Modified Tetrathiafulvalene as an Organic Conductor for Improving Performances of Li−O₂ Batteries', Angewandte Chemie International Edition, vol. 56, no. 29, pp. 8505-8509.
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AbstractLarge over‐potentials owing to the sluggish kinetics of battery reactions have always been the drawbacks of Li−O2 batteries, which lead to short cycle life. Although redox mediators have been intensively investigated to overcome this issue, side‐reactions are generally induced by the solvated nature of redox mediators. Herein, we report an alternative method to achieve more efficient utilization of tetrathiafulvalene (TTF) in Li−O2 batteries. By coordinating TTF+ with LiCl during charging, an organic conductor TTF+Clx− precipitate covers Li2O2 to provide an additional electron‐transfer pathway on the surface, which can significantly reduce the charge over‐potential, improve the energy efficiency of Li−O2 batteries, and eliminate side‐reactions between the lithium metal anode and TTF+. When a porous graphene electrode is used, the Li−O2 battery combined with TTF and LiCl shows an outstanding performance and prolonged cycle life.

Zhang, J, Sun, B, Zhao, Y, Kretschmer, K & Wang, G 2017, 'Modified Tetrathiafulvalene as an Organic Conductor for Improving Performances of Li−O₂ Batteries', Angewandte Chemie, vol. 129, no. 29, pp. 8625-8629.
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AbstractLarge over‐potentials owing to the sluggish kinetics of battery reactions have always been the drawbacks of Li−O2 batteries, which lead to short cycle life. Although redox mediators have been intensively investigated to overcome this issue, side‐reactions are generally induced by the solvated nature of redox mediators. Herein, we report an alternative method to achieve more efficient utilization of tetrathiafulvalene (TTF) in Li−O2 batteries. By coordinating TTF+ with LiCl during charging, an organic conductor TTF+Clx− precipitate covers Li2O2 to provide an additional electron‐transfer pathway on the surface, which can significantly reduce the charge over‐potential, improve the energy efficiency of Li−O2 batteries, and eliminate side‐reactions between the lithium metal anode and TTF+. When a porous graphene electrode is used, the Li−O2 battery combined with TTF and LiCl shows an outstanding performance and prolonged cycle life.

Zhang, X, Cao, J & Carroll, RJ 2017, 'Estimating Varying Coefficients for Partial Differential Equation Models', Biometrics, vol. 73, no. 3, pp. 949-959.
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Summary Partial differential equations (PDEs) are used to model complex dynamical systems in multiple dimensions, and their parameters often have important scientific interpretations. In some applications, PDE parameters are not constant but can change depending on the values of covariates, a feature that we call varying coefficients. We propose a parameter cascading method to estimate varying coefficients in PDE models from noisy data. Our estimates of the varying coefficients are shown to be consistent and asymptotically normally distributed. The performance of our method is evaluated by a simulation study and by an empirical study estimating three varying coefficients in a PDE model arising from LIDAR data.

Zhang, X, Li, P, Zang, R, Wang, S, Zhu, Y, Li, C & Wang, G 2017, 'Antimony/Porous Biomass Carbon Nanocomposites as High‐Capacity Anode Materials for Sodium‐Ion Batteries', Chemistry – An Asian Journal, vol. 12, no. 1, pp. 116-121.
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AbstractAntimony/porous biomass carbon nanocomposites have been prepared by a chemical reduction method and applied as anodes for sodium‐ion batteries. The porous biomass carbon derived from a black fungus had a large Brunauer–Emmett–Teller (BET) surface area of 2233 m2 g−1 in which antimony nanoparticles were uniformly distributed in the porous carbon. The as‐prepared antimony/porous biomass carbon nanocomposites exhibited a high reversible sodium storage capacity of 567 mA h g−1 at a current density of 100 mA g−1, extended cycling stability, and good rate capability.

Zhang, X, Wang, H, Ma, Y & Carroll, RJ 2017, 'Linear Model Selection When Covariates Contain Errors', Journal of the American Statistical Association, vol. 112, no. 520, pp. 1553-1561.
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© 2017 American Statistical Association. Prediction precision is arguably the most relevant criterion of a model in practice and is often a sought after property. A common difficulty with covariates measured with errors is the impossibility of performing prediction evaluation on the data even if a model is completely given without any unknown parameters. We bypass this inherent difficulty by using special properties on moment relations in linear regression models with measurement errors. The end product is a model selection procedure that achieves the same optimality properties that are achieved in classical linear regression models without covariate measurement error. Asymptotically, the procedure selects the model with the minimum prediction error in general, and selects the smallest correct model if the regression relation is indeed linear. Our model selection procedure is useful in prediction when future covariates without measurement error become available, for example, due to improved technology or better management and design of data collection procedures. Supplementary materials for this article are available online.

Zhao, CS, Yang, ST, Zhang, HT, Liu, CM, Sun, Y, Yang, ZY, Zhang, Y, Dong, BE & Lim, RP 2017, 'Coupling habitat suitability and ecosystem health with AEHRA to estimate E-flows under intensive human activities', Journal of Hydrology, vol. 551, pp. 470-483.
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© 2017 Elsevier B.V. Sustaining adequate environmental flows (e-flows) is a key principle for maintaining river biodiversity and ecosystem health, and for supporting sustainable water resource management in basins under intensive human activities. But few methods could correctly relate river health to e-flows assessment at the catchment scale when they are applied to rivers highly impacted by human activities. An effective method is presented in this study to closely link river health to e-flows assessment for rivers at the catchment scale. Key fish species, as indicators of ecosystem health, were selected by using the foodweb model. A multi-species-based habitat suitability model (MHSI) was improved, and coupled with dominance of the key fish species as well as the Index of Biological Integrity (IBI) to enhance its accuracy in determining the fish-preferred key hydrologic habitat variables related to ecosystem health. Taking 5964 fish samples and concurrent hydrological habitat variables as the basis, the combination of key variables of flow-velocity and water-depth were determined and used to drive the Adapted Ecological Hydraulic Radius Approach (AEHRA) to study e-flows in a Chinese urban river impacted by intensive human activities. Results showed that upstream urbanization resulted in abnormal river-course geomorphology and consequently abnormal e-flows under intensive human activities. Selection of key species based on the foodweb and trophic levels of aquatic ecosystems can reflect a comprehensive requirement on e-flows of the whole aquatic ecosystem, which greatly increases its potential to be used as a guidance tool for rehabilitation of degraded ecosystems at large spatial scales. These findings have significant ramifications for catchment e-flows assessment under intensive human activities and for river ecohealth restoration in such rivers globally.

Zhao, R, Xia, W, Lin, C, Sun, J, Mahmood, A, Wang, Q, Qiu, B, Tabassum, H & Zou, R 2017, 'A pore-expansion strategy to synthesize hierarchically porous carbon derived from metal-organic framework for enhanced oxygen reduction', Carbon, vol. 114, pp. 284-290.
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Zhao, Y, Zhang, J, Guo, X, Fan, H, Wu, W, Liu, H & Wang, G 2017, 'Fe₃C@nitrogen doped CNT arrays aligned on nitrogen functionalized carbon nanofibers as highly efficient catalysts for the oxygen evolution reaction', Journal of Materials Chemistry A, vol. 5, no. 37, pp. 19672-19679.
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Fe₃C based catalysts are found to be one of the most promising electrocatalysts for the oxygen evolution reaction (OER).

Zheng, M, Moriarty, NW, Xu, Y, Reimers, JR, Afonine, PV & Waller, MP 2017, 'Solving the scalability issue in quantum-based refinement: Q|R#1', Acta Crystallographica Section D Structural Biology, vol. 73, no. 12, pp. 1020-1028.
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Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately asnm, wherenis the number of atoms andm(≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package calledQ|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach inQ|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

Zheng, M, Reimers, JR, Waller, MP & Afonine, PV 2017, 'Q|R: quantum-based refinement', Acta Crystallographica Section D Structural Biology, vol. 73, no. 1, pp. 45-52.
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Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is twofold: firstly, the restraints have the potential to be more accurate, and secondly, the restraints can be more easily applied to new molecules such as drugs or novel cofactors. Here, a new project calledQ|Raimed at developing quantum-based refinement of biomacromolecules is under active development by researchers at Shanghai University together withPHENIXdevelopers. The central focus of this long-term project is to develop software that is built on top of open-source components. A development version ofQ|Rwas used to compare quantum-based refinements with standard refinement using a small model system.

Zheng, S, Kim, C, Meier, P, Sibbritt, D & Zaslawski, C 2017, 'Development of a Novel Questionnaire for the Traditional Chinese Medicine Pattern Diagnosis of Stress', Journal of Acupuncture and Meridian Studies, vol. 10, no. 4, pp. 276-285.
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© 2017. Currently, there is no definitive diagnosis or list of signs and symptoms for "stress" in either modern biomedicine or Chinese medicine (CM). While modern theories on stress relate to the neurological interaction of a stressor or stimuli on the autonomic nervous system, it is generally regarded as subjective in nature and as such each individual will likely present varying somatic or cognitive signs and symptoms. A questionnaire was therefore developed, based on textual research, that incorporated both general as well as gender specific signs and symptom responses to determine the most common CM patterns associated with individuals who report as feeling stressed. For the 45 females who completed the questionnaire, the mean percentage of symptoms per CM pattern showed that the pattern with the highest average percentage was heart qi deficiency (61.88%) followed by liver blood deficiency (60.23%) and then heart blood deficiency (60.12%). For males (n = 16), heart qi deficiency was also the highest scoring CM pattern with a scoring percentage of 54.81%. In males, however, heart blood deficiency was second with 53.29% followed by liver blood deficiency with 51.10%. Of the general non gender-specific symptoms collected (n = 65 symptoms), the symptom most commonly reported by both men and women was "anxious or racing thoughts", followed by "constant worrying" and "inability to concentrate". The CM diagnostic pattern results may prove useful for clinicians as the change in diagnostic understanding will also modify the treatment principle and subsequent treatment with acupuncture or herbal medicine. Future CM research studies should consider including the questionnaire either as a diagnostic aid or as an outcome measure for acupuncture or herbal medicine studies related to stress.

Zhou, Y, Rasmita, A, Li, K, Xiong, Q, Aharonovich, I & Gao, W-B 2017, 'Coherent control of a strongly driven silicon vacancy optical transition in diamond', Nature Communications, vol. 8, no. 1, pp. 1-8.
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AbstractThe ability to prepare, optically read out and coherently control single quantum states is a key requirement for quantum information processing. Optically active solid-state emitters have emerged as promising candidates with their prospects for on-chip integration as quantum nodes and sources of coherent photons connecting these nodes. Under a strongly driving resonant laser field, such quantum emitters can exhibit quantum behaviour such as Autler–Townes splitting and the Mollow triplet spectrum. Here we demonstrate coherent control of a strongly driven optical transition in silicon vacancy centre in diamond. Rapid optical detection of photons enabled the observation of time-resolved coherent Rabi oscillations and the Mollow triplet spectrum. Detection with a probing transition further confirmed Autler–Townes splitting generated by a strong laser field. The coherence time of the emitted photons is comparable to its lifetime and robust under a very strong driving field, which is promising for the generation of indistinguishable photons.

Zhu, A, Greaves, IK, Dennis, ES & Peacock, WJ 2017, 'Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage', BMC Genomics, vol. 18, no. 1, pp. 137-137.
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Hybrid vigour (heterosis) has been used for decades in cropping agriculture, especially in the production of maize and rice, because hybrid varieties exceed their parents in plant biomass and seed yield. The molecular basis of hybrid vigour is not fully understood. Previous studies have suggested that epigenetic systems could play a role in heterosis.In this project, we investigated genome-wide patterns of four histone modifications in Arabidopsis hybrids in germinating seeds. We found that although hybrids have similar histone modification patterns to the parents in most regions of the genome, they have altered patterns at specific loci. A small subset of genes show changes in histone modifications in the hybrids that correlate with changes in gene expression. Our results also show that genome-wide patterns of histone modifications in geminating seeds parallel those at later developmental stages of seedlings.Ler/C24 hybrids showed similar genome-wide patterns of histone modifications as the parents at an early germination stage. However, a small subset of genes, such as FLC, showed correlated changes in histone modification and in gene expression in the hybrids. The altered patterns of histone modifications for those genes in hybrids could be related to some heterotic traits in Arabidopsis, such as flowering time, and could play a role in hybrid vigour establishment.

Zhu, B, Qian, B, Liu, Y, Xu, C, Liu, C, Chen, Q, Zhou, J, Liu, X & Qiu, J 2017, 'A volumetric full-color display realized by frequency upconversion of a transparent composite incorporating dispersed nonlinear optical crystals', NPG Asia Materials, vol. 9, no. 6, pp. e394-e394.
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Zhu, L, Khachadorian, S, Hoffmann, A, Phillips, MR & Ton-That, C 2017, 'Chemical, vibrational and optical signatures of nitrogen in ZnO nanowires', Materials Science in Semiconductor Processing, vol. 69, pp. 57-61.
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© 2016 Elsevier Ltd ZnO nanowires with various concentrations of nitrogen molecules have been fabricated by remote plasma annealing. X-ray absorption near-edge spectroscopy (XANES) reveals that nitrogen exists mainly in two chemical states: atomic nitrogen substituting oxygen (NO) and molecular nitrogen (N2) weakly bound to the ZnO lattice; the latter state increases substantially with prolonged plasma time. Cathodoluminescence microanalysis of individual nanowires reveals a broad emission band at 3.24 eV at 10 K, attributable to the recombination of a shallow donor and a N2 acceptor state. The Raman modes at 547 and 580 cm−1 from the N-doped nanowires are found to rise in proportion to the N2 concentration, indicating they are related to N2 molecules or defects caused by the incorporation of N2 in the nanowires.

Zhu, L, Lem, LLC, Nguyen, T-P, Fair, K, Ali, S, Ford, MJ, Phillips, MR & Ton-That, C 2017, 'Indirect excitons in hydrogen-doped ZnO', Journal of Physics D: Applied Physics, vol. 50, no. 11, pp. 115104-115104.
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© 2017 IOP Publishing Ltd. We present a correlative experimental and theoretical study of bound excitons in hydrogen-doped ZnO, with a particular focus on the dynamics of their metastable state confined in the sub-surface region, using a combination of surface-sensitive characterisation techniques and density functional theory calculations. A metastable sub-surface emission at 3.31 eV found in H-doped ZnO is attributed to the radiative recombination of indirect excitons localised at basal plane stacking faults (BSFs) where the excitonic transition involves electrons bound to bond-centre hydrogen donors in the potential well of the BSF. Additionally, our work shows the electrical transport of ZnO Schottky junctions is dominated by electrons confined at BSFs in the near-surface region.

Zhu, Y, Ishizaka, J, Tripathy, SC, Wang, S, Sukigara, C, Goes, J, Matsuno, T & Suggett, DJ 2017, 'Relationship between light, community composition and the electron requirement for carbon fixation in natural phytoplankton', Marine Ecology Progress Series, vol. 580, pp. 83-100.
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© Inter-Research 2017. Fast repetition rate fluorometry (FRRF) provides a means to examine primary productivity at high resolution across broad scales, but must be coupled with independent knowledge of the electron requirement for carbon uptake (KC) to convert FRRF-measured electron transfer rate (ETR) to an inorganic carbon (C) uptake rate. Previous studies have demonstrated that variability of KC can be explained by key environmental factors (e.g. light, nutrients, temperature). However, how such reconciliation of KC reflects changes of phytoplankton physiological status versus that of community composition has not been well resolved. Therefore, using a dataset of coupled FRRF and C uptake measurements, we examined how the environmental dependency of KC potentially varied with parallel changes in phytoplankton community structure. Data were combined from 14 campaigns conducted during the summer season throughout 2007 to 2014 in the East China Sea (ECS) and Tsushima Strait (TS). KC varied considerably, but this variability was best explained by a linear relationship with light availability (R2 = 0.66). Co-variability between KC and light availability was slightly improved by considering data as 2 clusters of physico-chemical conditions (R2 = 0.74), but was best improved as 2 taxonomic clusters: samples dominated by micro-phytoplankton (>20 μm) versus small phytoplankton (nano + pico, <20 μm; R2 = 0.70-0.81). Interaction of phytoplankton community structure with light availability therefore explains the majority of variance of KC. The algorithms generated through our analysis therefore provide a means to examine C uptake with high resolution from future FRRF observations from these waters.

Zhu, Y, Xu, G, Zhang, X, Wang, S, Li, C & Wang, G 2017, 'Hierarchical porous carbon derived from soybean hulls as a cathode matrix for lithium-sulfur batteries', Journal of Alloys and Compounds, vol. 695, pp. 2246-2252.
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Zou, R, Huang, J, Shi, J, Huang, L, Zhang, X, Wong, K-L, Zhang, H, Jin, D, Wang, J & Su, Q 2017, 'Silica shell-assisted synthetic route for mono-disperse persistent nanophosphors with enhanced in vivo recharged near-infrared persistent luminescence', Nano Research, vol. 10, no. 6, pp. 2070-2082.
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© 2016, Tsinghua University Press and Springer-Verlag Berlin Heidelberg. Near-infrared (NIR) persistent-luminescence nanoparticles have emerged as a new class of background-free contrast agents that are promising for in vivo imaging. The next key roadblock is to establish a robust and controllable method for synthesizing monodisperse nanoparticles with high luminescence brightness and long persistent duration. Herein, we report a synthesis strategy involving the coating/etching of the SiO2 shell to obtain a new class of small NIR highly persistent luminescent ZnGa2O4:Cr3+,Sn4+ (ZGOCS) nanoparticles. The optimized ZGOCS nanoparticles have an excellent size distribution of ~15 nm without any agglomeration and an NIR persistent luminescence that is enhanced by a factor of 13.5, owing to the key role of the SiO2 shell in preventing nanoparticle agglomeration after annealing. The ZGOCS nanoparticles have a signal-to-noise ratio ~3 times higher than that of previously reported ZnGa2O4:Cr3+ (ZGC-1) nanoparticles as an NIR persistent-luminescence probe for in vivo bioimaging. Moreover, the persistent-luminescence signal from the ZGOCS nanoparticles can be repeatedly re-charged in situ with external excitation by a white lightemitting diode; thus, the nanoparticles are suitable for long-term in vivo imaging applications. Our study suggests an improved strategy for fabricating novel high-performance optical nanoparticles with good biocompatibility.

Agius, A, Morelato, M, Moret, S, Chadwick, S, Jones, K, Epple, R & Roux, C 1970, 'USING HANDWRITING TO INFER A WRITER'S COUNTRY OF ORIGIN FOR FORENSIC INTELLIGENCE PURPOSES', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 160-160.

Ajani, PA, Hallegraeff, GM, Allen, D, Coughlan, A, Richardson, AJ, Armand, L, Ingleton, I & Murray, SA 1970, 'Establishing baselines: eighty years of phytoplankton diversity and biomass in south-eastern Australia (Oral Presentation). ALSO Aquatic Science Meeting 2017, Hawaii'.

Ali, MK, Kim, R, Johnstone, D, Essilfie, A-T, Mayall, J, Karim, R, Pinkerton, J, Heidari, M, Donovan, C, Liu, G, Martin, K, Milward, L, Hansbro, P & Horvat, J 1970, 'ROLE OF INCREASED IRON LEVELS IN THE PATHOGENESIS OF LUNG DISEASE', RESPIROLOGY, WILEY, pp. 69-69.

Alqudah, A, McNally, R, Connell, A, Lyons, T, Grieve, D, Robson, T & McClements, L 1970, 'Irish Endocrine Society 41st Annual Meeting, 13th and 14th October 2017, Grand Hotel, Malahide, Dublin', Irish Journal of Medical Science (1971 -), Irish Endocrine Society 41st Annual Meeting, Springer Science and Business Media LLC, Malahide, Dublin, pp. 343-385.
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People with diabetes show five-fold higher incidence of cardiovascular disease, the leading causes of death globally. FKBPL is a novel angiogenesisrelated protein, with a critical role in physiological and pathological angiogenesis. A first-in-class clinical FKBPL peptide mimetic, ALM201, is currently in phase I/II clinical trials for treatment of solid tumours. More recently, in FKBPL knockdown (FKBPL+/-) mice, a pro-angiogenic phenotype was observed, accompanied by vascular dysfunction and a propensity to become overweight and glucose intolerant when fed a high fat diet. We now investigate a specific role for FKBPL in myocardial angiogenesis associated with diabetes. In streptozotocin (STZ) mice, cardiac FKBPL mRNA levels were significantly downregulated at 12 weeks post STZ injection versus vehicle controls (p<0.05, n=5), in association with diastolic dysfunction (e.g. mitral valve E/A ratio). This was in concert with a reduction of FKBPL protein in hearts from STZ-induced vs. control diabetic rats (p<0.01, n=3), also at 12 weeks. Complementary in vitro studies in cultured endothelial cells (HUVEC) demonstrated two-fold reduction in FKBPL protein levels following exposure to hypoxia (1%) for 24 h (p<0.01, n=6), indicating that reduced FKBPL levels observed in vivo may be, at least in part, driven by impaired oxygenation. Indeed, in an experimental mouse model of myocardial infarction (MI), associated with severe cardiac ischaemia/hypoxia and increased angiogenesis, FKBPL mRNA (p<0.05) and protein levels (p<0.01) were downregulated versus sham controls (n≥3). In conclusion, FKBPL may be a key early regulator of cardiac angiogenesis in diabetes, and may thereby hold novel biomarker and therapeutic potential.

Bannwarth, A, Morelato, M, Benaglia, L, Esseiva, P, Del, OM & Roux, C 1970, 'THE ANALYSIS OF ILLICIT DRUGS IN SYDNEY WASTEWATER', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 225-225.

Belic, NK, Padula, M, Milthorpe, B & Santos, J 1970, 'Multiple sclerosis: a disease in a dish', MULTIPLE SCLEROSIS JOURNAL, Progress in MS Research Conference, SAGE PUBLICATIONS LTD, MS Res Australia, Sydney, AUSTRALIA, pp. NP26-NP27.

Benner, L, Castro, EA, Whitworth, C, Cook, KR, Oliver, B & Lerit, DA 1970, 'Regulation of cell division by the intrinsic and extrinsic activities of small ovaries is required for germline development.', MOLECULAR BIOLOGY OF THE CELL, Annual Joint Meeting of the American-Society-for-Cell-Biology and the European-Molecular-Biology-Organization (ASCB/EMBO), AMER SOC CELL BIOLOGY, Philadelphia, PA.

Blanes, L, Dos Santos, RO, Diplock, M, Benson, N, Doble, P & Roux, C 1970, 'DEVELOPMENT OF AN ELECTRONIC EXPLOSIVE DETECTOR USING MICROFLUIDIC PAPER-BASED ANALYTICAL DEVICES', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 199-200.

Boudewijn, IM, Faiz, A, Steiling, K, van der Wiel, E, Telenga, E, Hoonhorst, S, ten Hacken, N, Brandsma, C-A, Kerstjens, H, Timens, W, Heijink, I, Jonker, M, de Bruin, H, Vroegop, S, Pasma, H, Boersma, W, Wielders, P, van den Elshout, F, Mansour, K, Spira, A, Lenburg, M, Postma, D & van den Berge, M 1970, 'A nasal gene expression profile differentiates individuals with and without COPD and overlaps bronchial gene expression', Genes and Environment, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Budden, K, Gellatly, S, Wood, D, Morrison, M, Cooper, M, Dennis, PG, Hugenholtz, P & Hansbro, P 1970, 'DIETARY FIBRE AND MICROBIAL METABOLITES PROTECT AGAINST CIGARETTE SMOKE‐INDUCED LUNG PATHOLOGY IN MICE', Respirology, Wiley, pp. 4-5.
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Buis, R, Rust, L, Nizio, K, Perrault, K, Rai, T, Stuart, B & Forbes, S 1970, 'IS HUMAN DECOMPOSITION FLUID A VALID TRAINING AID FOR CADAVER-DETECTION DOGS?', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 252-252.

Burke, C, Masters, DE, O'Sullivan, P & Sheu, L 1970, 'THE ROLE OF THIRD YEAR CLERKSHIP STUDENTS AND THE POTENTIAL FOR CHANGE', JOURNAL OF GENERAL INTERNAL MEDICINE, Annual National Meeting of the Society-of-General-Internal-Medicine (SGIM), SPRINGER, DC, Washington, pp. S350-S350.

Chadwick, S, de La Hunty, M, Morelato, M, Lam, R & Roux, C 1970, 'FORENSIC SCIENCE EDUCATION - FLAVOUR TO FOUNDATION', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 56-56.

Chadwick, S, Moret, S, Jayashanka, N, Lennard, C, Spindler, X & Roux, C 1970, 'INSIDE KNOWLEDGE OF THE FACTORS INFLUENCING FINGERMARK DETECTION', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 59-60.

Chadwick, S, Neskoski, M, Spindler, X, Lennard, C & Roux, C 1970, 'INVESTIGATION INTO THE EFFECT OF HAND SANITIZERS ON LATENT FINGERMARKS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 61-61.

Chen, H, Corboliou, V, Solntsev, AS, Choi, D-Y, Vincenti, MA, de Ceglia, D, De Angelis, C, Lu, Y & Neshev, D 1970, 'Hybrid integration of two-dimensional MoSe<inf>2</inf> on a silicon waveguide for second-order nonlinear optics', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe (CLEO/Europe) & European Quantum Electronics Conference (EQEC), IEEE, Munich, GERMANY.
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Chen, H, Corboliou, V, Solntsev, AS, Choi, D-Y, Vincenti, MA, de Ceglia, D, De Angelis, C, Lu, Y & Neshev, DN 1970, 'Enhanced second-harmonic generation from two-dimensional MoSe2 by waveguide integration', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, CA, USA, pp. 1-2.
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© 2017 IEEE. We demonstrate enhanced second-harmonic generation from a monolayer MoSe2 through Si waveguide integration. This is achieved by exciting the monolayer through the guided mode, which dramatically increases the interaction length and allows for phasematching.

Chimankar, V, Harrison, C, Rahman, A, Sahu, P, Scott, R, Watkins, N & Hansbro, P 1970, 'Investigating the Genetics of the Development of Lung Cancer', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, pp. 28-28.

Collison, A, Li, J, De Siqueira, AP, Lv, X, Toop, HD, Morris, JC, Starkey, MR, Hansbro, PM, Zhang, J & Mattes, J 1970, 'THE E3 UBIQUITIN LIGASE MID1 PROMOTES IDIOPATHIC PULMONARY FIBROSIS', RESPIROLOGY, WILEY, pp. 168-168.

Coupland, M, Solina, D & Cave, G 1970, 'Mastery Learning: Improving the Model', 40 years on: We are still learning! Proceedings of the 40th Annual Conference of the Mathematics Education Research Group of Australasia, 40 years on: We are still learning! Proceedings of the 40th Annual Conference of the Mathematics Education Research Group of Australasia, MERGA : Mathematics Education Research Group of Australasia, Melbourne, pp. 189-196.
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In this paper, we report on developments in the Mastery Learning (ML) curriculum and assessment model that has been successfully implemented in a metropolitan university for teaching first-year mathematics. Initial responses to ML were positive; however, we askwhether the nature of the ML tests encourages a focus on shallow learning of procedures, and whether the structure of the assessment regime provides sufficient motivation for learning more complex problem solving. We analysed assessment data, as well as student reports and survey responses in an attempt to answer these questions.

Davies, JM, Ebert, E, Huete, A, Newbigin, E, Silver, J & Beggs, P 1970, 'Aerobiological, biogeographical, and meteorological features of the November 2016 fatal thunderstorm asthma event in Melbourne, Australia', ALLERGY, Congress of the European-Academy-of-Allergy-and-Clinical-Immunology, WILEY, Helsinki, FINLAND, pp. 803-804.

Davila, YC & Griffiths, N 1970, 'Removing the cloak of invisibility: Developing scientific writing practices for commencing science students', Proceedings of the Australian Conference on Science and Mathematics Education, Australian Conference on Science and Mathematics Education, Monash University, pp. 32-32.

Durmus, E, Mohanty, M, Taspinar, S, Uzun, E & Memon, N 1970, 'Image carving with missing headers and missing fragments', 2017 IEEE Workshop on Information Forensics and Security (WIFS), 2017 IEEE Workshop on Information Forensics and Security (WIFS), IEEE, Rennes, FR POLYNESIA.
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Eapen, M, Hansbro, P, McAlinden, K, Kim, R, Hackett, T-L, Ward, C, Walters, H & Sohal, SS 1970, 'Abnormal M1/M2 macrophage switching in small airway wall and lumen of smokers and COPD patients', Airway Cell Biology and Immunopathology, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Eapen, M, Hansbro, P, Mcalinden, K, Ward, C, Hackett, T-L, Walters, H & Sohal, SS 1970, 'ABNORMAL M1/M2 MACROPHAGE PHENOTYPE SWITCHING OCCURS DIFFERENTIALLY IN THE SMALL AIRWAY WALL AND LUMEN IN SMOKERS AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD)', Respirology, Wiley, pp. 30-30.
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Eapen, M, Hansbro, P, Tan, E, Ward, C, Walters, H & Sohal, SS 1970, 'INCREASED UPREGULATION OF LYSOSOMAL‐ASSOCIATED MEMBRANE PROTEIN 1 (LAMP‐1) IN THE AIRWAY WALL OF COPD IS ASSOCIATED WITH DECREASED PHYSIOLOGICAL OUTCOMES AND POTENTIAL ROLE IN AUTOPHAGY', Respirology, Wiley, pp. 31-31.
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Espinoza Vergara, G, Noorian, P, Sun, S & McDougald, D 1970, 'Intracellular trafficking of Vibrio cholerae in Acanthamoeba castellanii', Vibrio Meeting 2017. The Biology of Vibrios, Vibrio Meeting 2017. The Biology of Vibrios, American Society for Microbiology, Chicago.

Faiz, A, Wisman, M, Hiemstra, PS, Timens, W, Woodruff, P, Christenson, S, Van Den Berge, M, Heijink, IH & Koppelman, GH 1970, 'Late Breaking Abstract - Functional investigation of the corticosteroid resistance candidate FKBP5 using a CRISPR-Cas9 knockout model', Molecular Pathology and Functional Genomics, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Fan, G & Mohanty, M 1970, 'Privacy-preserving Disease Susceptibility Test with Shamir’s Secret Sharing', Proceedings of the 14th International Joint Conference on e-Business and Telecommunications, 14th International Conference on Security and Cryptography, SCITEPRESS - Science and Technology Publications, pp. 525-533.
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Copyright © 2017 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved. Recent advances in genomics have facilitated the development of personalized medicine, in which a patient's susceptibility to certain diseases and her compatibility with certain medications can be determined from her genetic makeup. Although this technology has many advantages, privacy of the patient is one of the major concerns due to the sensitivity of genomic data. In this paper, we propose a privacy-preserving scheme for computing a patient's susceptibility to a particular disease. Our scheme stores genomic data in hidden form and performs the disease susceptibility test in the hidden domain. To hide the data, we use Shamir's (l, n) secret sharing, which can be homomorphic to a fixed number of multiplications and unlimited additions. Using Shamir's secret sharing, we create n shares and store the shares at n datacenters. The datacenters perform the susceptibility test on their shares and send the result (which is also hidden) to a hospital. Finally, the hospital obtains the secret result of the test by accessing at least k datacenters, where k = 2l-1. In comparison to other works, our approach is more practical as it minimizes the involvement of the patient and incurs less overhead.

Fu, LB, Shi, BY, Jin, DY & Chung, R 1970, 'Versatile upconversion surfaces evaluation platform for bio-nano surface selection for nervous system', 2017 IEEE 17th International Conference on Nanotechnology (IEEE-NANO), 2017 IEEE 17th International Conference on Nanotechnology (IEEE-NANO), IEEE, Pittsburgh, PA, USA, pp. 932-933.
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© 2017 IEEE. Neurodegenerative disorder diseases have been perplexing physicians and scientists for many years. There is considerable interest in developing diagnostic nanotools for diagnosis and therapeutic treatment strategies for the neuron diseases. However, a key challenge remains in selection of suitable surface to overcome the nano-bio interface issue as many nanoparticles indicate instability when administered into biological environments and show serious cytotoxicity to sensitive central nervous system. We have developed new-generation upconversion nanoparticles (UCNPs) which represent a promising model nanoparticle for suitable evaluation due to its superior properties in bio photonics.

Gachon, CMM, Badis, Y, Klochkova, TA, Strittmatter, M, Garvetto, A, Murua, P, Ostrowski, M, Tringe, S, Prochnik, S, Sanderson, C & Kim, GH 1970, 'HIDDEN DIVERSITY IN THE OOMYCETE GENUS OLPIDIOPSIS IS A GLOBAL THREAT TO RED ALGAL CULTIVATION', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 54-55.

Ge, Q, Wang, J, Simcock, D, Kanabar-Raivadera, V, Hirst, S, Ward, J, Sawant, S, Van De Velde, R, Oliver, BG, Ashton, A & Burgess, JK 1970, 'Connective Tissue Growth Factor (ctgf) - A Key Factor In Asthmatic Airway Angiogenesis', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Gentle, AR, Nuhoglu, A, Arnold, MD & Smith, GB 1970, '3D printable optical structures for sub-ambient sky cooling', Thermal Radiation Management for Energy Applications, Thermal Radiation Management for Energy Applications, SPIE, San Diego, CA.
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Gerace, D, Martiniello-Wilks, R, Nassif, NT, Ren, B & Simpson, AM 1970, 'Ex Vivo Expanded Murine Mesenchymal Stem Cells as Targets for the Generation of a Cell Replacement Therapy for Type 1 Diabetes', DIABETES, 77th Scientific Sessions of the American-Diabetes-Association, AMER DIABETES ASSOC, San Diego, CA, pp. A83-A83.

Godecke, E, Armstrong, E, Middleton, S, Ciccone, N, Rai, T, Holland, A, Whitworth, A, Rose, M, Ellery, F, Cadilhac, D, Hankey, G & Bernhardt, J 1970, 'Therapy fidelity and trial progress in the Very Early Rehabilitation in SpEech (VERSE) trial', INTERNATIONAL JOURNAL OF STROKE, Annual Scientific Meeting of the Stroke Society of Australasia, SAGE PUBLICATIONS LTD, Queenstown, New Zealand, pp. 14-15.

Griffiths, N & Davila, YC 1970, 'Doing Science Write: technology‐enhanced learning of discipline specific scientific writing practices', 9th Conference of the European Association for Teaching Academic Writing, Royal Holloway, University of London, pp. 88-88.
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A key practice in science is the use of the scientific literature to communicate research findings and inform further research. To help commencing university Science students attain the level of writing proficiency expected and understand the discipline‐specific academic discourses required, it is recommended that explicit teaching of writing skills be introduced early in the curriculum (Coil et al 2010), and embedded and scaffolded (Amos and McGowan 2012). To address this our project aimed to introduce first year students to the conventions of scientific writing, develop their scientific report writing practices and build their confidence in writing. We achieved this by taking a technology‐enhanced student‐centred approach, intentionally designing and integrating targeted online interactive tutorials and face‐to‐face workshops into a first year, first semester Science subject. Using this blended learning approach enables inclusivity, accessibility and flexibility thus supporting our increasingly diverse student cohort (Devlin et al 2012). A pre and post semester paired‐comparison showed that students’ confidence in their scientific report writing increased after completing the online tutorials and workshops. Their academic performance in theassessment task also improved compared to previous cohorts in the subject. Students commented that the well‐targeted, in‐depth analysis provided on how to write a scientific report helped them to understand theimportance of good scientific writing, and how to write according to university and scientific standards. Based on our success in embedding discipline specific, contextualised writing practices resources, werecommend that this approach be used to demystify scientific writing in the first year curriculum.References:Amos, K.J. and McGowan, U. (2012) Integrating academic reading and writing skills development with core content in science and engineering. Journal of Learning Development in Higher Education, ...

Griffiths, N & Davila, YC 1970, 'Write right: embedding academic integrity resources into science writing', 8th Asia Pacific Conference on Educational Integrity, University of Sydney.

Grosso, G, Moon, H, Lienhard, B, Ali, S, Furchi, MM, Walsh, M, Efetov, DK, Jarillo-Herrero, P, Ford, MJ, Aharonovich, I & Englund, D 1970, 'Tunable Quantum Emission from Atomic Defects in Hexagonal Boron Nitride', Conference on Lasers and Electro-Optics, CLEO: Applications and Technology, OSA, San Jose, CA, USA, pp. 1-2.
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© 2016 Optical Society of America. We demonstrate that strain control of exfoliated hexagonal boron nitride allows spectral tuning of single photon emitters over 6 meV. We propose a material processing that sharply improves the single-photon purity with g(2)(0) = 0.077, and brightness with emission rate exceeding 107counts/sec at saturation.

Hadaddi, N, McGowan, E & Nassif, N 1970, 'Alteration of Cellular Function by Cancer-Associated PTEN Mutations.', Frontiers in Cancer Science 6-8th Nov, Singapore, Singapore.

Haddadi, N, McGowan, E & Nassif, N 1970, 'Cancer-associated PTEN mutations alter PTEN cellular function.', Australasian Genomic Technologies Association (AGTA) Annual Conference 2017, Hobart, Tasmania.

Hallegraeff, G, Bolch, C, Condie, S, Dorantes-Aranda, J, Murray, SA, Quinlan, R, Ruvindy, R, Turnbull, A, Ugalde, S & Wilson, K 1970, 'Unprecedented Alexandrium blooms in a previously low biotoxin risk area of Tasmania, Australia.', Proceedings of the 17th International Conference on Harmful Algae, 17th International Conference on Harmful Algae, ICHA, Brazil, pp. 38-41.
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During October 2012, a shipment of blue mussels (Mytilus galloprovincialis) from the poorly monitored east coast of Tasmania, Australia, was tested by Japanese import authorities and found to be contaminated with unacceptable levels of Paralytic Shellfish Toxins (PSTs; 10 mg/kg). Subsequently local oysters, scallops, clams, the viscera of abalone and rock lobsters were also found to be contaminated. This led to a global product recall and loss to the local economy of AUD 23M. Following low toxicity during 2013 and 2014 and implementation of minimal shellfish farm closures, a more severe bloom event occurred during July-November 2015 and again June-September 2016 (up to 300,000 Alexandrium cells/L; 24 mg/kg PST in mussels, 6 mg/kg in Crassostrea gigas oysters), also causing 4 human illnesses resulting in hospitalization after consumption of wild shellfish. While Alexandrium tamarense had been detected in low concentrations in southeastern Australia since 1987, all cultured strains belonged to the mostly non-toxic group 5 (now designated A. australiense; detected since 1987) and weakly toxic group 4 (A. pacificum; detected in 1997).In contrast, the 2012 to 2016 outbreaks were dominated by highly toxic group 1 (A. fundyense) neverdetected previously in the Australian region. Molecular analyses suggest that A. fundyense may have been a cryptic ribotype previously present in Tasmania, but newly stimulated by altered water column stratificationconditions driven by changing rainfall and temperature patterns. Increased seafood and plankton monitoring of the area now include the implementation of Alexandrium qPCR, routine Neogen™ immunological and HPLC PST tests, but ultimately may also drive change in harvesting strategies and aquaculture species selection by the local seafood industry.

Ho-Le, TP, Center, JR, Eisman, JA, Nguyen, TV & Nguyen, HT 1970, 'Prediction of hip fracture in post-menopausal women using artificial neural network approach', 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), IEEE, Jeju Island, Korea, pp. 4207-4210.
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Hip fracture is one of the most serious health problems among post-menopausal women with osteoporosis. It is very difficult to predict hip fracture, because it is affected by multiple risk factors. Existing statistical models for predicting hip fracture risk yield area under the receiver operating characteristic curve (AUC) ~0.7-0.85. In this study, we trained an artificial neural network (ANN) to predict hip fracture in one cohort, and validated its predictive performance in another cohort. The data for training and validation included age, bone mineral density (BMD), clinical factors, and lifestyle factors which had been obtained from a longitudinal study that involved 1167 women aged 60 years and above. The women had been followed up for up to 10 years, and during the period, the incidence of new hip fractures was ascertained. We applied feed-forward neural networks to learn from the data, and then used the learning for predicting hip fracture. Results of prediction showed that the accuracy of model I (which included only lumbar spine and femoral neck BMD) and model II (which included non-BMD factors) was 82% and 84%, respectively. When both BMD and non-BMD factors were combined (Model III), the accuracy increased to 87%. The AUC for model III was 0.94. These findings indicate that ANNs are able to predict hip fracture more accurately than any existing statistical models, and that ANNs can help stratify individuals for clinical management.

Horvat, J, Pinkerton, J, Rae, B, Mayall, J, Brown, A, Ali, MK, Goggins, B, Essilfie, A-T, Starkey, M, Bosco, A, Kim, R & Hansbro, P 1970, 'IMPAIRED INDUCTION OF SLC26A4 PROMOTES RESPIRATORY ACIDOSIS AND SEVERE, STEROID-INSENSITIVE ASTHMA', RESPIROLOGY, WILEY, pp. 65-65.

Horvat, JC, Ali, MK, Johnstone, D, Kim, RY, Mayall, JR, Karim, R, Pinkerton, JW, Heidari, M, Martin, KL, Donovam, C, Liu, G, Milward, EA & Hansbro, PM 1970, 'Role for dysregulated iron in the pathogenesis of murine models of lung disease', JOURNAL OF IMMUNOLOGY, Annual Meeting of the American-Association-of-Immunologists (AAI), AMER ASSOC IMMUNOLOGISTS, Washington, DC.

Horvat, JC, Mayall, JR, Mangan, NE, Brown, AC, Chevalier, A, Starkey, MR, Kim, RY, Hertzog, P & Hansbro, PM 1970, 'IFN-epsilon regulated innate immune responses in the female reproductive tract during Chlarnydia infection', JOURNAL OF IMMUNOLOGY, Annual Meeting of the American-Association-of-Immunologists (AAI), AMER ASSOC IMMUNOLOGISTS, Washington, DC.

Irga, PJ & Torpy, FR 1970, 'Can urban forestry really reduce air pollution? A field study on a city scale.', Green Infrastructure: Nature Based Solutions for Sustainable and Resilient Cities, Green Infrastructure: Nature Based Solutions for Sustainable and Resilient Cities, Orvieto, Italy.

Kalatzis, G, Lees, T, Nassif, N, Zaslawski, C & Lal, S 1970, 'Exploring cognitive function in diabetes and non-diabetes samples using electroencephalography (EEG) and psychometric assessment: a comparative study', 37th Annual Scientific Meeting of the Australasian Neuroscience Society.

Khuu, A, Chadwick, S, Spindler, X, Moret, S, Gunn, P & Roux, C 1970, 'THE IMPACT OF ONE-STEP LUMINESCENT CYANOACRYLATES ON SUBSEQUENT DNA ANALYSIS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 246-246.
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Fingermarks can be exploited for both their ridge detail and touch DNA. One-step luminescent cyanoacrylate (CA) fuming techniques used for fingermark enhancement, such as PolyCyano UV (Foster+Freeman Ltd) and Lumicyano™ (Crime Science Technology), claim to be compatible with DNA analysis as they reduce the need for post‐staining to increase contrast of the developed fingermark. The aim of this study was to determine the impact that these one-step luminescent cyanoacrylates have on DNA analysis and how they compare to conventional CA techniques. Four donors each deposited five sets of natural fingermarks, to which a known amount of washed saliva cells was dispensed onto half of each set of fingermarks. Each set was treated with either a conventional CA technique or a one‐step luminescent CA technique prior to collection and processing of DNA, with one set left as a non-fumed control. It was found that DNA was still recoverable and detectable following each of the treatments. Lumicyano™ had a similar impact on DNA profiles as conventional CA fuming and with post‐stain, however, the degradation effect of PolyCyano UV on DNA was greater than the conventional treatments. For quantities of DNA such as that from touch DNA, the use of PolyCyano UV to enhance fingermarks may impact subsequent DNA analysis by causing allele drop out at larger fragment sizes.

Kianinia, M, Tawfik, SA, Regan, B, Tran, TT, Ford, MJ, Aharonovich, I & Toth, M 1970, 'Robust Solid State Quantum System Operating at 800 K', Conference on Lasers and Electro-Optics, CLEO: Applications and Technology, OSA, p. jtu5a.24.
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Kim, JH, Wang, P, Park, BS, Kim, J, Patidar, SK, Ajani, PA, Murray, SA, Lim, HC, Lim, PT & Han, M 1970, 'Revealing the hybrid zone and genetic polymorphisms of genetic sub-populations within Pseudo-nitzschia pungens the cosmopolitan diatom species (Oral Presentation). 10th EASTHAB Symposium, Harmful Algal Blooms in East Asia, Dec 2017, Hokkaido, Japan'.

Kim, JH, Wang, P, Park, BS, Paditar, KS, Ajani, PA, Murray, SA, Lim, HC & Lim, PT 1970, 'Revealing the hybrid zone and genetic polymorphisms of genetic sub-populations within Pseudo-nitzschia pungens the cosmopolitan diatom species (Oral Presentation). H-HABs Working Group, 3rd Symposium, Nov 2017, Korea Institute of Ocean Science & Technology, South Korea'.

Kim, R, Sunkara, K, Jarnicki, A, Bracke, K, Haw, TJ, Wark, P, Conickx, G, Brusselle, G, Horvat, J, Foster, P & Hansbro, P 1970, 'MicroRNA-21 DRIVES EXPERIMENTAL CHRONIC OBSTRUCTIVE PULMONARY DISEASE THROUGH A SATB1/S100A9/NF-kappa B AXIS', RESPIROLOGY, WILEY, pp. 71-71.

Kim, RYH, Pinkerton, JW, Rae, BE, Mayall, JR, Brown, AC, Ali, MK, Goggins, BJ, Essilfie, A-T, Starkey, MR, To, C, Bosco, A, Horvat, JC & Hansbro, PM 1970, 'Impaired induction of Slc26a4 promotes respiratory acidosis and severe, steroid-resistant asthma', The Journal of Immunology, International Conference of the American-Thoracic-Society (ATS), The American Association of Immunologists, Washington, DC, pp. 53.9-53.9.
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Abstract CO2 produced by systemic cellular respiration is hydrated into carbonic acid (H2CO3) that dissociates into H+ and HCO3−. These are transported in the plasma to the lungs where HCO3− is converted back into H2CO3 and CO2 that are expelled through breathing. Evidence suggests that dysfunction of the mechanisms that govern these processes may result in the development of respiratory acidosis (RA) and the cardinal features of severe, steroid-resistant (SSR) asthma. Reduced lung function, which occurs in SSR asthma, impairs removal of volatile H2CO3 and CO2, resulting in acid accumulation and increased arterial PaCO2. Patients with severe asthma often develop complications from increased PaCO2, which skews the PaCO2/HCO3− ratio resulting in increased H+ concentration and reduced pH. We developed three mouse models of respiratory infection and ovalbumin-induced SSR allergic airways disease (SSRAAD) that are highly representative of SSR asthma in humans. We used these models to show a role for impaired homeostatic acid-base balance in SSR asthma. All three infections suppress the induction of the expression of the chloride (Cl−)/HCO− pump, Slc26a4, in the airway mucosa in AAD. Importantly, SSRAAD is associated with increased levels of free H+ ions in bronchoalveolar lavage fluid. Administration of Slc26a4-specific siRNA in steroid-sensitive AAD, which mimics the effect of decreased Slc26a4 responses in SSRAAD, induced RA and steroid-resistant airway inflammation and AHR. Importantly, treatment of RA with NaHCO3 during infection-induced SSRAAD suppressed steroid-resistant AHR. Thus, we have identified a previously unrecognised role for deficient Slc26a4 responses that result in the development of RA and the pathogenesis of SSRAAD.

Kim, RYH, Pinkerton, JW, Rae, BE, Mayall, JR, Brown, AC, Nli, MK, Goggins, BJ, Essilfie, A-T, Starkey, MR, To, C, Bosco, A, Horvat, JC & Hansbro, PM 1970, 'Impaired induction of Slc26a4 promotes respiratory acidosis and severe, steroid-resistant asthma', JOURNAL OF IMMUNOLOGY, Annual Meeting of the American-Association-of-Immunologists (AAI), AMER ASSOC IMMUNOLOGISTS, Washington, DC.

Kingkam, P, Visser, S, Brown, J, Woodcock, S, Baird, T, Jackson, D & Morgan, L 1970, 'THE ARGUMENT FOR A BRONCHIECTASIS SPECIFIC AR‐DRG: ANALYSIS OF HOSPITAL DISCHARGE DATA (2012‐2016) FOR PATIENTS REGISTERED TO THE AUSTRALIAN BRONCHIECTASIS REGISTRY', Respirology, 22nd Congress of the APSR, Wiley, Sydney, pp. 206-207.
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Kota, A, Xenaki, D, Deshpande, DA, Oliver, BG & Sharma, P 1970, 'Ask1 Inhibition Prevented Mitogen-Induced Human Airway Smooth Muscle Growth In Chronic Obstructive Pulmonary Disease', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Kusrini, E, Lukita, M, Gozan, M, Susanto, BH, Nasution, DA, Rahman, A & Gunawan, C 1970, 'Enrichment process of biogas using simultaneous Absorption - Adsorption methods', AIP Conference Proceedings, RENEWABLE ENERGY TECHNOLOGY AND INNOVATION FOR SUSTAINABLE DEVELOPMENT: Proceedings of the International Tropical Renewable Energy Conference (i-TREC) 2016, Author(s), i-TREC.
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© 2017 Author(s). Removal of CO2in biogas is an essential methods to the purification and upgrading of biogas. Natural Clinoptilolite zeolites were evaluated as sorbents for purification of biogas that produced from palm oil mill effluent (POME) by anerobic-digestion method. The absorption and adsorption experiments were conducted in a fixed-bed two column adsorption unit by simultaneous absorption-adsorption method. The Ca(OH)2solution with concentration of 0.062 M was used as absorption method. Sorbent for removal of CO2in biogas have been prepared by modifying of Clinoptilolite zeolites with an acid (HCl, 2M) and alkaline (NaOH, 2M), calcined at 450°C and then coated using chitosan (0.5 w/v%) in order to increase their adsorption capacity. The removal of CO2in biogas was achieved about ∼83% using 2.5?g of sorbent zeolite (2M)/chitosan dosage for each column, breakthrough time of 30?min, and flow rate of 100?mL/min. Clinoptilolite zeolites with modifications of an acid-alkaline and chitosan (zeolite (2M)/chitosan) are promising sorbents due to the amine groups from chitosan and high surface-volume ratio are one of important factors in a simultaneous absorption-adsorption method.

Kusrini, E, Prassanti, R, Nurjaya, DM & Gunawan, C 1970, 'Multifunctional microsphere formulation of fluorescent magnetic properties for drug delivery system', AIP Conference Proceedings, BIOMEDICAL ENGINEERING’S RECENT PROGRESS IN BIOMATERIALS, DRUGS DEVELOPMENT, AND MEDICAL DEVICES: Proceedings of the First International Symposium of Biomedical Engineering (ISBE 2016), Author(s).
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© 2017 Author(s). The microsphere formulations of Chit/TPP/Sm/Fe3O4/Rn were prepared by an ionic gelation technique, where Chit=chitosan, TPP=tripolyphosphate, Sm=samarium and Rn=ranitidine. Optimum of microsphere formulation exhibit magnetic and fluorescent properties with adsorption efficiency of ∼92% was obtained for Chit/TPP/Sm/Fe3O4/Rn with ratio 400:500:50:1:20. Fluorescence intensity of microsphere formulations increased with the cumulative amount release of ranitidine, so that the changing of fluorescence intensity at wavelength of 590 nm referring to the Sm3+ ion could be used as indicator in DDS. With the demonstration of sustained release from microsphere formulation, it allows to investigate the applications to other drugs.

Lam, R, Barone, A, Morrell, W, Malone, A, Moret, S, Roux, C, Spikmans, V & Lennard, C 1970, 'EXCESSIVE FUMING WITH CYANOACRYLATE FOR THE DETECTION OF LATENT FINGERMARKS ON POLYMER BANKNOTES', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 62-62.

Lam, R, Ruscito, A, Derosa, MC, Spindler, X, Lennard, C & Roux, C 1970, 'FINGERMARK-SELEX: A NOVEL APPROACH TO DEVELOP DNA APTAMERS FOR FINGERMARK DETECTION', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 52-52.

Lee, PL, Moret, S, de la Hunty, M, Spindler, X, Lennard, C & Roux, C 1970, 'SINGLE METAL DEPOSITION VS. PHYSICAL DEVELOPER, A COMPARISON OF TWO FINGERMARK DETECTION TECHNIQUES', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 191-191.

Lee, R, Comber, B, Abraham, J, Lennard, C, Spindler, X & Roux, C 1970, 'SUPPORTING FINGERPRINT IDENTIFICATION ASSESSMENTS USING A SKIN STRETCH MODEL', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 3-3.

Lenzini, F, Poddubny, AN, Titchener, J, Fisher, P, Boes, A, Kasture, S, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 1970, 'Quantum tomography of a nonlinear photonic circuit by classical sum-frequency generation measurements', 2017 Conference on Lasers and Electro-Optics Pacific Rim (CLEO-PR), 2017 Conference on Lasers and Electro-Optics Pacific Rim (CLEO-PR), IEEE, Singapore, Singapore, pp. 1-2.
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© 2017 Institute of Electrical and Electronics Engineers Inc. All rights reserved. We propose and demonstrate a new method for the characterization of nonlinear multimode integrated devices that reconstruct the biphoton state produced trough spontaneous parametric down-conversion (SPDC) using classical sum-frequency generation measurements. The proposed method is experimentally demonstrated by predicting the state generated from a multi-channel integrated nonlinear waveguide device.

Lin, Y, Chen, H & McGowan, E 1970, 'A promising alternative in prevention and treatment of cardiovascular diseases-Nattokinase', eProceedings of APSA-ASCEPT 2017 Joint Scientific Meeting, APSA-ASCEPT 2017 Joint Scientific Meeting, European Association of Remote Sensing Laboratories, Brisbane, pp. 32-32.
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Yiguang Lin1, Hongjie Chen2, Eileen McGowan1. School of Life Sciences, University of Technology Sydney1, Broadway NSW Australia. Dept of TCM, 3rd Affiliated Hospital of Sun Yat-sen University2, Guangzhou, China.Introduction. Nattokinase (NK), the most active ingredient of Natto, possesses a variety of favourable cardiovascular effects and the consumption of Natto has been linked to the reduction of cardiovascular disease (CVD) mortality. However, the effect of NK on atherosclerosis in human has never been studied.Aims. This study was designed to evaluate the efficacy of oral NK in the reduction of common carotid artery intimal medial thickness (CCA-IMT) and carotid artery plaque size, lowering blood lipids, and to explore the underlying mechanism of action of NK. We further explored NK’s potential as an alternative treatment to Statin (ST) in the clinic.Methods. All enrolled patients were randomly assigned to one of two groups, NK and ST. 26 weeks’ treatment applied to both NK Group (NK were given at a daily dose of 6000 FU) and ST Group (treated with statin-simvastatin 20 mg daily). CCA-IMT, carotid plaque size and blood lipid of the patients were measured before and after treatment.Results. A total of 90 patients were enrolled in the study and 81 patients (NK=43, ST=38) completed the study. Following the treatments for 26 weeks, there was a significant reduction in CCA-IMT and carotid plaque size in both groups compared with the baseline before treatment. The carotid plaque size and CCA-IMT reduced from 0.25±0.12cm2 to 0.16±0.10cm2 and from 1.15±0.12mm to 1.02±0.11mm, respectively. The reduction in the NK group was significantly more profound (P<0.01, 36.6% reduction in plaque size in NK group versus 11.5% change in ST group). Both treatments reduced total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG). While the reduction in both groups was shown to be statistically significant (P<0.01), the reduction of TC, L...

Liu, G, Cooley, MA, Jarnicki, AG, Hsu, AC-Y, Nair, PM, Haw, TJ, Tjin, G, Jones, B, Harrison, CL, Fricker, M, Inman, MD, Walker, MM, Horvat, JC, Oliver, BG, Argraves, WS, Knight, DA, Burgess, JK & Hansbro, PM 1970, 'FIUBLIN-1C PLAYS CRITICAL ROLES IN LUNG REMODELLING IN IDIOPATHIC PULMONARY FIBROSIS', RESPIROLOGY, WILEY, pp. 70-70.

Lobo, C 1970, 'Directed deposition and etching of functional nanostructures using electron beam and plasma irradiation', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, AMER CHEMICAL SOC, CA, San Francisco.

Maitre, M, Kirkbride, P, Horder, M, Roux, C & Beavis, A 1970, 'PERSISTENCE OF ORGANIC GUNSHOT RESIDUES EVIDENCE', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 157-157.

Mang, NE, De Geus, E, Mielke, L, Gould, J, Cumming, H, Woodhouse, I, Gearing, LJ, Matthews, A, deweerd, N, Belz, G, Hansbro, P & Hertzog, P 1970, 'Interferon epsilon in the regulation of mucosal innate immune responses in the female reproductive tract', CYTOKINE, 5th Annual Meeting of the International-Cytokine-and-Interferon-Society (ICIS), ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, Int Cytokine & Interferon Soc, Kanazawa, JAPAN, pp. 162-163.

Marino, G, Solntsev, AS, Xu, L, Gili, V, Carletti, L, Poddubny, AN, Smirnova, D, Chen, H, Zhang, G, Zayats, A, De Angelis, C, Leo, G, Kivshar, YS, Sukhorukov, AA & Neshev, DN 1970, 'Sum-Frequency Generation and Photon-Pair Creation in AlGaAs Nano-Scale Resonators', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, CA, USA, pp. 1-2.
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©2017 IEEE We demonstrate experimentally sum-frequency generation in AlGaAs nano-resonators, establishing a quantum-classical correspondence with spontaneous parametric down-conversion. We predict that AlGaAs nano-resonators can be utilized as high-rate sources of photon pairs with non-classical correlations.

Marino, G, Solntsev, AS, Xu, L, Gili, V, Carletti, L, Poddubny, AN, Smirnova, D, Chen, H, Zhang, G, Zayats, AV, De Angelis, C, Leo, G, Kivshar, YS, Sukhorukov, AA & Neshev, DN 1970, 'Sum-frequency generation and photon-pair creation in AIGaAs nano-disks', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe (CLEO/Europe) & European Quantum Electronics Conference (EQEC), IEEE, Munich, Germany.
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All-dielectric and semiconductor nonlinear nanophotonics is an emerging field enabling efficient optical interactions between magnetic and electric resonances at sub-wavelength scales, thereby achieving high directionality and high figures of merit due to very low losses [1, 2]. It was shown that AlGaAs nanodisks with quadratic nonlinear susceptibility can provide second harmonic generation (SHG) with record-high efficiency of 10 -4 [3], opening to a wide range of possible applications, including nonlinear microscopy and holography. In this work, we show experimentally that the strong quadratic nonlinearity in AlGaAs nano-disks allows efficient sum-frequency generation (SFG) with nontrivial polarization dependencies. By using the established classical-quantum analogy [4], we predict that these nano-resonators can facilitate efficient generation of quantum entangled photon pairs with higher than kHz biphoton rate and strong angular correlations.

McAlinden, KD, Chan, YL, Kota, A, Chen, H, Oliver, BG & Sharma, P 1970, 'Maternal E-Cigarette Vaping Enhances Development Of Allergic Asthma In The Offspring', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.
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Rationale: E-cigarettes (eCig) are being considered as an alternative to quit cigarette smoking (CS) while their long-term safety and effect on lung patho-physiology are not known. Maternal eCig-vaping may be considered as a safer CS-replacement during pregnancy. Thus the effect of maternal eCig vaping needs further assessment, particularly the effect this has on offspring and development of allergic asthma later in life. Combining mouse models of maternal vaping and allergic asthma and human airway smooth muscle cells (ASM) in vitro we tested whether maternal eCig vaping enhances features of allergic asthma in the offspring. Methods: Female BALB/c mice were vaped with either eCig vapour (± nicotine) or CS+eCig (+nicotine) or room air (control group). The eCig vaping was started prior to mating and continued during gestation and lactation while CS-exposure was used prior to mating and replaced with eCig during gestation and mating. The female offspring from these mothers were subjected to an ovalbumin (OVA)-induced allergic asthma model. 24 hours after the last aerosolized OVA or saline challenge, lung function measurements were performed using flexiVent (Scireq, Canada) to increasing concentration of methacholine (MCh). Airway inflammation was assessed by counting total immune cell influx in BAL fluid. Human ASM cells were treated with varying concentrations of eCig liquid condensate and key parameters of mitochondrial function were measured with a Seahorse XF analyzer. Results: Repeated allergen-exposure induced Th2-driven inflammation in OVA-exposed mice, characterized by massive influx of leukocytes predominantly eosinophils (OVA: 3x105±8.3x104 vs Saline: 1.1x102±1x102) and to some extent neutrophils (OVA: 1.3x104±4.4x103 vs Saline: 1.3x102±1.1x102) into the airways. The effect of allergen on airway eosinophilia was significantly enhanced in the offsprings from eCig OVA (+Nic)-exposed mothers when compared with eCig OVA (-Nic) or CS+eCig animals. OVA-exposed ...

Mcalinden, KD, Chan, YL, Tan, B, Chen, H, Oliver, B, Sharma, P & Chapman, D 1970, 'MATERNAL E-CIGARETTE VAPING ENHANCES DEVELOPMENT OF ALLERGIC ASTHMA IN THE OFFSPRING', RESPIROLOGY, WILEY, pp. 104-104.

Mccabe, R, Spikmans, V, Spindler, X, Wuhrer, R & Lennard, C 1970, 'INDANEDIONE METHODS FOR FINGERMARK DETECTION: NORMAL TREATMENT, VACUUM DEVELOPMENT AND DRY-TRANSFER.', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 163-163.

McClements, L, McNally, R, Alqudah, A, Robson, T, Watson, C & Lyons, T 1970, '53 rd EASD Annual Meeting of the European Association for the Study of Diabetes', Diabetologia, 53 rd EASD Annual Meeting of the European Association for the Study of Diabetes, Springer Science and Business Media LLC, Lisbon, Portugal, pp. 1-608.
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Background and aims: Diabetic vascular complications are closely related to irregular angiogenesis, oxidative stress and lipid peroxidation.Preeclampsia (PE) is a pregnancy condition characterised by high bloodpressure, proteinuria and multi-organ dysfunction. PE occurs in 4-6% ofpregnancies; however in women with diabetes the incidence of PE isincreased four-fold. Furthermore, PE does not only have short-term risks,but long-term is associated with cardiovascular disease and/or Type 2diabetes in both mothers and offspring. Despite research efforts in thisarea, currently there are no reliable early biomarkers, preventative ortreatment strategies for PE, other than delivery. Moreover, paucity ofmechanistic data is impeding the development of successful preventativeand curative therapies of PE, particularly in the context of diabetes. The novel angiogenesis-related protein, FKBPL, is a critical regulator of developmental and pathological angiogenesis and closely associated with nutrient-sensing protein, SIRT-1. Therefore, FKBPL may play a key role in the pathophysiology of PE associated with diabetes.Materials and methods: Three different trophoblast cells lines(HTR8.SV.neo, BeWo and Jar) were exposed to diabetic stimuli: normalvs. high glucose (5.5 vs. 10, 20, 40 mM), native vs. highly oxidised,glycated low density lipoprotein (N- vs. HOG-LDL; 25 μg protein/ml),or hypoxia (1%); then FKBPL and SIRT-1 protein expression and mRNAlevels were measured in cell lysates. FKBPL and SIRT-1 were also measured in placental extracts using western blotting.Results: FKBPL and SIRT-1 protein expression differed across the threetrophoblast cell lines, with Jar cells expressing the highest levels ofFKBPL and SIRT-1, BeWo cells expressing the lowest level of SIRT-1and HTR8.SV.neo cells expressing the lowest level of FKBPL. In BeWocells treated with high vs. normal glucose (48 h), FKBPL mRNA levelswere increased 1.3-fold (10mM; p=0.001; n=3), 1.21-fold (...

Medek, D, Katelaris, C, Erbas, B, Lampugnani, ER, Newbiggin, E, Haberle, S, Huete, A, Beggs, PJ, Ebert, B, van Klinken, R & Davies, JM 1970, 'P56: IMPLEMENTATION OF THE AUSPOLLEN PARTNERSHIP PROJECT AND PRE‐EVALUATION SURVEY OF USER PERCEPTION OF THE VALUE OF LOCAL POLLEN INFORMATION', Internal Medicine Journal, Wiley, pp. 21-21.
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Meng, Q, Wu, J, Ellis, J & Kennedy, PJ 1970, 'Dynamic island model based on spectral clustering in genetic algorithm', 2017 International Joint Conference on Neural Networks (IJCNN), 2017 International Joint Conference on Neural Networks (IJCNN), IEEE, Anchorage, AK, USA, pp. 1724-1731.
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© 2017 IEEE. How to maintain relative high diversity is important to avoid premature convergence in population-based optimization methods. Island model is widely considered as a major approach to achieve this because of its flexibility and high efficiency. The model maintains a group of sub-populations on different islands and allows sub-populations to interact with each other via predefined migration policies. However, current island model has some drawbacks. One is that after a certain number of generations, different islands may retain quite similar, converged sub-populations thereby losing diversity and decreasing efficiency. Another drawback is that determining the number of islands to maintain is also very challenging. Meanwhile initializing many sub-populations increases the randomness of island model. To address these issues, we proposed a dynamic island model (DIM-SP) which can force each island to maintain different sub-populations, control the number of islands dynamically and starts with one sub-population. The proposed island model outperforms the other three state-of-the-art island models in three baseline optimization problems including job shop scheduler, travelling salesmen, and quadratic multiple knapsack.

Michelot, H, Morelato, M, Chadwick, S, Roux, C & Tahtouh, M 1970, 'CHEMOMETRICS APPLIED TO CHEMICAL PROFILES OF COCAINE SEIZURES: A FORENSIC INTELLIGENCE APPROACH', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 229-230.

Michelot, H, Morelato, M, Chadwick, S, Roux, C & Tahtouh, M 1970, 'THE ANALYSIS OF CUTTING AGENTS IN AUSTRALIAN SEIZURES OF COCAINE AND HEROIN OVER SIX YEARS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 227-227.

Michelot, H, Morelato, M, Chadwick, S, Tahtouh, M & Roux, C 1970, 'ION MOBILITY SPECTROMETRY VERSUS ION TRAP TANDEM MASS SPECTROMETRY TO DETECT NARCOTICS ON PASSPORTS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 227-227.

Mitchell, A, Mourad, B, Benzimra, M, Malouf, M, Morgan, L, Oliver, B & Glanville, A 1970, 'A SINGLE CENTRE, PROSPECTIVE, LONGITUDINAL STUDY OF THE HUMAN RESPIRATORY VIROME AFTER LUNG TRANSPLANTATION', RESPIROLOGY, WILEY, pp. 34-34.

Mitchell, AB, Calligaro, GL, Malouf, MA, Benzimra, M, Rigby, A, Pearson, R, Havryk, A, Plit, M, Morgan, L, Oliver, BG & Glanville, AR 1970, 'Transplanting The Human Respiratory Microbiome', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Mitchell, AB, Mourad, B, Malouf, M, Benzimra, M, Morgan, LC, Oliver, BGG & Glanville, AR 1970, 'The human respiratory virome after lung transplantation for COPD: A single centre, prospective, longitudinal study', Respiratory Medicine, Elsevier BV, pp. 276-277.
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Mitchell, AB, Mourad, B, Malouf, MA, Benzimra, M, Morgan, LC, Oliver, BG & Glanville, AR 1970, 'Transplanting the Human Respiratory Virome', JOURNAL OF HEART AND LUNG TRANSPLANTATION, 37th Annual Meeting and Scientific Sessions of the International-Society-for-Heart-and-Lung-Transplantation (ISHLT), ELSEVIER SCIENCE INC, San Diego, CA, pp. S148-S149.

Mitchell, AB, Mourad, B, Malouf, MA, Benzimra, M, Stark, D, Morgan, LC, Oliver, BG & Glanville, AR 1970, 'COMMUNITY ACQUIRED RESPIRATORY VIRUS DETECTION: COMPARING THE DIAGNOSTIC LABORATORY WITH THE RESEARCH LABORATORY', RESPIROLOGY, WILEY, pp. 62-62.

Moheimani, F, Williams, T, Koops, J, Reid, AT, Hansbro, PM, Wark, PAB & Knight, D 1970, 'Micrornas As Potential Epigenetic Targets To Restore The Airway Epithelium Integrity In Asthmatics', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Morelato, M, Broseus, J, Rhumorbarbe, D, Staehli, L, Roux, C & Rossy, Q 1970, 'A GEOGRAPHICAL ANALYSIS OF TRAFFICKING ON EVOLUTION, A POPULAR DARKNET MARKETPLACE', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 246-246.

Moret, S, Lee, PL, Spindler, X, Lennard, C & Roux, C 1970, 'LUMINESCENT SILICON OXIDE NANOPARTICLES FOR FINGERMARK DETECTION', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 232-232.

Paull, NJ, Irga, PJ & Torpy, FR 1970, 'Active green wall technology for the phytoremediation of indoor air pollutants', Green Infrastructure: Nature Based Solutions for Sustainable and Resilient Cities, Green Infrastructure: Nature Based Solutions for Sustainable and Resilient Cities.

Pavlidis, S, Faiz, A, Postma, D, Timens, W, Van Den Berg, M, Chihhsi Kuo, S, Chung, KF, Adcock, I, Guo, Y, Sterk, PJ, Djukanovic, R, Hiemstra, PS & Rowe, A 1970, 'Gene signatures from U-BIOPRED transcriptomic-associated clusters exist in COPD', Airway Pharmacology and Treatment, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Pierce, JE, Foster, A, Hurley, M, O'Halloran, R, Rose, M, Nickels, L, Togher, L, Meinzer, M, Copland, D, Rai, T, Godecke, E, Joosup, K & Cadilhac, D 1970, 'Treatment for people with chronic aphasia - Investigation of high and low intensity, constraint and multimodal treatments', INTERNATIONAL JOURNAL OF STROKE, Smart Strokes, SAGE PUBLICATIONS LTD, Gold Coast, QLD, pp. 7-7.

Pinkerton, J, Kim, R, Mayall, J, Ali, MK, Starkey, M, Robertson, A, O'Neill, L, Cooper, M, Hansbro, P & Horvat, J 1970, 'HIGH FAT DIET-INDUCED OBESITY PROMOTES STEROID-RESISTANT ASTHMA THROUGH AN NLRP3 INFLAMMASOME-DEPENDENT MECHANISM', RESPIROLOGY, WILEY, pp. 65-65.

Platen, E 1970, 'Long-Term Risk of a Well-Diversified Equity Index', 5th Asian Quantitative Finance Conference, Seoul, South Korea.

Platen, E 1970, 'Preparing Financial Regulation for Forthcoming Crises', AUT Mathematical Sciences Symposium, Aukland, New Zealand.

Platen, E & Schmutz, M 1970, 'Preparing Financial Regulation', 5th NUS Workshop on Risk and Regulation, Singapore.

Poulton, CG, Mirnaziry, SR & Wolff, C 1970, 'Stimulated brillouin scattering in plasmonic waveguides: Trade-offs and prospects', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe (CLEO/Europe) & European Quantum Electronics Conference (EQEC), IEEE, Munich, Germany.
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Summary form only given. The nonlinear optomechanical phenomenon known as Stimulated Brillouin Scattering (SBS) has attracted much recent attention in photonics, having a diverse range of important applications in such areas as sensing, narrow-linewidth sources, microwave photonics and spectroscopy [1]. Generating and using SBS is challenging in many platforms because the conditions for optical confinement (high refractive index of the core) are often at odds with the conditions for guidance of the acoustic wave, which are that the core material is mechanically compliant [2]. However there exists a class of materials - metals - that are both mechanically “soft”, and can also be used to strongly confine the optical field, in the form of Surface Plasmon Polaritons (SPPs). One might assume that the high optical loss and associated short propagation constants of SPPs indicate that these structures are not conducive to SBS. On the other hand, surface plasmons are associated with strong optical field gradients, which might be expected to assist SBS; in addition it is expected that a strong overlap between optical and acoustic modes can be achieved. The question of whether or not SBS can be harnessed, and useful gain measured, is therefore an open and interesting physical problem.Here we examine the theoretical properties of SBS in plasmonic waveguides. We show that metallic nanowires can indeed be used to guide both optical and acoustic waves, and that enhanced radiation pressure [3] at the metal-dielectric interface significantly enhances the SBS process. Indeed, we find that surface plasmon modes of silver nanowires embedded in silica can give rise to SBS gains orders of magnitude higher than that of recently-demonstrated integrated waveguides [4,5]. However there is a trade-off for this high gain: we show that the maximum Stokes amplification is limited by the power-handling capability of the waveguide, which is in turn dependent on the waveguide's thermal propertie...

Pyne, SG, Jatisatienr, A, Mungkornasawakul, P, Ung, AT, Limtrakul, P, Sastraruji, T, Sastraruji, K, Chaiyong, S, Umsumarng, S, Baird, MC, Dau, XD & Ramli, RA 1970, 'Phytochemical, Synthetic and Biological Studies on Stemona and Stichoneuron Plants and Alkaloids: A Personal Perspective', NATURAL PRODUCT COMMUNICATIONS, International Symposium on Natural Products for the Future (ISNPF), NATURAL PRODUCTS INC, JAPAN, Tokushima Bunri Univ, Tokushima, pp. 1365-1369.

Rahmani, M, Kruk, S, Camacho-Morales, R, Xu, L, Wang, L, Miroshnichenko, AE, Smimova, D, Tan, H, Karouta, F, Naureen, S, Vora, K, Solntsev, AS, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 1970, 'Giant enhancement and control of second-harmonic radiation from AlGaAs nanoantennas', 2017 Conference on Lasers and Electro-Optics Pacific Rim (CLEO-PR), 2017 Conference on Lasers and Electro-Optics Pacific Rim (CLEO-PR), IEEE, Singapore, Singapore, pp. 1-3.
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© 2017 Institute of Electrical and Electronics Engineers Inc. All Rights Reserved. We fabricate AlGaAs nanoantennas on a glass substrate and demonstrate the highest nonlinear conversion efficiency of 10-4 with the capability for shaping the radiation patterns and polarization of the second harmonic emission in both forward and backward directions. We also decode dynamic multipolar contributions to the second harmonic generation within such nanoantennas.

Rahmani, M, Kruk, S, Camacho-Morales, R, Xu, L, Wang, L, Miroshnichenko, AE, Smirnova, D, Tan, H, Karouta, F, Naureen, S, Vora, K, Solntsev, AS, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 1970, 'Giant enhancement and control of second-harmonic radiation from AlGaAs nanoantennas', Optics InfoBase Conference Papers.
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We fabricate AlGaAs nanoantennas on a glass substrate and demonstrate the highest nonlinear conversion efficiency of 10-4 with the capability for shaping the radiation patterns and polarization of the second harmonic emission in both forward and backward directions. We also decode dynamic multipolar contributions to the second harmonic generation within such nanoantennas.

Rees, M, Meier, P & Brown, J 1970, 'EVALUATION OF EFFECTIVENESS OF LASER ACUPUNCTURE ON OSTEOARTHRITIS KNEE PAIN - RANDOMISED, DOUBLE-BLINDED, PLACEBO-CONTROLLED TRIAL', LASERS IN SURGERY AND MEDICINE, Annual Meeting of the American-Society-for-Laser-Medicine-and-Surgery (ASLMS), WILEY, San Diego, CA, pp. 45-45.

Reid, AT, Moheimani, F, Nichol, K, Bartlett, N, Wark, PAB, Grainge, C, Hansbro, PM & Knight, D 1970, 'Short-Term Inhibition Of Notch Signalling Ablates Muc5ac Production In Human Airway Epithelial Cells From Asthmatic, Non-Asthmatic And COPD Donors', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Reimers, JR, McKemmish, LK, McKenzie, RH & Hush, NS 1970, 'Diabatic models with transferrable parameters for generalized chemical reactions', Journal of Physics: Conference Series, 23rd International Symposium on the Jahn-Teller Effect - Vibronic Coupling and Electron-Phonon Interactions in Molecules and Crystals, IOP Publishing, Tartu, ESTONIA, pp. 012014-012014.
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Abstract Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative corr...

Reyna Zeballos, JL, Hanham, J, Meier, P, Vlachopoulos, P & Geronimo, F 1970, 'Exploring Self-Regulation in Learner-Generated Digital Media (LGDM) Assignments in First Year Science Students.', Australian Association for Research in Education Conference, Australian Association for Research in Education Conference, Canberra, ACT.

Reyna, J, Horgan, F, Ramp, D & Meier, P 1970, 'USING LEARNER-GENERATED DIGITAL MEDIA (LGDM) AS AN ASSESSMENT TOOL IN GEOLOGICAL SCIENCES', INTED proceedings, International Technology, Education and Development Conference, IATED, Valencia, SPAIN, pp. 40-50.
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This study explores learner-generated digital media (LGDM) as an assessment tool in Geological Sciences. The aim was to engage students with the geology subject further and to develop their digital media literacies. For this purpose, a cohort of 97 students from the undergraduate Geological Processes subject (Autumn 2016) at the University of Technology Sydney, were randomly allocated to groups of 2-5 students. The students were asked to produce a five-minute digital media presentation on a chosen study topic. A lecture and workshop on digital media principles were delivered to prepare the students for the task early in the semester. Support and feedback were provided across the entire semester by the lecturer and digital media tutor through computer practicals and preparatory assignments. Group contribution was monitored using the SPARKPlus application. An online questionnaire was used at the end of the semester to gauge students’ attitude towards LGDM. The survey assessed demographics, digital media support, attitudes toward the assignment, and the contribution of LGDM to skills development. Methodological triangulation was used with data sets from the questionnaire, group work and marks obtained. Our preliminary results indicate that students had a positive attitude towards LGDM as an assessment tool and that the assessment provided a novel opportunity for students to apply attributes such as ‘creativity’ to their learning experience of geology. Implications for teaching and learning are discussed.

Rodgers, K, Chan, S & Steele, J 1970, 'Administration of L-tyrosine with levodopa could be neuroprotective in Parkinson's disease', JOURNAL OF NEUROCHEMISTRY, Biennial Meeting of the International-Society-for-Neurochemistry and European-Society-for-Neurochemistry (ISN-ESN), WILEY, Paris, FRANCE, pp. 245-245.

Rodgers, K, Steele, J & Padula, M 1970, 'A novel approach to detect the presence of levodopa (lDOPA) in the polypeptide chains of proteins', JOURNAL OF NEUROCHEMISTRY, Biennial Meeting of the International-Society-for-Neurochemistry and European-Society-for-Neurochemistry (ISN-ESN), WILEY, Paris, FRANCE, pp. 164-164.

Rutting, S, Wood, L, Hansbro, P & Oliver, B 1970, 'INTERACTION OF DIETARY FATTY ACIDS WITH OBESITY-INDUCED CYTOKINES IN PRIMARY PULMONARY FIBROBLASTS', RESPIROLOGY, WILEY, pp. 40-40.

Rutting, S, Xenaki, D, Ge, Q, Wood, L, Hansbro, P & Oliver, B 1970, 'DIETARY OMEGA‐6, BUT NOT OMEGA‐3 POLYUNSATURATED OR SATURATED FATTY ACIDS INCREASE INFLAMMATION IN HUMAN PULMONARY FIBROBLASTS', Respirology, Wiley, pp. 17-17.
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Seckiner, D, Maynard, P, Roux, C & Mallett, X 1970, 'FORENSIC GAIT ANALYSIS: MORPHOMETRIC BODY ASSESSMENT WITH ASSOCIATED CCTV IMAGE QUANTIFICATION', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 246-246.

Sharma, P, McAlinden, K, Chan, Y, Kota, A, Komalla, V, Chen, H & Oliver, B 1970, 'Maternal eCigarette vaping enhances Th2 driven asthma in the offspring', Airway Pharmacology and Treatment, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Shuttleworth, LA, Deutscher, AT, Osborne, T, Khan, MAM, Collins, D, Burke, C, Chapman, T, Darling, A, Riegler, M & Reynolds, OL 1970, 'Area wide integrated pest management incorporating the sterile insect technique: gut microbiota impacts on tephritid fitness and performance.', CABI, pp. 292-293.
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Smith, GB, Bilokur, M, Gentle, AR, Arnold, MD & Cortie, MB 1970, 'An advanced plasmonic cermet solar absorber for high temperature solar energy conversion applications', Nanostructured Thin Films X, Nanostructured Thin Films X, SPIE, San Diego, CA.
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Smith, GB, Gali Labarias, MA, Arnold, MD & Gentle, AR 1970, 'Super-cool paints: optimizing composition with a modified four-flux model', Thermal Radiation Management for Energy Applications, Thermal Radiation Management for Energy Applications, SPIE.
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© 2017 SPIE. The scope for maximizing the albedo of a painted surface to produce low cost new and retro-fitted super-cool roofing is explored systematically. The aim is easy to apply, low cost paint formulations yielding albedos in the range 0.90 to 0.95. This requires raising the near-infrared (NIR) spectral reflectance into this range, while not reducing the more easily obtained high visible reflectance values. Our modified version of the four-flux method has enabled results on more complex composites. Key parameters to be optimized include; fill factors, particle size and material, using more than one mean size, thickness, substrate and binder materials. The model used is a variation of the classical four-flux method that solves the energy transfer problem through four balance differential equations. We use a different approach to the characteristic parameters to define the absorptance and scattering of the complete composite. This generalization allows extension to inclusion of size dispersion of the pigment particle and various binder resins, including those most commonly in use based on acrylics. Thus, the pigment scattering model has to take account of the matrix having loss in the NIR. A paint ranking index aimed specifically at separating paints with albedo above 0.80 is introduced representing the fraction of time at a sub-ambient temperature.

Smith, GB, Tai, M, Arnold, MD & Gentle, AR 1970, 'Optical anisotropy due to perpendicular azimuth serial bideposition', Nanostructured Thin Films X, Nanostructured Thin Films X, SPIE, USA.
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© 2017 SPIE. Angled columnar structures produced by oblique angle deposition possess useful optical polarization effects. It is well known that this is due to structural anisotropy but the relative contributions of factors affecting this anisotropy are not fully understood in all cases. Serial bideposited films where the azimuth is changed during deposition can have greater birefringence if the azimuths are directly opposed. In contrast, in this article the properties of perpendicular azimuth films are studied: silicon films at tilt angles 50-80° were deposited and analyzed. Electron microscopy confirmed that the silicon nanostructures were formed off-axis, meaning they did not develop along the deposition axes but followed the averaged azimuth. Optical measurements confirm that the maximum birefringence occurs closer to glancing angles, and optical modelling demonstrates that in contrast to fixed azimuth films the birefringence in these perpendicular azimuth films is primarily modulated by depolarization factors.

Smith, MJA, Wolff, C, De Sterke, CM, Lapine, M & Poulton, CG 1970, 'Metamaterials for enhanced acousto-optic interactions', 13th International Conference on Theoretical and Computational Acoustics, ICTCA 2017, International Conference on Theoretical and Computational Acoustics, Vienna, Austria, pp. 91-91.

Smith, MJA, Wolff, C, Lapine, M, de Sterke, CM & Poulton, CG 1970, 'Metamaterials for opto-acoustic interactions', AIP Conference Proceedings, ADVANCES IN ELECTRICAL AND ELECTRONIC ENGINEERING: FROM THEORY TO APPLICATIONS: Proceedings of the International Conference on Electrical and Electronic Engineering (IC3E 2017), Author(s), Vladivostok, RUSSIA.
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Solntsev, AS, Kumar, P, Pertsch, T, Setzpfandt, F & Sukhorukov, AA 1970, 'Integrated Quantum Spectroscopy on a Nonlinear Chip', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, CA, USA, pp. 1-2.
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©2017 IEEE We demonstrate experimentally on-chip-integrated quantum spectroscopy by generating biphotons in a LiNbO3 waveguide through spontaneous parametric down-conversion, and using signal photon detection in the NIR to study the dynamics of idler photons in the MIR.

Solntsev, AS, Kumar, P, Pertsch, T, Sukhorukov, AA & Setzpfandt, F 1970, 'Quantum spectroscopy on a nonlinear photonic chip', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe (CLEO/Europe) & European Quantum Electronics Conference (EQEC), IEEE, Munich, Germany.
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Quantum spectroscopy is a powerful tool that is based on classically detecting one of the photons of a biphoton state to study how the other photon experiences the environment [1]. It is especially useful, since the signal photon can be read out in the visible range, where the detection is simple and affordable, while the idler photon can probe the optical properties in mid-infrared (MIR) and far-infrared (FIR) ranges, which typically requires expensive and bulky solutions when using conventional spectroscopic approaches. Quantum spectroscopy has been utilized to measure broadband refractive index dispersion [2] and domain structure [3] of solids in a single shot of a non-tunable continuous-wave laser, as well as to precisely determine the optical properties of gases [4].

Spindler, X, Lau, V & Roux, C 1970, 'WHEN ARE FIBRES RELEVANT: DAILY ACTIVITY AND BACKGROUND EXTRANEOUS FIBRES ON T-SHIRTS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 58-58.

Spindler, X, Scott, E, Barone, A, Liang, K, Roux, C, Moret, S & Lennard, C 1970, 'THE DETECTION OF LATENT FINGERMARKS USING LUMINESCENT METAL-ORGANIC FRAMEWORKS', FORENSIC SCIENCE INTERNATIONAL, 21st Triennial Meeting of the International-Association-of-Forensic-Sciences (IAFS), ELSEVIER IRELAND LTD, Toronto, CANADA, pp. 61-61.

Starkey, MR, Dua, K, Hsu, AC, Nair, PM, Haw, TJ, Nguyen, DH, Kim, RY, Horvat, JC, Godfrey, DI, McKenzie, A, Lukacs, NW, Wark, PAB & Hansbro, PM 1970, 'Interleukin-13 Predisposes To More Severe Influenza Infection In Mice And Human Epithelial Cells By Suppressing Interferon Responses And Activating The Microrna-21/pi3k Signaling Pathway', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Starkey, MR, Nguyen, DH, Kim, RY, Nair, PM, Haw, T, Horvat, JC, Godfrey, DI, McKenzie, AN & Hansbro, PM 1970, 'Early-life respiratory bacterial infection-induced chronic lung disease is driven by a novel TLR2/IL-13/miR-21/PI3K-dependent, but MyD88-independent signalling pathway', The Journal of Immunology, International Conference of the American-Thoracic-Society (ATS), The American Association of Immunologists, Washington, DC, pp. 131.5-131.5.
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Abstract There is a critical window in early-life where the lung is still maturing and susceptible to infection. Indeed, severe respiratory infections in early-life are a risk factor for the development of chronic lung diseases. The aim of this study was to identify the mechanisms involved. Neonatal wild-type (WT), TLR2 deficient (−/−), IL-13−/−, MyD88−/− and STAT6−/− mice were infected with the natural mouse bacterial pathogen Chlamydia muridarum, as a model of severe respiratory tract infection in early-life. In some experiments WT mice were treated with miR-21 antagomirs, PI3K inhibitors, or relevant controls during early-life infection. The impact of targeting these specific immune molecules during early-life on infection-induced impairment of lung function and structure were assessed. Neonatal Chlamydia respiratory infection increased TLR2, IL-13-receptor, miR-21 and PI3K expression and/or activity in the lung. TLR2 signalling induced IL-13-receptor expression, IL-13 signalling induced miR-21 expression and miR-21 increased PI3K activity. TLR2 signalling also increased IL-13+ ILC2s in the lung. TLR2−/− and IL-13−/− mice were protected against infection-induced airway hyperresponsiveness (AHR), but not emphysema-like alveolar enlargement. This TLR2/IL-13 mediated phenotype was independent of MyD88, but dependent on STAT6. Specific targeting of miR-21 prevented AHR but not emphysema. Pan-PI3K inhibition did not affect AHR, but protected against emphysema. Interestingly, early-life infection-induced AHR was steroid insensitive. This study identifies a novel signalling network that may be targeted for the prevention of the long-term deleterious effects of early-life infection on lung function and structure.

Starkey, MR, Nguyen, DH, Kim, RY, Nair, PM, Haw, T, Horvat, JC, Godfrey, DI, McKenzie, AN & Hansbro, PM 1970, 'Early-life respiratory bacterial infection-induced chronic lung disease is driven by a novel TLR2/IL-13/miR-21/PI3K-dependent, but MyD88-independent signalling pathway', JOURNAL OF IMMUNOLOGY, Annual Meeting of the American-Association-of-Immunologists (AAI), AMER ASSOC IMMUNOLOGISTS, Washington, DC.

Tay, HL, Hsu, A, Nguyen, T, Donovan, C, Collison, A, Mattes, J, Kaiko, GE, Yang, M, Hansbro, PM & Foster, PS 1970, 'Interleukin-36 gamma: Roles in lungs innate immunity, inflammation and allergy', CYTOKINE, 5th Annual Meeting of the International-Cytokine-and-Interferon-Society (ICIS), ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, Int Cytokine & Interferon Soc, Kanazawa, JAPAN, pp. 114-114.

Tayebi, A & Rice, SA 1970, 'Plasmonic superradiant antennas', AIP Conference Proceedings, PROCEEDINGS OF THE 43RD INTERNATIONAL CONFERENCE APPLICATIONS OF MATHEMATICS IN ENGINEERING AND ECONOMICS: (AMEE’17), Author(s), MI, Michigan State Univ, Nat Superconducting Cyclotron Lab, Facil Rear Isotope, East Lansing.
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Teherani, FH, Rogers, DJ, Sandana, VE, Bove, P, Ton-That, C, Lem, LLC, Chikoidze, E, Neumann-Spallart, M, Dumont, Y, Huynh, T, Phillips, MR, Chapon, P, McClintock, R & Razeghi, M 1970, 'A study into the impact of sapphire substrate orientation on the properties of nominally-undoped β-Ga₂O₃ thin films grown by pulsed laser deposition', SPIE Proceedings, SPIE OPTO, SPIE, San Francisco.
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© 2017 SPIE. Nominally-undoped Ga2O3 layers were deposited on a-, c- and r-plane sapphire substrates using pulsed laser deposition. Conventional x-ray diffraction analysis for films grown on a- and c-plane sapphire showed the layers to be in the β-Ga2O3 phase with preferential orientation of the (-201) axis along the growth direction. Pole figures revealed the film grown on r-plane sapphire to also be in the β-Ga2O3 phase but with epitaxial offsets of 29.5°, 38.5° and 64° from the growth direction for the (-201) axis. Optical transmission spectroscopy indicated that the bandgap was ∼5.2eV, for all the layers and that the transparency was > 80% in the visible wavelength range. Four point collinear resistivity and Van der Pauw based Hall measurements revealed the β-Ga2O3 layer on r-plane sapphire to be 4 orders of magnitude more conducting than layers grown on a- and c-plane sapphire under similar conditions. The absolute values of conductivity, carrier mobility and carrier concentration for the β-Ga2O3 layer on r-sapphire (at 20Ω-1.cm-1, 6 cm2/Vs and 1.7 x 1019 cm-3, respectively) all exceeded values found in the literature for nominally-undoped β-Ga2O3 thin films by at least an order of magnitude. Gas discharge optical emission spectroscopy compositional depth profiling for common shallow donor impurities (Cl, F, Si and Sn) did not indicate any discernable increase in their concentrations compared to background levels in the sapphire substrate. It is proposed that the fundamentally anisotropic conductivity in β-Ga2O3 combined with the epitaxial offset of the (-201) axis observed for the layer grown on r-plane sapphire may explain the much larger carrier concentration, electrical conductivity and mobility compared with layers having the (-201) axis aligned along the growth direction.

Thomas, M, Bjorhall, K, Israelsson, E, LammBergstrom, E, Horvat, J, Kim, R, Maciewicz, R, Muthas, D, Nordberg, M, RodrigoBlomqvist, S, Saarne, T, Winkler, C, Karabelas, K, Adcock, I, Chung, F, Hansbro, P, Malmgren, A & Perry, M 1970, 'Phosphoinositide-3-kinase gamma/delta isoform signalling defines a mixed T cell severe asthmatic endotype', Airway Cell Biology and Immunopathology, ERS International Congress 2017 abstracts, European Respiratory Society.
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Titchener, J, Grafe, M, Heilmann, R, Solntsev, AS, Szameit, A & Sukhorukov, AA 1970, 'Scalable on-chip quantum state tomography', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe (CLEO/Europe) & European Quantum Electronics Conference (EQEC), IEEE.
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Titchener, J, Gräfe, M, Heilmann, R, Solntsev, AS, Szameit, A & Sukhorukov, AA 1970, 'Scalable quantum tomography in a photonic chip', Conference on Lasers and Electro-Optics, CLEO: Applications and Technology, OSA, San Jose, CA, USA, pp. 1-2.
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© 2017 IEEE. We formulate a method of quantum tomography that scales linearly with the number of photons and involves only one optical transformation. We demonstrate it experimentally for two-photon entangled states using a special photonic chip.

Toan, TT, Elbadawi, C, Totonjian, D, Lobo, CJ, Grosso, G, Moon, H, Englund, DR, Ford, MJ, Aharonovich, I & Toth, M 1970, 'Robust Multicolor Single Photon Emission from Point Defects in Hexagonal Boron Nitride', 2017 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics (CLEO), IEEE, CA, San Jose.
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We demonstrates engineering of quantum emitters in hBN multi-layers using either electron beam irradiation or annealing. The defects exhibit a broad range of multicolor room-temperature single photon emissions across the visible and the near-infrared ranges.

Tran, NN, Huete, A & Hardtke, L 1970, 'Impact of bidirectional reflectance distribution function on modis vegetation indices in southeast Asia tropical forests', 38th Asian Conference on Remote Sensing - Space Applications: Touching Human Lives, ACRS 2017, Asian Conference on Remote Sensing, AARS, Delhi, India, pp. 1-6.
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Tropical forests play important roles on global climate and biodiversity. The Moderate Resolution Imaging Spectroradiometer (MODIS), with high temporal resolution, provide a useful tool to study tropical forest dynamics, including seasonality and inter-annual variation. However, optical satellite data have cloud, aerosol and bidirectional reflectance distribution function (BRDF) effects, that create uncertainty in tropical forest studies. In the Amazon, some researchers demonstrated the difficulties in separating true forest dynamics from BRDF artefacts and seasonal cloud and aerosol influences. Lastly, optical reflectance saturation in dense tropical forests may restrict the retrieval of phenology information. In this study, we investigated the impact of BRDF effects on MODIS vegetation indices (VI) in Southeast Asia (SEA) tropical forests, the least studied area compared to other major tropical forests (South America and Central Africa). Moreover, unlike Amazon tropical forests, VI seasonality in SEA forests is not synchronous with sun-sensor geometries. We used 10-year data of daily MODIS BRDF (MCD43A1) collection 6 product, a kernel-driven model product that allows us to retrieve VI values for a range of fixed solar zenith angles (SZA). We compared these with the standard VI products (MOD13A1, MYD13A1) to analyse BRDF influences. The results show significant BRDF effects in all forest sites. Generally, smaller SZA yielded higher VI signals in forests. We found tradeoff's between VI robustness to BRDF effects and saturation that impacted upon the retrievals of phenology parameters.

Turturice, BA, McGee, H, Oliver, BG, Baraket, M, Ascoli, C, Ranjan, R, Perkins, DL & Finn, PW 1970, 'Genetically Encoded Metabolic Pathways In Airway Microbiota As Mediators Of Airway Inflammation In Asthma', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Wang, J, Ge, Q, Oliver, BG, Ashton, A, Dong, L & Burgess, J 1970, 'Runt-Related Transcription Factor 2 (runx2) Is A Potential Regulator Of Connective Tissue Growth Facor (ctgf) In Asthmatic Airway Smooth Muscle', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, Washington, DC.

Wang, K, Kruk, SS, Xu, L, Parry, M, Chung, H-P, Solntsev, AS, Titchener, J, Kravchenko, I, Chen, Y-H, Kivshar, YS, Neshev, DN & Sukhorukov, AA 1970, 'Quantum imaging with dielectric metasurfaces for multi-photon polarization tomography', Conference on Lasers and Electro-Optics, CLEO: Applications and Technology, OSA, San Jose, CA, USA, pp. 1-2.
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© 2017 IEEE. We suggest and realize experimentally dielectric metasurfaces with high transmission efficiency for quantum multi-photon tomography, allowing for full reconstruction of pure or mixed quantum polarization states across a broad bandwidth.

Wang, K, Kruk, SS, Xu, L, Parry, M, Chung, H-P, Solntsev, AS, Titchener, J, Kravchenko, I, Chen, Y-H, Kivshar, YS, Neshev, DN & Sukhorukov, AA 1970, 'Quantum polarization tomography with all-dielectric metasurfaces', 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2017 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), IEEE, Munich, Germany.
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Measurements of quantum states of photons are conventionally performed with series of optical elements in bulk setups [1] or optical chips incorporating multiple tunable beam splitters. Here, we suggest and develop experimentally, for the first time to our knowledge, a new concept of quantum-polarization measurements with a single all-dielectric resonant metasurface [2]. The operating principle is presented in Fig. 1(a): A metasurface spatially splits different components of photon polarization states, which then enables full reconstruction of the photon state based on the photon correlations with simple polarization-insensitive single-photon detectors or EMCCD cameras. The subwavelength thin structure provides an ultimate miniaturization, and can facilitate quantum tomography by spatially-resolved imaging without a need for reconfiguration. Such parallel-detection approach promises not only better robustness and scalability, but also the possibility to study the dynamics of quantum states in real-time.

Wang, K, Kruk, SS, Xu, L, Parry, M, Chung, H-P, Titchener, J, Kravchenko, I, Chen, Y-H, Solntsev, AS, Kivshar, YS, Neshev, DN & Sukhorukov, AA 1970, 'Quantum tomography with all-dielectric metasurfaces', Frontiers in Optics 2017, Frontiers in Optics, OSA, Munich, Germany.
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© OSA 2017. We suggest and realize experimentally dielectric metasurfaces with high transmission efficiency for quantum multi-photon tomography, allowing for full reconstruction of pure or mixed quantum polarization states across a broad bandwidth.

Wolff, C, Stiller, B, Steel, MJ, Eggleton, BJ & Poulton, CG 1970, 'Theory of cascaded forward brillouin scattering', Optics InfoBase Conference Papers, The European Conference on Lasers and Electro-Optics 2017, Munich, Germany.
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Brillouin Scattering (SBS) is the scattering of light from acoustic vibrations in matter and manifests in three different configurations (see Fig. 1a): The first case is when light is back-scattered and is referred to as stimulated Brillouin scattering (SBS) in the strict sense. The second case is when light is forward-scattered into a different optical mode. This inter-modal scattering process has many similarities with (backward) SBS. The third case is when light is forward-scattered into the same optical mode, which is known as intra-mode forward Brillouin scattering (FBS). In bulk and bulk-like systems, backward SBS is self-amplifying and a promising mechanism for the implementation of applications ranging from novel light sources such as Brillouin lasers or on-chip frequency combs to microwave photonics [1]. However, recent studies [2,3] conducted in nano-scale waveguides showed that FBS can exhibit opto-mechanical coupling in excess of backward SBS and for this reason it has attracted considerable attention. So far, the analysis of many FBS experiments has been based on theory developed for backward SBS. Unfortunately, this turns out not to be applicable. The most striking discrepancy is that simple backward SBS theory predicts exponential growth of Stokes and sound wave, while FBS without optical dispersion does not exhibit any growth at all of the sound wave and oscillatory behaviour in the Stokes signals. The reason for this very different behavior is that in intra-mode FBS and unlike in backward SBS all Stokes orders are coupled by the same acoustic mode and therefore the scattering process can cascade very efficiently [4].

Wong, S, Chen, L, Oliver, B, Padula, M & Sukkar, M 1970, 'SPARC EXPRESSION IN AIRWAY SMOOTH MUSCLE CELLS IS REGULATED BY THE UNFOLDED PROTEIN RESPONSE AND MAY BE DIMINISHED IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE', Respirology, Wiley, pp. 31-32.
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Xu, J, Su, D & Wang, G 1970, 'Co₃O₄-Carbon Cloth free standing cathode for lithium sulfur battery', IOP Conference Series: Materials Science and Engineering, International Conference on Energy Materials and Applications, IOP Publishing, Hiroshima, Japan, pp. 012013-012013.
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© Published under licence by IOP Publishing Ltd. Lithium-sulfur (Li-S) battery has been considered to be one of the most promising next-generation electrochemical energy-storage systems due to its high theoretical energy of 2600 Wh kg-1 with low cost. The insulating nature of both sulfur and the dissolution of polysulfides are the two primary challenges for the application of lithium sulfur batteries. Here, we developed a binder-free cathode by chemisorption of Co3O4 to carbon cloth (CC), which was used as a 3D current collector to accommodate a large amount of sulfur, multiwall carbon nanofiber (MWCNF) and carbon black (CB) hybrids within the conductive scaffold, enabling the fabrication of ultrahigh sulfur loaded electrodes. The interconnected carbon fibers established a long-range conductive matrix for an efficient electron transport, the multiple conductive pathways guarantee high sulfur utilization. More importantly, the high electrolyte absorbability of the Co3O4-CC-S current collector facilitates well-localized polysulfides within the Co3O4-CC-S, meanwhile, the polar Co3O4 could also effectively entrapped the intermediated polysulfides preventing their free diffusion to the lithium anode, guaranteeing good cycling stability. Consequently, the Co3O4-CC-S electrodes exhibit excellent electrochemical performance with sulfur loading of 4.3 mg cm-2.

Yang, X, Ma, C, Wang, F, Jin, D & Xi, P 1970, 'Long-term ultra-low-level power STED nanoscopy', International Conference on Photonics and Imaging in Biology and Medicine, International Conference on Photonics and Imaging in Biology and Medicine, OSA.
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Through the strategic application of upconversion rare-earth nanoparticles (UCNPs), this work has reduced the intensity of the traditional super-resolution by 2-3 orders of magnitude. It reveals a new mechanism of stimulated emission caused by the photon avalanche effect. With only 30mW continuous laser, resolution down to 28nm has been attained, which is only 1/36 of the excitation wavelength.

Yang, X, Xie, H, Alonas, E, Liu, Y, Chen, X, Santangelo, PJ, Ren, Q, Xi, P & Jin, D 1970, 'Mirror enhanced STED super-resolution microscopy', 2017 Conference on Lasers and Electro-Optics, CLEO 2017 - Proceedings, Conference on Lasers and Electro-Optics, IEEE, San Jose, CA, USA, pp. 1-2.
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Through reflective interference, the axial thickness of confocal point spread function can be easily improved to 100 nm. Six-fold of axial resolution and two-fold of lateral resolution can be obtained for STED nanoscopy.

Zakarya, R, Chen, H, Brandsma, C-A, Adcock, IM & Oliver, BGG 1970, 'Epigenetic control of TGFβ induced fibrosis in COPD', Molecular Pathology and Functional Genomics, ERS International Congress 2017 abstracts, European Respiratory Society, Milan, ITALY.
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Irga, PJ, Paull, NJ, Abdo, P, Huynh, BP, Avakian, V, Nguyen, T & Torpy, F 2017, DEVELOPING THE JUNGLEFY BREATHING WALL FOR ENHANCED INDOOR AIR QUALITY REMEDIATION, Sydney, Australia.
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KEY RESEARCH HIGHLIGHTSOperational parameters of the Junglefy Breathing Wall system were determined and characterised. Data collected included system water loss, pressure drop, air distribution and the system’s effect on ambient temperature and relative humidity.Clean air delivery rates were calculated utilising the removal efficiencies. The system produced 25.86¬–28.70 m3/h per module, depending on particle size and airflow rate. A typical Breathing Wall of 10 m2, utilising 40 modules would thus produce up to 12,700 m3/h of particle-free air.Tests were conducted to identify the most appropriate plant species for survival in high pollution environments. All of the plant species tested, which are currently used in commercial applications of the Breathing Wall, recorded moderate air pollutant tolerance, and thus the system using the current plant species could possibly be used in industrial applications. Pollutant effect on air filled porosity of the substrate was negligible, even under extremely high pollutant loads.Air quality tests were conducted at the Lend Lease Head Office, and the efficiency of the first Breathing Wall installation was monitored. The Breathing Wall is successfully reducing ambient particulate matter and carbon dioxide relative to outdoors and other areas throughout the building. Additionally, air pollutants including carbon monoxide, volatile organic compounds and sulphur dioxide were below the detection limit of the equipment being used, indicating excellent indoor environmental quality. The results indicate that the Breathing Wall is working as intended.

Lassudrie, M, Ajani, PA & Murray, SA 2017, Microalgal Community Composition Assessment in Warringah Lagoons 2016-2017, 1-33.

Pettit, T, Irga, P, Abdo, P, Huynh, B, Stephen, J & Torpy, FR UTS 2017, DEVELOPMENT AND AUGMENTATION THE JUNGLEFY BREATHING WALL, Sydney, Australia.

Plant, RA, Cunningham, R, Berry, F, Madden, B, Hageer, Y & Huete, A 2017, Measuring Urban Green Space in Australia, no. GC15004, pp. 1-133, Sydney, Australia.
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The Hort Innovation Green Cities project “Measuring Australia’s Green Space Asset” (MUGS) undertook a global review of urban green space (UGS) measurement research and engaged with Australian stakeholders to gauge current practice. The overall aim of the project was to foster best-practice UGS planning and management by juxtaposing the scientific state of the art with the contextualised needs expressed by potential Australian end users. The synthesis of findings informed a ‘blueprint’ which sketches the contours of a possible nationally consistent UGS decision-support framework. The framework is illustrated with a worked example from Australia (rapid assessment of urban green space assets using satellite imagery).

Berhane, AM, Jeong, K-Y, Bradac, C, Walsh, M, Englund, D, Toth, M & Aharonovich, I 2017, 'Photophysics of GaN single photon sources in the visible spectral range'.

Bottomley, A, Mann, R, Monahan, L, Sonenshein, A & Harry, E 2017, 'We Are What We Eat Identifying a regulatory crosstalk between central carbon metabolism and cell division in bacteria'.

Bouman, HA, Platt, T, Doblin, M, Figueiras, FG, Gudmudsson, K, Gudfinnsson, HG, Huang, B, Hickman, A, Hiscock, M, Jackson, T, Lutz, VA, Mélin, F, Rey, F, Pepin, P, Segura, V, Tilstone, GH, van Dongen-Vogels, V & Sathyendranath, S 2017, 'Photosynthesis-irradiance parameters of marine phytoplankton: synthesis of a global data set', Copernicus GmbH.
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Abstract. The photosynthetic performance of marine phytoplankton varies in response to a variety of factors, environmental and taxonomic. One of the aims of the MArine primary Production: model Parameters from Space (MAPPS) project of the European Space Agency is to assemble a global database of photosynthesis-irradiance (P-E) parameters from a range of oceanographic regimes as an aid to examining the basin-scale variability in the photophysiological response of marine phytoplankton and to use this information to improve the assignment of P-E parameters in the estimation of global marine primary production using satellite data. The MAPPS P-E Database, which consists of over 5000 P-E experiments, provides information on the spatio-temporal variability in the two P-E parameters (the assimilation number, PmB, and the initial slope, αB, where the superscripts B indicate normalisation to concentration of chlorophyll) that are fundamental inputs for models (satellite-based and otherwise) of marine primary production that use chlorophyll as the state variable. Quality-control measures consisted of removing samples with abnormally-high parameter values and flags were added to denote whether the spectral quality of the incubator lamp was used to calculate a broad-band value of αB. The MAPPS database provides a photophysiological dataset that is unprecedented in number of observations and in spatial coverage. The database would be useful to a variety of research communities, including marine ecologists, biogeochemical modellers, remote-sensing scientists and algal physiologists. The compiled data are available at https://doi.org/10.1594/PANGAEA.874087 (Bouman et al., 2017).

Bray, K, Cheung, L, Aharonovich, I, Valenzuela, SM & Shimoni, O 2017, 'Versatile Multicolor Nanodiamond Probes for Intracellular Imaging and Targeted Labeling', Cold Spring Harbor Laboratory.
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AbstractDiamond nanoparticles that host bright luminescent centers are attracting attention for applications in bio-labeling and bio-sensing. Beyond their unsurpassed photostability, diamond can host multiple color centers, from the blue to the near infra-red spectral range. While nanodiamonds hosting nitrogen vacancy defects have been widely employed as bio-imaging probes, production and fabrication of nanodiamonds with other color centers is a challenge. In this work, a large scale production of fluorescent nanodiamonds (FNDs) containing a near infrared (NIR) color center – namely the silicon vacancy (SiV) defect, is reported. More importantly, a concept of application of different color centers for multi-color bio-imaging to investigate intercellular processes is demonstrated. Furthermore, two types of FNDs within cells can be easily resolved by their specific spectral properties, where data shows that SiV FNDs initially dispersed throughout the cell interior while NV FNDs localized in a close proximity to nucleus. The reported results are the first demonstration of multi-color labeling with FNDs that can pave the way for the wide-ranging use of FNDs in applications, including bio-sensing, bio-imaging and drug delivery applications.

Bray, K, Kato, H, Previdi, R, Sandstrom, R, Ganesan, K, Ogura, M, Makino, T, Yamasaki, S, Magyar, AP, Toth, M & Aharonovich, I 2017, 'Single crystal diamond membranes for nanoelectronics'.

Capistrano, SJ, Zakarya, R, Chen, H & Oliver, BG 2017, 'BIOMASS SMOKE EXPOSURE ENHANCES RHINOVIRUS-INDUCED INFLAMMATION', WILEY, pp. 122-122.

Cardona, T, Sánchez-Baracaldo, P, Rutherford, AW & Larkum, AWD 2017, 'Early Archean origin of Photosystem II', Cold Spring Harbor Laboratory.
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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 and had already evolved some level of protection against the formation of reactive oxygen species, which would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

Dietrich, A, Bürk, M, Steiger, ES, Antoniuk, L, Tran, TT, Nguyen, M, Aharonovich, I, Jelezko, F & Kubanek, A 2017, 'Narrowband quantum emitters over large spectral range with Fourier-limited linewidth in hexagonal boron nitride'.
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Single defect centers in layered hexagonal boron nitride (hBN) are promisingcandidates as single photon sources for quantum optics and nanophotonicsapplications. However, until today spectral instability hinders manyapplications. Here, we perform resonant excitation measurements and observeFourier-Transform limited (FL) linewidths down to $\approx 50$ MHz. Weinvestigate optical properties of more than 600 quantum emitters (QE) in hBN.The QEs exhibit narrow zero-phonon lines (ZPL) distributed over a spectralrange from 580 nm to 800 nm and with dipole-like emission with highpolarization contrast. The emission frequencies can be divided into four mainregions indicating distinct families or crystallographic structures of the QEs,in accord with ab-initio calculations. Finally, the emitters withstand transferto a foreign photonic platform - namely a silver mirror, which makes themcompatible with photonic devices such as optical resonators and paves the wayto quantum photonics applications including quantum commmunications and quantumrepeaters.

Duong, H, Chen, Y, Tawfik, SA, Wen, S, Parviz, M, Ford, MJ, Shimoni, O & Jin, D 2017, 'Systematic Investigation of Functional Ligands for Colloidal Stable Upconversion Nanoparticles', American Chemical Society (ACS).
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Despite intense efforts on surface functionalization to generate hydrophilic upconversion nanoparticles (UCNPs), long-term colloidal stability in physiological buffers remains a major concern. Here we quantitatively investigate the competitive adsorption of phosphate, carboxylic acid and sulphonic acid onto the surface of UCNPs and study their binding strength to identify the best conjugation strategy. To achieve this, we designed and synthesized three di-block copolymers composed of poly(ethylene glycol) methyl ether acrylate and a polymer block bearing phosphate, carboxylic or sulphonic acid anchoring groups prepared by an advanced polymerization technique, Reversible Addition Fragmentation Chain Transfer (RAFT). Analytical tools provide the evidence that phosphate ligands completely replaced all the oleic acid capping molecules on the surface of the UCNPs compared with incomplete ligand exchange by carboxylic and sulphonic acid groups. In the meanwhile, simulated quantitative adsorption energy measurements confirmed that among three functional groups, calculated adsorption strength for phosphate anchoring ligands is higher which is in good agreement with experimental results regarding the best colloidal stability especially in phosphate buffer solution. The finding suggests that polymers with multiple anchoring negatively charged phosphate moieties provide excellent colloidal stability for lanthanide ion-doped luminescent nanoparticles for various potential applications.

Faizi, M, Zavřel, T, Loureiro, C, Cerveny, J & Steuer, R 2017, 'A minimal model of protein allocation during phototrophic growth', Cold Spring Harbor Laboratory.
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AbstractPhotoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.

Fergusson, K & Platen, E 2017, 'Less-Expensive Valuation of Long Term Annuities Linked to Mortality, Cash and Equity'.
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This paper proposes a paradigm shift in the valuation of long term annuities, away from classical no-arbitrage valuation towards valuation under the real world probability measure. Furthermore, we apply this valuation method to two examples of annuity products, one having annual payments linked to a mortality index and the savings account and the other having annual payments linked to a mortality index and an equity index with a guarantee that is linked to the same mortality index and the savings account. Out-of-sample hedge simulations demonstrate the effectiveness of real world valuation. In contrast to risk neutral valuation, which is a form of relative valuation, the long term average excess return of the equity market comes into play. Instead of the savings account, the num\'eraire portfolio is employed as the fundamental unit of value in the analysis. The num\'eraire portfolio is the strictly positive, tradable portfolio that when used as benchmark makes all benchmarked nonnegative portfolios supermartingales. The benchmarked real world value of a benchmarked contingent claim equals its real world conditional expectation. This yields the minimal possible value for its hedgeable part and minimizes the fluctuations for its benchmarked hedge error. Under classical assumptions, actuarial and risk neutral valuation emerge as special cases of the proposed real world valuation. In long term liability and asset valuation, the proposed real world valuation can lead to significantly lower values than suggested by classical approaches when an equivalent risk neutral probability measure does not exist.

Fourment, M, Claywell, BC, Dinh, V, McCoy, C, Matsen, FA & Darling, AE 2017, 'Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals', Cold Spring Harbor Laboratory.
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AbstractModern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phy-logenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein new data can be continuously incorporated to update the estimate of the posterior probability distribution. In this paper we describe and evaluate several different online phylogenetic sequential Monte Carlo (OPSMC) algorithms. We show that proposing new phylogenies with a density similar to the Bayesian prior suffers from poor performance, and we develop ‘guided’ proposals that better match the proposal density to the posterior. Furthermore, we show that the simplest guided proposals can exhibit pathological behavior in some situations, leading to poor results, and that the situation can be resolved by heating the proposal density. The results demonstrate that relative to the widely-used MCMC-based algorithm implemented in MrBayes, the total time required to compute a series of phylogenetic posteriors as sequences arrive can be significantly reduced by the use of OPSMC, without incurring a significant loss in accuracy.

Grüning, B, Dale, R, Sjödin, A, Chapman, BA, Rowe, J, Tomkins-Tinch, CH, Valieris, R, Caprez, A, Batut, B, Haudgaard, M, Cokelaer, T, Beauchamp, KA, Pedersen, BS, Hoogstrate, Y, Bretaudeau, A, Ryan, D, Corguillé, GL, Yusuf, D, Luna-Valero, S, Kirchner, R, Brinda, K, Wollmann, T, Raden, M, Heeringen, SJV, Soranzo, N, Pantano, L, Charlop-Powers, Z, Unneberg, P, Smet, MD, Martin, M, Kuster, GV, Antao, T, Miladi, M, Thornton, K, Brueffer, C, Beek, MVD, Maticzka, D, Blank, C, Will, S, Gravouil, KE, Wolff, J, Holtgrewe, M, Fallmann, J, Piro, VC, Shlyakhter, I, Yousif, A, Mabon, P, Zhang, X-O, Shen, W, Cabral, J, Thomas, C, Enns, E, Brown, J, Boekel, J, Hollander, MD, Kelleher, J, Turaga, N, Ruiter, JRD, Bouvier, D, Gladman, S, Choudhary, S, Harding, N, Eggenhofer, F, Kratz, A, Fang, Z, Kleinkauf, R, Timm, H, Cock, PJA, Seiler, E, Brislawn, C, Nguyen, H, Stovner, EB, Ewels, P, Chambers, M, Johnson, JE, Hägglund, E, Ye, S, Guimera, RV, Pruesse, E, Dunn, WA, Parsons, L, Patro, R, Koppstein, D, Grassi, E, Wohlers, I, Reynolds, A, Cornwell, M, Stoler, N, Blankenberg, D, He, G, Bargull, M, Junge, A, Farouni, R, Freeberg, M, Singh, S, Bogema, DR, Cumbo, F, Wang, L-B, Larson, DE, Workentine, ML, Devisetty, UK, Laurent, S, Roger, P, Garnier, X, Agren, R, Khan, A, Eppley, JM, Li, W, Stöcker, BK, Rausch, T, Taylor, J, Wright, PR, Taranto, AP, Chicco, D, Sennblad, B, Baaijens, JA, Gopez, M, Abdennur, N, Milne, I, Preussner, J, Pinello, L, Srivastava, A, Chande, AT, Kensche, PR, Pirola, Y, Knudsen, M, Bruijn, ID, Blin, K, Gonnella, G, Enache, OM, Rai, V, Waters, NR, Hiltemann, S, Bendall, ML, Stahl, C, Miles, A, Boursin, Y, Perez-Riverol, Y, Schmeier, S, Clarke, E, Arvai, K, Jung, M, Domenico, TAD, Seiler, J, Rasche, E, Kornobis, E, Beisser, D, Rahmann, S, Mikheyev, AS, Tran, C, Capellades, J, Schröder, C, Salatino, AE, Dirmeier, S, Webster, TH, Moskalenko, O, Stephen, G & Köster, J 2017, 'Bioconda: A sustainable and comprehensive software distribution for the life sciences', Cold Spring Harbor Laboratory.
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Hortle, E, Starrs, L, Brown, F, Jane, S, Curtis, D, McMorran, BJ, Foote, SJ & Burgio, G 2017, 'KCC1 Activation protects Mice from the Development of Experimental Cerebral Malaria', Cold Spring Harbor Laboratory.
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Irga, PJ, Pettit, TJ, Paull, N & Torpy, FR 2017, 'Functional green infrastructure for sustainable urban environmental quality'.

Kelleway, JJ, Saintilan, N, Macreadie, PI, Baldock, JA & Ralph, PJ 2017, 'Sediment and carbon accumulation vary among vegetation assemblages in a coastal saltmarsh', Copernicus GmbH, Copernicus GmbH.
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Abstract. Coastal saltmarshes are dynamic, intertidal ecosystems which are increasingly being recognised for their contributions to ecosystem services, including carbon (C) accumulation and storage. The survival of saltmarshes and their capacity to store C under rising sea levels, however, is partially reliant upon surface sedimentation rates and influenced by a combination of physical and biological factors. In this study, we use several complementary methods to assess short-term (days) deposition and medium-term (months) accretion dynamics within three saltmarsh vegetation types common throughout southeast (SE) Australia. We found that surface accretion varies among vegetation assemblages, with medium-term (19 month) bulk accretion rates in the upper marsh rush (Juncus) assemblage (1.74 ± 0.13 mm y−1) consistently in excess of estimated local sea level rise (1.15 mm y−1). Accretion was lower and less consistent in both the succulent (Sarcocornia) (0.78 ± 0.18 mm y−1) and grass (Sporobolus) (0.88 ± 0.22 mm y−1) assemblages located lower in the tidal frame. Short-term (6 d) experiments showed deposition within Juncus plots to be dominated by autochthonous organic inputs with C deposition rates ranging from 0.41 ± 0.15 g C cm−2 y−1 (neap tidal period) to 0.87 ± 0.16 g C cm−2 y−1 (spring tidal period), while minerogenic inputs and lower C deposition dominated Sarcocornia (0.03 ± 0.01 to 0.23 ± 0.03 g C cm−2 y−1) and Sporobolus (0.06 ± 0.01 to 0.15 ± 0.03 g C cm−2 y−1) assemblages. Elemental (C : N), isotopic (δ13C), mid infrared (MIR) and 13C NMR analyses revealed little difference in either the source or character of materials being deposited among neap versus spring tidal periods. Instead, these analyses point to substantial redistribution of materials within the Sarcocornia and Sporobolus assemblages, compared to high retention and preservation of organic inputs in the Juncus assemblage. By combining medium-term accretion quantification with short-term d...

Kumar, M & Ralph, P 2017, 'Systems Biology of Marine Ecosystems', Springer International Publishing, pp. 1-351.
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© Springer International Publishing AG 2017. This book describes the latest advances in systems biology in four plant-based marine ecosystems: seaweeds, seagrasses, microalgae, and corals. Marine organisms that inhabit the oceanic environment experience a diverse range of environmental fluctuations, anthropogenic stress, and threats from invasive species and pathogens. System biology integrates physiology, genomics, transcriptomics, proteomics, and metabolomics into numerical models and is emerging as an important approach to elucidate the functional adaptations of marine organisms to adverse environmental conditions. This book focuses on how ecophysiology, omics platforms, their integration (a systems biology perspective), and next generation sequencing tools are being used to address the stress response of marine seaweeds, seagrasses, corals, marine microbe diversity, and micro-and macroalgae/corals-bacterial interactions to global climate change and anthropogenic activities. The contents of the book are of special interest to graduate and postgraduate marine biology students and marine biology researchers, particularly those interested in marine ecology, stress physiology of marine macrophytes/corals/phytoplankton, and environmental microbiology. This book would also be of interest to marine engineers engaged in the management and conservation of our valuable marine resources.

Leisen, D & Platen, E 2017, 'Investing for the Long Run'.
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This paper studies long term investing by an investor that maximizes either expected utility from terminal wealth or from consumption. We introduce the concepts of a generalized stochastic discount factor (SDF) and of the minimum price to attain target payouts. The paper finds that the dynamics of the SDF needs to be captured and not the entire market dynamics, which simplifies significantly practical implementations of optimal portfolio strategies. We pay particular attention to the case where the SDF is equal to the inverse of the growth-optimal portfolio in the given market. Then, optimal wealth evolution is closely linked to the growth optimal portfolio. In particular, our concepts allow us to reconcile utility optimization with the practitioner approach of growth investing. We illustrate empirically that our new framework leads to improved lifetime consumption-portfolio choice and asset allocation strategies.

Liu, M, Worden, P, Monahan, LG, DeMaere, MZ, Burke, CM, Djordjevic, SP, Charles, IG & Darling, AE 2017, 'Evaluation of ddRADseq for reduced representation metagenome sequencing', Cold Spring Harbor Laboratory.
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ABSTRACTBackground‘Who is doing what’ is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection.ResultsWe assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling.ConclusionAlthough ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

Maharaj, S, Lees, T, Zaslawski, C, Fatima-Shad, K & Lal, S 2017, 'Assessing the link between negative mental states and cognitive performance in health professionals'.

Maharaj, S, Lees, T, Zaslawski, C, Fatima-Shad, K & Lal, S 2017, 'The prevalence of depression in a cohort of Australian Nurses'.

McWalter, T, Rudd, R, Kienitz, J & Platen, E 2017, 'Appendix: Recursive Marginal Quantization of Higher-Order Schemes'.

Mitchell, AB, Mourad, B, Malouf, MA, Benzimra, M, Morgan, LC, Oliver, BG & Glanville, AR 2017, 'TRANSPLANTING THE HUMAN RESPIRATORY VIROME', WILEY, pp. 93-93.

Platen, E & Rendek, R 2017, 'Market Efficiency and Growth Optimal Portfolio'.
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The paper predicts an Efficient Market Property for the equity market, wherestocks, when denominated in units of the growth optimal portfolio (GP), havezero instantaneous expected returns. Well-diversified equity portfolios areshown to approximate the GP, which explains the well-observed good performanceof equally weighted portfolios. The proposed hierarchically weighted index(HWI) is shown to be an even better proxy of the GP. It sets weights equalwithin industrial and geographical groupings of stocks. When using the HWI asproxy of the GP the Efficient Market Property cannot be easily rejected andappears to be very robust.

Platen, E & Taylor, D 2017, 'Loading Pricing of Long-Dated, Insurance-Type Contracts'.

Reyna, J, Meier, P, Hanham, J, Vlachopoulos, P & Rodgers, K 2017, 'LEARNER-GENERATED DIGITAL MEDIA (LGDM) FRAMEWORK'.
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Learner-Generated Digital Media (LGDM) has been incorporated as a tool to assess students in K-12 and higher education in the last decade. There are frameworks developed for video making in the classroom that considers technical know-how and a model that incorporate pedagogies. However, there is the absence of a practical framework to inform academics and students on the implementation of digital presentations as an assessment tool in the curricula. The aim of this poster is to propose a model for how to design, implement and evaluate LGDM as assessment tools in tertiary education. This evidence-based framework considers the following elements: (1) pedagogy; (2) student training; (3) hosting of videos; (4) marking schemes; (5) group contribution; (6) feedback; (7) reflection, and; (8) evaluation. The model serves as a conduit between theory and good practice.

Rudd, R, McWalter, TA, Kienitz, J & Platen, E 2017, 'Fast Quantization of Stochastic Volatility Models'.
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Recursive Marginal Quantization (RMQ) allows fast approximation of solutions to stochastic differential equations in one-dimension. When applied to two factor models, RMQ is inefficient due to the fact that the optimization problem is usually performed using stochastic methods, e.g., Lloyd’s algorithm or Competitive Learning Vector Quantization. In this paper, a new algorithm is proposed that allows RMQ to be applied to two-factor stochastic volatility models, which retains the efficiency of gradient-descent techniques. By margining over potential realizations of the volatility process, a significant decrease in computational effort is achieved when compared to current quantization methods. Additionally, techniques for modelling the correct zero-boundary behaviour are used to allow the new algorithm to be applied to cases where the previous methods would fail. The proposed technique is illustrated for European options on the Heston and Stein-Stein models, while a more thorough application is considered in the case of the popular SABR model, where various exotic options are also priced.

Schell, AW, Takashima, H, Tran, TT, Aharonovich, I & Takeuchi, S 2017, 'Coupling quantum emitters in 2D materials with tapered fibers'.

Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Dröge, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jørgensen, TS, Shapiro, N, Blood, PD, Gurevich, A, Bai, Y, Turaev, D, DeMaere, MZ, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvoit, M, Hansen, LH, Sørensen, SJ, Chia, BKH, Denis, B, Froula, JL, Wang, Z, Egan, R, Kang, DD, Cook, JJ, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, SW, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, M, Lingner, T, Lin, H-H, Liao, Y-C, Silva, GGZ, Cuevas, DA, Edwards, RA, Saha, S, Piro, VC, Renard, BY, Pop, M, Klenk, H-P, Göker, M, Kyrpides, NC, Woyke, T, Vorholt, JA, Schulze-Lefert, P, Rubin, EM, Darling, AE, Rattei, T & McHardy, AC 2017, 'Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software', Cold Spring Harbor Laboratory.
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AbstractIn metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

Sharma, P, Yi, R, Nayak, AP, Wang, N, Tang, F, Knight, MJ, Pan, S, Oliver, B & Deshpande, DA 2017, 'Bitter Taste Receptor Agonists Mitigate Features of Allergic Asthma in Mice', Springer Science and Business Media LLC.
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AbstractAsthma is characterized by airway inflammation, mucus secretion, remodeling and hyperresponsiveness (AHR). Recent research has established the bronchodilatory effect of bitter taste receptor (TAS2R) agonists in various models. Comprehensive pre-clinical studies aimed at establishing effectiveness of TAS2R agonists in disease models are lacking. Here we aimed to determine the effect of TAS2R agonists on features of asthma. Further, we elucidated a mechanism by which TAS2R agonists mitigate features of asthma. Asthma was induced in mice using intranasal house dust mite or aerosol ova-albumin challenge, and chloroquine or quinine were tested in both prophylactic and treatment models. Allergen challenge resulted in airway inflammation as evidenced by increased immune cells infiltration and release of cytokines and chemokines in the lungs, which were significantly attenuated in TAS2R agonists treated mice. TAS2R agonists attenuated features of airway remodeling including smooth muscle mass, extracellular matrix deposition and pro-fibrotic signaling, and also prevented mucus accumulation and development of AHR in mice. Mechanistic studies using human neutrophils demonstrated that inhibition of immune cell chemotaxis is a key mechanism by which TAS2R agonists blocked allergic airway inflammation and exerted anti-asthma effects. Our comprehensive studies establish the effectiveness of TAS2R agonists in mitigating multiple features of allergic asthma.

Shrestha, J 2017, 'The Situation and Clinical Research in Nepal'.
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Genomic Medicine 2017 conference in Ho Chi Min City, Vietnam

Su, D, Cortie, M & Wang, G 2017, 'Lithium‐Sulfur Batteries: Fabrication of N‐doped Graphene–Carbon Nanotube Hybrids from Prussian Blue for Lithium–Sulfur Batteries (Adv. Energy Mater. 8/2017)', Wiley.
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Vine, M, Lees, T, Nassif, N, Simpson, A & Lal, S 2017, 'Investigating the associations between ADHD symptomology and chronic illness: cardiovascular disease and diabetes mellitus'.

Wang, JJ & Suzanne, P 2017, 'Intensive correction orders versus short prison sentence: a comparison of re-offending.', NSW Bureau of Crime Statistics and Research, pp. 1-20.

Wang, KYX, Menzies, AM, Silva, IP, Wilmott, JS, Yan, Y, Wongchenko, M, Kefford, RF, Scolyer, RA, Long, GV, Tarr, G, Mueller, S & Yang, JYH 2017, 'bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays', Cold Spring Harbor Laboratory.
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Woodcock, S 2017, 'How predictable are the Oscars? More than you might think', The Conversation.

Woodcock, S 2017, 'Paradoxes of probability and other statistical strangeness', The Conversation.

Wu, P-J, Kabakova, I, Ruberti, J, Sherwood, JM, Dunlop, IE, Paterson, C, Török, P & Overby, DR 2017, 'Brillouin microscopy, what is it really measuring?'.
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Brillouin microscopy measures compressibility, but is being increasingly usedto assess stiffness of cells and tissues. Using hydrogels with tunableproperties, we demonstrate that Brillouin microscopy is insensitive tostiffness of hydrated materials, but depends strongly on water content,consistent with a theoretical model of biphasic compressibility. Empiricalcorrelations between Brillouin measurements and stiffness arise due to theirmutual dependence on water content, but correlations vanish once hydration iscontrolled.

Xu, Z-Q, Elbadawi, C, Tran, TT, Kianinia, M, Hoffman, TB, Edgar, JH, Toth, M & Aharonovich, I 2017, 'Atomic Engineering of Single Photon Sources in 2D Boron Nitride Zai-Quan'.
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Artificial atomic systems in solids such as single photon emitters arebecoming increasingly important building blocks in quantum informationprocessing and scalable quantum nanophotonic networks. Here, we report on acontrollable way to engineer emitters in two-dimensional (2D) hexagonal boronnitride (hBN) crystals using plasma processing. The method is robust, andyields a 7-fold increase in the density of emitters in hBN, which is promisingfor their deployment in practical devices. While as-fabricated emitters sufferfrom blinking and bleaching, a subsequent annealing step yields photo-stableemitters. The presented process is the first step towards controllableplacement of quantum emitters in hBN for integrated on-chip quantumnanophotonics based on 2D materials.

Yam, JKH, Aung, TT, Chua, SL, Cheng, Y, Kohli, GS, Zhou, J, Constancias, F, Liu, Y, Cai, Z, Salido, MMS, Drautz-Moses, DI, Rice, SA, Schuster, SC, Wu, B, Kjelleberg, S, Tolker-Nielsen, T, Beuerman, RW, Givskov, M & Yang, L 2017, 'Cyclic-di-GMP is required for corneal infection byPseudomonas aeruginosaand modulates host immunity', Cold Spring Harbor Laboratory.
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Zaman, G, Jung, IH, Torres, DFM & Zeb, A 2017, 'Mathematical Modeling and Control of Infectious Diseases', Hindawi Limited, pp. 1-1.
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