Publications

Eamus, D, Huete, A & Yu, Q 2016, Vegetation Dynamics, Cambridge University Press.
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Brings together plant ecophysiology, remote sensing and modelling of vegetation and landscape function for advanced students and researchers.

Ajani, P, Hallegraeff, G, Allen, D, Coughlan, A, Richardson, A, Armand, L, Ingleton, T & Murray, S 2016, 'Oceanography and Marine Biology', CRC Press, pp. 387-412.
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Establishing trends in phytoplankton diversity and biomass, particularly in relation to climate change, is challenging and requires reference to baseline observations. Detecting changes over seasonal, interannual, and interdecadal timescales requires the collection of long-term datasets. Australian marine ecosystems and their constituent phytoplankton have been studied only in the last approximately 100 years, focused on the south-eastern coast of Australia, as this is the site of the major population centres. The coastline of south-eastern Australia is dominated by the dynamic East Australian Current, as well as a diverse range of estuaries, each with its own distinct riverine inputs, tidal cycles, and flushing times. Warming of the East Australian Current over the past century at two to three times the global average, combined with increased nutrient loads and encroaching coastal urbanization, is likely to have had an impact on the coastal environment, ecosystems, and supported phytoplankton communities. Even though sporadic research has been undertaken into the diversity, distribution, and ecology of marine and estuarine phytoplankton over the past 80 years, the first long-term time-series investigations have only recently been completed. In this review, we conducted a meta-analysis of 90 phytoplankton studies from 1933 to 2015 and examined the major themes covered and methodologies used. We examined five datasets spanning the past 50 years from the long-term coastal station off shore from Port Hacking, Sydney. Whilst species composition and distribution appear to have changed over time, our knowledge of their systematics and identification has also expanded. Sixty-three species, 5 genera, and about 19 potentially harmful species have been described from south-eastern Australian waters over the past 30 years, and many represent first-time Australian records. The emerging use of next-generation sequencing and quantitative molecular methods for phytoplankton ide...

Ajani, PA, Hallegraeff, GM, Allen, D, Coughlan, A, Richardson, AJ, Armand, LK, Ingleton, T & Murray, SA 2016, 'ESTABLISHING BASELINES: EIGHTY YEARS OF PHYTOPLANKTON DIVERSITY AND BIOMASS IN SOUTH-EASTERN AUSTRALIA' in Oceanography and Marine Biology: An Annual Review: Volume 54, pp. 387-412.
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Establishing trends in phytoplankton diversity and biomass, particularly in relation to climate change, is challenging and requires reference to baseline observations. Detecting changes over seasonal, interannual, and interdecadal timescales requires the collection of long-term datasets. Australian marine ecosystems and their constituent phytoplankton have been studied only in the last approximately 100 years, focused on the south-eastern coast of Australia, as this is the site of the major population centres. The coastline of south-eastern Australia is dominated by the dynamic East Australian Current, as well as a diverse range of estuaries, each with its own distinct riverine inputs, tidal cycles, and flushing times. Warming of the East Australian Current over the past century at two to three times the global average, combined with increased nutrient loads and encroaching coastal urbanization, is likely to have had an impact on the coastal environment, ecosystems, and supported phytoplankton communities. Even though sporadic research has been undertaken into the diversity, distribution, and ecology of marine and estuarine phytoplankton over the past 80 years, the first long-term time-series investigations have only recently been completed. In this review, we conducted a meta-analysis of 90 phytoplankton studies from 1933 to 2015 and examined the major themes covered and methodologies used. We examined five datasets spanning the past 50 years from the long-term coastal station off shore from Port Hacking, Sydney. Whilst species composition and distribution appear to have changed over time, our knowledge of their systematics and identification has also expanded. Sixty-three species, 5 genera, and about 19 potentially harmful species have been described from south-eastern Australian waters over the past 30 years, and many represent first-time Australian records. The emerging use of next-generation sequencing and quantitative molecular methods for phytopl...

Alexander, J, Ashmore, J, Baker, A & Chadwick, S 2016, 'NMR Spectroscopy in First-Year Chemistry at the University of Technology Sydney' in Soulsby, D, Anna, L & Wallner, AS (eds), ACS Symposium Series, American Chemical Society, pp. 13-29.
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First-year general chemistry classes at large universities typically enroll students with diverse backgrounds. The vast majority of these students are not chemistry majors. NMR instrumentation was introduced to this class to engage these students in their learning and to represent modern chemistry to students for whom this course might be their only chemistry experience. We have incorporated NMR spectroscopy into the general chemistry laboratory experiments at the University of Technology Sydney in Sydney, Australia. Benchtop NMR spectrometers now mean that students can have close and frequent access to instrumentation. This chapter describes the use of the picoSpin-45 NMR spectrometer in the introductory laboratory, the types of experiments performed, quiz and survey results, and implementation challenges and successes.

Ao, Z, Jiang, Q, Li, S, Dou, S & Wang, G 2016, 'Effect of external electric fields on the multifunctional applications of graphene' in Graphene Science Handbook, pp. 235-254.
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Graphene has shown promising applications as ultrasensitive gas sensors, transparent electrodes in liquid crystal display devices, large capacity electrodes in batteries, etc. External electric fields, which are often met in practical applications, could induce changes of graphene-based materials in geometry, binding energies, vibrational spectra, chemical activities, and electronic properties, thus further widening their application fields. In this chapter, the dissociative adsorption of H2 and H2O molecules on graphene and N2O decomposition on Mn-embedded graphene in the presence of electric fields based on density functional calculations are reviewed. It is shown that electric fields could act as catalysts to facilitate these chemical reactions, which can widen the applications of graphene as an atomic hydrogen storage material, for reversible tuning of graphene's wettability between hydrophobic and hydrophilic, and reducing the pollution of N2O.

Ao, Z, Jiang, Q, Li, S, Dou, S & Wang, G 2016, 'Graphene-Based Polymer Nanocomposites' in Graphene Science Handbook, CRC Press, USA, pp. 163-178.
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Volume One: Fabrication Methods Volume Two: Nanostructure and Atomic Arrangement Volume Three: Electrical and Optical Properties Volume Four: Mechanical and Chemical Properties Volume Five: Size-Dependent Properties Volume Six: Applications ...

Care, A, Bergquist, PL & Sunna, A 2016, 'Solid-Binding Peptides: Immobilisation Strategies for Extremophile Biocatalysis in Biotechnology' in Grand Challenges in Biology and Biotechnology, Springer International Publishing, pp. 637-674.
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Castorina, A 2016, 'Multiple Actions of Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP) in Schwann Cell Biology' in Current Topics in Neurotoxicity, Springer International Publishing, pp. 459-479.
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Choi, AH, Ben-Nissan, B, Bendavid, A & Latella, B 2016, 'Mechanical behavior and properties of thin films for biomedical applications' in Thin Film Coatings for Biomaterials and Biomedical Applications, Elsevier, pp. 117-141.
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Coupland, M, Dunn, PK, Galligan, L, Oates, G & Trenholm, S 2016, 'Tertiary Mathematics Education' in Makar, K, Dole, S, Visnovska, J, Bennison, A & Fry, K (eds), Research in Mathematics Education in Australasia 2012-2015, Springer Singapore, Singapore, pp. 187-211.
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This review aims to critically promote quality research and focus on the building of research capacity in Australasia.

Eamus, D, Fu, B, Springer, AE & Stevens, LE 2016, 'Groundwater Dependent Ecosystems: Classification, Identification Techniques and Threats' in Jakeman, AJ, Barreteau, O, Hunt, RJ, Rinaudo, JD & Ross, A (eds), Integrated Groundwater Management, Springer International Publishing, Cham, pp. 313-346.
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© The Author(s) 2016. This chapter begins by briefly discussing the three major classes of groundwater dependent ecosystems (GDEs), namely: (I) GDEs that reside within groundwater (e.g. karsts; stygofauna); (II) GDEs requiring the surface expression of groundwater (e.g. springs; wetlands); and (III) GDEs dependent upon sub-surface availability of groundwater within the rooting depth of vegetation (e.g. woodlands; riparian forests). We then discuss a range of techniques available for identifying the location of GDEs in a landscape, with a primary focus of class III GDEs and a secondary focus of class II GDEs. These techniques include inferential methodologies, using hydrological, geochemical and geomorphological indicators, biotic assemblages, historical documentation, and remote sensing methodologies. Techniques available to quantify groundwater use by GDEs are briefly described, including application of simple modelling tools, remote sensing methods and complex modelling applications. This chapter also outlines the contemporary threats to the persistence of GDEs across the world. This involves a description of the “natural” hydrological attributes relevant to GDEs and theprocesses that lead to disturbances to natural hydrological attributes as a result of human activities (e.g. groundwater extraction). Two cases studies, (1) Class III: terrestrial vegetation and (2) Class II: springs, are discussed in relation to these issues.

El Saliby, I, McDonagh, A, Erdei, L & Kyong Shon, H 2016, 'Water Reclamation by Heterogeneous Photocatalysis over Titanium Dioxide' in Green Technologies for Sustainable Water Management, American Society of Civil Engineers, pp. 679-704.
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© 2016 American Society of Civil Engineers. This chapter presents the fundamentals and basic principles of water reclamation by heterogeneous photocatalysis (HP). The effects of important operational parameters on the overall treatment efficiency of photocatalytic system are addressed in the chapter in terms of photocatalyst loading, pollutant concentration, pH and temperature of water, dissolved oxygen, and light intensity. The most popular semiconductor used in HP is Titanium dioxide (TiO2) for being relatively inexpensive, chemically stable, and nontoxic. Most water remediation technologies generate a significant amount of wastewater that requires costly retreatment or discharge to evaporation ponds, rivers, and oceans. HP processes that decompose aqueous contaminants are highly dependent on the reaction conditions and the setup of photocatalytic reactors. Visible-light responsive photocatalysts promise a more effective utilization of solar energy. Doping and co-doping of titania is a practical approach toward obtaining improved visible-light active photocatalysts.

Fu, S 2016, 'Adulterants in Urine Drug Testing' in Makowski, GS (ed), Advances in Clinical Chemistry, Elsevier, Burlington, pp. 123-163.
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Urine drug testing plays an important role in monitoring licit and illicit drug use for both medico-legal and clinical purposes. One of the major challenges of urine drug testing is adulteration, a practice involving manipulation of a urine specimen with chemical adulterants to produce a false negative test result. This problem is compounded by the number of easily obtained chemicals that can effectively adulterate a urine specimen. Common adulterants include some household chemicals such as hypochlorite bleach, laundry detergent, table salt, and toilet bowl cleaner and many commercial products such as UrinAid (glutaraldehyde), Stealth® (containing peroxidase and peroxide), Urine Luck (pyridinium chlorochromate, PCC), and Klear® (potassium nitrite) available through the Internet. These adulterants can invalidate a screening test result, a confirmatory test result, or both. To counteract urine adulteration, drug testing laboratories have developed a number of analytical methods to detect adulterants in a urine specimen. While these methods are useful in detecting urine adulteration when such activities are suspected, they do not reveal what types of drugs are being concealed. This is particularly the case when oxidizing urine adulterants are involved as these oxidants are capable of destroying drugs and their metabolites in urine, rendering the drug analytes undetectable by any testing technology. One promising approach to address this current limitation has been the use of unique oxidation products formed from reaction of drug analytes with oxidizing adulterants as markers for monitoring drug misuse and urine adulteration. This novel approach will ultimately improve the effectiveness of the current urine drug testing programs.

Gerace, D, Martiniello-Wilks, R & Simpson, AM 2016, 'Viral-Mediated Gene Therapy for the Generation of Artificial Insulin-Producing Cells as a Therapeutic Treatment for Type 1 Diabetes Mellitus' in Hardikar, AA (ed), Stem Cell Biology and Regenerative Medicine, Springer International Publishing, Germany, pp. 241-255.
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Over the past decade, several approaches have been employed to develop cell and gene therapy strategies that generate artificial insulin-producing cells (IPCs) for potential therapeutic applications in the treatment of type 1 diabetes mellitus (T1D) . The genetic engineering of functional IPCs necessitates a broad understanding of the pancreatic developmental process and the β cell transcription factors that govern mature β cell differentiation and function. To successfully obtain functional IPCs, the type of vectors utilised for gene transfer and the selection of a suitable target cell for subsequent differentiation into IPCs is of fundamental importance. Techniques for manufacturing IPCs include the dedifferentiation and directed transdifferentiation of autologous or allogeneic cells ex vivo followed by transplantation and the in vivo transdifferentiation of target tissue via viral gene transfer. Ultimately, the goal is to construct IPCs that have the capacity to process, store and secrete insulin in response to fluctuating blood glucose levels, whilst avoiding the administration of immunosuppressants and recurrent autoimmune destruction, thereby indefinitely restoring normoglycaemia.

Hare, DJ, Rembach, A & Roberts, BR 2016, 'The Emerging Role of Metalloproteomics in Alzheimer’s Disease Research' in Methods in Molecular Biology, Springer New York, pp. 379-389.
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Metals are increasingly recognized to have an important role in molecular processes underlying Alzheimer's disease (AD). This chapter discusses the current role of metals in AD and expands on the development of metalloproteomics and how the recent advances in analytical technology will allow detailed investigation of metalloproteins. Investigation of individual metalloproteins will yield new mechanistic details about the role of metals in AD.

Kanodarwala, FK & Stride, JA 2016, 'Phase transition in CdSe quantum dots and deposition of cdse quantum dots on graphene sheets' in Nanomaterials: Science and Applications, pp. 203-230.
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To date, quantum dots (QDs) have been synthesized through a number of different processes ranging from colloidal synthesis and electrochemical methods to chemical vapor deposition (CVD). This chapter focuses on the synthesis of high-quality CdSe nanocrystals through a bench-top colloidal synthesis, paying particular attention to the effects on the size and crystallinity of the QDs of varying the reaction temperature and reagent concentrations. Powder X-ray diffraction (PXRD) analysis and high-resolution transmission electron microscopy (HRTEM) have been used to highlight a transition of the crystallite phases obtained, from cubic zinc blende to hexagonal wurtzite and back again to the cubic phase as a function of reaction time. The nature of this phase shift is believed to be due to the rapid growth along the (111) crystallite facets, with the facial facets then 'catching up,' to restore the cubic symmetry. High-quality trioctylphosphine/trioctylphosphine oxide (TOP/ TOPO)-capped CdSe QDs displaying a narrow emission band were then grafted onto graphene nanosheets through a simple wetchemical procedure. A significant red shift of both the broad absorption and the narrow emission spectrum of the QDs was observed upon attachment to graphene, as determined by UV-Vis absorption and photoluminescence spectroscopies, whilst HRTEM data clearly show the successful decoration of the graphene sheets with CdSe QDs. This type of nanocomposite may have potential applications in the fields of optics, biological imaging, and sensing.

Larkum, AW 2016, 'Photosynthesis and Light Harvesting in Algae' in The Physiology of Microalgae, Springer International Publishing, pp. 67-87.
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Meakin, G 2016, 'Transfer' in Jamieson, A & Bader, S (eds), A Guide to Forensic DNA Profiling, John Wiley & Sons, United Kingdom, pp. 71-76.
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Following extensive introductory chapters covering forensic DNA profiling and forensic genetics, this comprehensive volume presents a substantial breadth of material covering: Fundamental material – including sources of DNA, validation, ...

Mondal, A & Wang, G 2016, 'Advances in Solar Photovoltaic Power Plants' in Islam, MR, Rahman, F & Xu, W (eds), Advances in Solar Photovoltaic Power Plants, Springer Berlin Heidelberg, Berlin Heidelberg, pp. 231-251.
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Among various renewable energy resources, solar energy has gained tremendous attention for future energy because of its cleanliness, availability and environmental friendliness. Many countries around the globe are intensely considering solar energy technologies for their future energy expansion. The major disadvantage for use of solar technology is its intermittent and unpredictable nature. This influence the power quality and consistency of the power grid, particularly at large-scale solar energy systems. Solar power is the conversion of sunlight into electricity, either directly using photovoltaic (PV) or indirectly using concentrated solar power. The variation of sun light may lead to over-production of electricity at one time and lack of production at another time. The variable nature of solar power causes significant challenges for the electric grid operators. To smooth out the intermittency of solar energy production, electrical energy storage technology will become necessary. In order to increase the solar energy penetration with appropriate reliability, this chapter presents a range of energy storage systems that could technically and economically be used in association with solar photovoltaic energy.

Warner, ME & Suggett, DJ 2016, 'The Photobiology of Symbiodinium spp.: Linking Physiological Diversity to the Implications of Stress and Resilience' in The Cnidaria, Past, Present and Future, Springer International Publishing, pp. 489-509.
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© Springer International Publishing Switzerland 2016. Over the past two decades, our knowledge of Symbiodinium genetic diversity and ecological distribution has grown at an incredible pace, while the physiological diversity and how it may be compared to the phylogenetic and evolutionary constraints of these dinoflagellates is still catching up. Our knowledge of the photobiology of Symbiodinium has been driven largely by the desire to explain cellular mechanisms of stress and reaction to global events driven by climate change. We tend to focus more on the former in this chapter since this is where the majority of work has been performed to date. However, it is imperative that we return to the first principles of phytoplankton physiological ecology to form a more complete understanding of the photobiology of these algae and the physiological constraints expected in an algal cell capable of living benthic, pelagic and symbiotic life styles. In order to understand not only the pathways of cellular dysfunction, but also resilience, we address specific patterns of light harvesting balance, reaction centre turnover, inorganic carbon acquisition and utilisation, and alternative electron transport across this genus. Symbiodinium - focused research, and physiology in particular, poses several challenges that demand a broad perspective gleaned from working with these algae in culture as well as in hospite in controlled ‘model’ and natural cnidarian hosts across many different environments. We outline several key processes related to photosynthesis as well as new directions integrating many of these processes that are required to more fully understand how environmental change shapes the role of photobiology in governing the ecological success of these important algae.

Wilkinson, S & Torpy, F 2016, 'Urban Food Production on Retrofitted Rooftops' in Wilkinson, SJ & Dixon, TJ (eds), Muscle Disease: Pathology and Genetics: Second Edition, Wiley, uk, pp. 158-188.
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© 2016 John Wiley & Sons, Ltd. All rights reserved. Human populations are becoming increasingly urbanised and thus distanced, both physically and psychologically, from the sources of their food. Decentralising food production from remote rural regions to within urban centres will address both the growing sense of disconnect and the growing costs associated with food transport. This chapter describes the social, environmental and economic aspects of local-scale urban food production as well as setting out typical specifications and considerations in respect of bed systems, with a focus on the health and safety, technical, environmental and economic aspects of larger-scale food rooftop production. Our empirical observations demonstrate that there is great potential in most cities for the expansion of urban rooftop farming, and that many of the traditional barriers to growing food in cities, such as fears over food safety, can be overcome in virtually all situations.

Zhou, J & Qiu, J 2016, 'Upconversion Luminescence Behavior of Single Nanoparticles' in Phosphors, Up Conversion Nano Particles, Quantum Dots and Their Applications, Springer Singapore, pp. 311-331.
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Afshinnekoo, E, Ahsanuddin, S, Ghedin, E, Read, T, Fraser, C, Dudley, J, Bowler, C, Mason, CE, Chernomoretz, A, Stolovitzky, G, Łabaj, PP, Graf, AB, Darling, A, Burke, C, Noushmehr, H, Dias-Neto, E, Guo, Y, Xie, Z, Lee, PKH, Shi, L, Ruiz-Perez, CA, Zambrano, MM, Siam, R, Ouf, A, Richard, H, Lafontaine, I, Wieler, LH, Semmler, T, Prithiviraj, B, Nedunuri, N, Mehr, S, Banihashemi, K, Lista, F, Anselmo, A, Suzuki, H, Kuroda, M, Yamashita, R, Sato, Y, Kaminuma, E, Aranda, CMA, Martinez, J, Dada, C, Dybwad, M, Oliveira, M, Schuster, S, Siwo, GH, Jang, S, Seo, SC, Hwang, SH, Ossowski, S, Bezdan, D, Chaker, S, Chatziefthimiou, AD, Udekwu, K, Liungdahl, P, Sezerman, U, Meydan, C, Elhaik, E, Gonnet, G, Schriml, LM, Mongodin, E, Huttenhower, C, Gilbert, J, Eisen, J, Hirschberg, D, Hernandez, M, McGrath, K, McGrath, L, Gray, A, Osuolale, O, Segata, N, Fillo, S, Iraola, G, Zhou, Y, Chang, Y, Li, Y, Zhend, Y, Hou, W, Ramirez, A, Cepeda, M, Desnues, C, Rascovan, N, Baron, C, Nagarajan, N, Ercolini, D, Menary, W, Tighe, S, Donia, M, Levy, S, Benito, J, Jones, A, Kasarskis, A, Maritz, J, Jorgensen, E, Neches, R, Livelli, T, Barnetche, JM, Pasolli, E, Greenfield, N & Hasan, N 2016, 'The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report', Microbiome, vol. 4, no. 1.
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© 2016 The MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

Aharonovich, I, Englund, D & Toth, M 2016, 'Solid-state single-photon emitters', Nature Photonics, vol. 10, no. 10, pp. 631-641.
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Aili, SR, Touchard, A, Koh, JMS, Dejean, A, Orivel, J, Padula, MP, Escoubas, P & Nicholson, GM 2016, 'Comparisons of Protein and Peptide Complexity in Poneroid and Formicoid Ant Venoms', JOURNAL OF PROTEOME RESEARCH, vol. 15, no. 9, pp. 3039-3054.
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© 2016 American Chemical Society. Animal venom peptides are currently being developed as novel drugs and bioinsecticides. Because ants use venoms for defense and predation, venomous ants represent an untapped source of potential bioactive toxins. This study compared the protein and peptide components of the poneroid ants Neoponera commutata, Neoponera apicalis, and Odontomachus hastatus and the formicoid ants Ectatomma tuberculatum, Ectatomma brunneum, and Myrmecia gulosa. 1D and 2D PAGE revealed venom proteins in the mass range <10 to >250 kDa. NanoLC-ESI-QTOF MS/MS analysis of tryptic peptides revealed the presence of common venom proteins and also many undescribed proteins. RP-HPLC separation followed by MALDI-TOF MS of the venom peptides also revealed considerable heterogeneity. It was found that the venoms contained between 144 and 1032 peptides with 5-95% of peptides in the ranges 1-4 and 1-8 kDa for poneroid and formicoid ants, respectively. By employing the reducing MALDI matrix 1,5-diaminonapthalene, up to 28 disulfide-bonded peptides were also identified in each of the venoms. In particular, the mass range of peptides from poneroid ants is lower than peptides from other venoms, indicating possible novel structures and pharmacologies. These results indicate that ant venoms represent an enormous, untapped source of novel therapeutic and bioinsecticide leads.

Ajani, P, Hallegraeff, G, Allen, D, Coughlan, A, Richardson, A, Armand, L, Ingleton, T & Murray, S 2016, 'The Contrasting Ecology of Temperate Macrotidal and Microtidal Estuaries', vol. 54, pp. 387-412.
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Establishing trends in phytoplankton diversity and biomass, particularly in relation to climate change, is challenging and requires reference to baseline observations. Detecting changes over seasonal, interannual, and interdecadal timescales requires the collection of long-term datasets. Australian marine ecosystems and their constituent phytoplankton have been studied only in the last approximately 100 years, focused on the south-eastern coast of Australia, as this is the site of the major population centres. The coastline of south-eastern Australia is dominated by the dynamic East Australian Current, as well as a diverse range of estuaries, each with its own distinct riverine inputs, tidal cycles, and ushing times. Warming of the East Australian Current over the past century at two to three times the global average, combined with increased nutrient loads and encroaching coastal urbanization, is likely to have had an impact on the coastal environment, ecosystems, and supported phytoplankton communities. Even though sporadic research has been undertaken into the diversity, distribution, and ecology of marine and estuarine phytoplankton over the past 80 years, the rst long-term time-series investigations have only recently been completed. In this review, we conducted a meta-analysis of 90 phytoplankton studies from 1933 to 2015 and examined the major themes covered and methodologies used. We examined ve datasets spanning the past 50 years from the long-term coastal station off shore from Port Hacking, Sydney. Whilst species composition and distribution appear to have changed over time, our knowledge of their systematics and identication has also expanded. Sixty-three species, 5 genera, and about 19 potentially harmful species have been described from south-eastern Australian waters over the past 30 years, and many represent rst-time Australian records. The emerging use of next-generation sequencing and quantitative molecular methods for phytoplankton ide...

Ajani, P, Kim, JH, Han, MS & Murray, SA 2016, 'The first report of the potentially harmful diatom Pseudo‐nitzschia caciantha from Australian coastal waters', Phycological Research, vol. 64, no. 4, pp. 312-317.
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SUMMARYThe diatom Pseudo‐nitzschia is a significant component of coastal waters worldwide and a producer of the potent neurotoxin, domoic acid. Sixteen species belonging to this genus have been reported from Australian waters, but the potentially toxic species P. caciantha has not been previously known from this region. Two clonal strains of P. caciantha were isolated from Coogee Beach, south‐east Australia, and the morphological, molecular and toxicological evidence for this species delineation were examined using light and transmission electron microscopy, phylogenetic analysis based on sequences of the second internal transcribed spacer and domoic acid production as measured by liquid chromatography–mass spectrometry. The results unambiguously confirmed that these isolates are the potentially toxic species P. caciantha, being only the second report of this species in the Southern Hemisphere. The potential for further hidden Pseudo‐nitzschia diversity in these waters is considerable.

Ajani, P, Larsson, ME, Rubio, A, Bush, S, Brett, S & Farrell, H 2016, 'Modelling bloom formation of the toxic dinoflagellates Dinophysis acuminata and Dinophysis caudata in a highly modified estuary, south eastern Australia', Estuarine, Coastal and Shelf Science, vol. 183, pp. 95-106.
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© 2016 Elsevier Ltd Dinoflagellates belonging to the toxigenic genus Dinophysis are increasing in abundance in the Hawkesbury River, south-eastern Australia. This study investigates a twelve year time series of abundance and physico-chemical data to model these blooms. Four species were reported over the sampling campaign - Dinophysis acuminata, Dinophysis caudata, Dinophysis fortii and Dinophysis tripos-with D. acuminata and D. caudata being most abundant. Highest abundance of D. acuminata occurred in the austral spring (max. abundance 4500 cells l−1), whilst highest D. caudata occurred in the summer to autumn (max. 12,000 cells l−1). Generalised additive models revealed abundance of D. acuminata was significantly linked to season, thermal stratification and nutrients, whilst D. caudata was associated with nutrients, salinity and dissolved oxygen. The models’ predictive capability was up to 60% for D. acuminata and 53% for D. caudata. Altering sampling strategies during blooms accompanied with in situ high resolution monitoring will further improve Dinophysis bloom prediction capability.

Ajani, PA, Armbrecht, LH, Kersten, O, Kohli, GS & Murray, SA 2016, 'Diversity, temporal distribution and physiology of the centric diatomLeptocylindrusCleve (Bacillariophyta) from a southern hemisphere upwelling system', Diatom Research, vol. 31, no. 4, pp. 351-365.
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© 2016 The International Society for Diatom Research. The marine diatom Leptocylindrus is a major component of phytoplankton blooms in coastal ecosystems and upwelling regions worldwide, however, little is known about this genus in the southern hemisphere. Whilst Leptocylindrus danicus has been reported from south-eastern (SE) Australia since the 1930s, there has been neither unequivocal species identification nor focused examination of the temporal abundance of Leptocylindrus in this region. Such investigations are crucial in the context of climate change and the strengthening of the East Australian Current, which is expected to result in alterations to the seasonal abundance and distribution of Leptocylindrus along the east Australian coast. Thus we also describe the temporal distribution of Leptocylindrus based on 50 years of records, revealing that this diatom is a key component of the seasonal phytoplankton cycle, with greatest abundance in the austral spring and summer. Using light and transmission electron microscopy and molecular phylogenetics based on the nuclear-encoded ITS1–5.8S–ITS2 rDNA region, our study unambiguously revealed three species, L. danicus, Leptocylindrus convexus and Leptocylindrus aporus from 34 clonal isolates from SE Australia, with the majority (82%) of strains identified as L. danicus. Furthermore, we investigated the growth, auxospore and resting spore formation of the most commonly occurring species, L. danicus, under four temperature and irradiance scenarios. The diatom reached maximum growth rates (µMax, 1.71 divisions day−1) under relatively high temperatures (25°C) and light conditions (100 µmol photons m−2 s−1) between days 2 and 7 of the experiment. When temperature and light regimes were reduced (18°C, 50 µmol photons m−2 s−1) auxospores and resting spores were formed. The rapid growth rate and potential of L. danicus to form auxospores are important survival mechanisms in coastal upwelling systems and likely to ...

Al Khamici, H, Hossain, K, Cornell, B & Valenzuela, S 2016, 'Investigating Sterol and Redox Regulation of the Ion Channel Activity of CLIC1 Using Tethered Bilayer Membranes', Membranes, vol. 6, no. 4, pp. 51-51.
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The Chloride Intracellular Ion Channel (CLIC) family consists of six conserved proteins in humans. These are a group of enigmatic proteins, which adopt both a soluble and membrane bound form. CLIC1 was found to be a metamorphic protein, where under specific environmental triggers it adopts more than one stable reversible soluble structural conformation. CLIC1 was found to spontaneously insert into cell membranes and form chloride ion channels. However, factors that control the structural transition of CLIC1 from being an aqueous soluble protein into a membrane bound protein have yet to be adequately described. Using tethered bilayer lipid membranes and electrical impedance spectroscopy system, herein we demonstrate that CLIC1 ion channel activity is dependent on the type and concentration of sterols in bilayer membranes. These findings suggest that membrane sterols play an essential role in CLIC1’s acrobatic switching from a globular soluble form to an integral membrane form, promoting greater ion channel conductance in membranes. What remains unclear is the precise nature of this regulation involving membrane sterols and ultimately determining CLIC1’s membrane structure and function as an ion channel. Furthermore, our impedance spectroscopy results obtained using CLIC1 mutants, suggest that the residue Cys24 is not essential for CLIC1’s ion channel function. However Cys24 does appear important for optimal ion channel activity. We also observe differences in conductance between CLIC1 reduced and oxidized forms when added to our tethered membranes. Therefore, we conclude that both membrane sterols and redox play a role in the ion channel activity of CLIC1.

Alacid, E, Park, MG, Turon, M, Petrou, K & Garces, E 2016, 'A Game of Russian Roulette for a Generalist Dinoflagellate Parasitoid: Host Susceptibility Is the Key to Success', FRONTIERS IN MICROBIOLOGY, vol. 7, no. MAY, pp. 1-13.
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© 2016 Alacid, Park, Turon, Petrou and Garcés. Marine microbial interactions involving eukaryotes and their parasites play an important role in shaping the structure of phytoplankton communities. These interactions may alter population densities of the main host, which in turn may have consequences for the other concurrent species. The effect generalist parasitoids exert on a community is strongly dependent on the degree of host specificity. Parvilucifera sinerae is a generalist parasitoid able to infect a wide range of dinoflagellates, including toxic-bloom-forming species. A density-dependent chemical cue has been identified as the trigger for the activation of the infective stage. Together these traits make Parvilucifera-dinoflagellate hosts a good model to investigate the degree of specificity of a generalist parasitoid, and the potential effects that it could have at the community level. Here, we present for the first time, the strategy by which a generalist dinoflagellate parasitoid seeks out its host and determine whether it exhibits host preferences, highlighting key factors in determining infection. Our results demonstrate that in its infective stage, P. sinerae is able to sense potential hosts, but does not actively select among them. Instead, the parasitoids contact the host at random, governed by the encounter probability rate and once encountered, the chance to penetrate inside the host cell and develop the infection strongly depends on the degree of host susceptibility. As such, their strategy for persistence is more of a game of Russian roulette, where the chance of survival is dependent on the susceptibility of the host. Our study identifies P. sinerae as a potential key player in community ecology, where in mixed dinoflagellate communities consisting of hosts that are highly susceptible to infection, parasitoid preferences may mediate coexistence between host species, reducing the dominance of the superior competitor. Alternatively, it ...

ALEXANDER, S, NOVIKOV, A & KORDZAKHIA, N 2016, 'BOUNDS ON PRICES FOR ASIAN OPTIONS VIA FOURIER METHODS', The ANZIAM Journal, vol. 57, no. 3, pp. 299-318.
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The problem of pricing arithmetic Asian options is nontrivial, and has attracted much interest over the last two decades. This paper provides a method for calculating bounds on option prices and approximations to option deltas in a market where the underlying asset follows a geometric Lévy process. The core idea is to find a highly correlated, yet more tractable proxy to the event that the option finishes in-the-money. The paper provides a means for calculating the joint characteristic function of the underlying asset and proxy processes, and relies on Fourier methods to compute prices and deltas. Numerical studies show that the lower bound provides accurate approximations to prices and deltas, while the upper bound provides good though less accurate results.

Alexeeff, SE, Carroll, RJ & Coull, B 2016, 'Spatial measurement error and correction by spatial SIMEX in linear regression models when using predicted air pollution exposures', Biostatistics, vol. 17, no. 2, pp. 377-389.
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© 2015 The Author 2015. Published by Oxford University Press. All rights reserved. Spatial modeling of air pollution exposures is widespread in air pollution epidemiology research as a way to improve exposure assessment. However, there are key sources of exposure model uncertainty when air pollution is modeled, including estimation error and model misspecification. We examine the use of predicted air pollution levels in linear health effect models under a measurement error framework. For the prediction of air pollution exposures, we consider a universal Kriging framework, which may include land-use regression terms in the mean function and a spatial covariance structure for the residuals. We derive the bias induced by estimation error and by model misspecification in the exposure model, and we find that a misspecified exposure model can induce asymptotic bias in the effect estimate of air pollution on health. We propose a new spatial simulation extrapolation (SIMEX) procedure, and we demonstrate that the procedure has good performance in correcting this asymptotic bias. We illustrate spatial SIMEX in a study of air pollution and birthweight in Massachusetts.

Ali, H & Singh, SK 2016, 'Biological Voyage of Solid Lipid nanoparticles: A Proficient Carrier in Nanomedicine', Therapeutic Delivery, vol. 7, no. 10, pp. 691-709.
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Ali, H, Kanodarwala, FK, Majeed, I, Stride, JA & Nadeem, MA 2016, 'La₂O₃Promoted Pd/rGO Electro-catalysts for Formic Acid Oxidation', ACS Applied Materials & Interfaces, vol. 8, no. 47, pp. 32581-32590.
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High activity, a low rate of CO poisoning, and long-term stability of Pd electro-catalysts are necessary for practical use as an anode material in direct formic acid fuel cells. Achieving a high degree of Pd nanoparticle dispersion on a carbon support, without agglomeration, while maintaining a facile electron transfer through the catalyst surface are two challenging tasks to be overcome in fulfilling this aim. Herein, we report the effect of addition of La/La-oxides on the efficiency of Pd nanoparticles supported on reduced graphene oxide (rGO) for formic acid electro-oxidation reaction. A series of electro-catalysts with different Pd-La molar ratios were successfully synthesized and characterized using a range of techniques including PXRD, XPS, TEM, FTIR, and Raman spectroscopy and then tested as anode materials for direct formic acid fuel cells. We explore that the lanthanum species (La/La-oxide) significantly promote the activity and stability of Pd catalyst toward electrocatalytic oxidation of formic acid. The metallic ratio is found to be critical, and the activity order of various catalysts is observed as follows; Pd30La70/rGO > Pd80La20/rGO > Pd70La30 rGO. The obtained mass specific activity for Pd30La70/rGO (986.42 A/g) is 2.18 times higher than that for Pd/rGO (451 A/g) and 16 times higher than that for Pd/C (61.5 A/g) at given onset peak potentials. The high activity and stability of the electro-catalysts are attributed to the uniform dispersion of Pd nanoparticles over the rGO support, as evidenced from TEM images. It is believed that the role of La species in promoting the catalyst activity is to disperse the catalyst particles during synthesis and to facilitate the electron transfer via providing a suitable pathway during electrochemical testing.

Ali, Z, Tahir, M, Cao, C, Mahmood, A, Mahmood, N, Butt, FK, Tanveer, M, Shakir, I, Rizwan, M, Idrees, F, Aslam, I & Zou, J-J 2016, 'Solid waste for energy storage material as electrode of supercapacitors', Materials Letters, vol. 181, pp. 191-195.
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Alqarni, B, Colley, B, Klebensberger, J, McDougald, D & Rice, SA 2016, 'Expression stability of 13 housekeeping genes during carbon starvation of Pseudomonas aeruginosa', Journal of Microbiological Methods, vol. 127, pp. 182-187.
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© 2016 Elsevier B.V. Quantitative real-time polymerase chain reaction (qRT-PCR) is a reliable technique for quantifying mRNA levels when normalised by a stable reference gene/s. Many putative reference genes are known to be affected by physiological stresses, such as nutrient limitation and hence may not be suitable for normalisation. In this study of Pseudomonas aeruginosa, the expression of 13 commonly used reference genes, rpoS, proC, recA, rpsL, rho, oprL, anr, tipA, nadB, fabD, ampC, algD and gyrA, were analysed for changes in expression under carbon starvation and nutrient replete conditions. The results showed that rpoS was the only stably expressed housekeeping gene during carbon starvation. In contrast, other commonly used housekeeping genes were shown to vary by as much as 10-100 fold under starvation conditions. This study has identified a suitable reference gene for qRT-PCR in P. aeruginosa during carbon starvation. The results presented here highlight the need to validate housekeeping genes under the chosen experimental conditions.

Andreasson, JG, Shevchenko, PV & Novikov, A 2016, 'Optimal Consumption, Investment and Housing with Means-tested Public Pension in Retirement', Insurance: Mathematics and Economics, vol. 75, pp. 32-47.
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In this paper, we develop an expected utility model for the retirementbehavior in the decumulation phase of Australian retirees with sequentialfamily status subject to consumption, housing, investment, bequest andgovernment provided means-tested Age Pension. We account for mortality risk andrisky investment assets, and introduce a health proxy to capture the decreasinglevel of consumption for older retirees. Then we find optimal housing atretirement, and optimal consumption and optimal risky asset allocationdepending on age and wealth. The model is solved numerically as a stochasticcontrol problem, and is calibrated using the maximum likelihood method onempirical data of consumption and housing from the Australian Bureau ofStatistics 2009-2010 Survey. The model fits the characteristics of the datawell to explain the behavior of Australian retirees. The key findings are thefollowing: First, the optimal policy is highly sensitive to means-tested AgePension early in retirement but this sensitivity fades with age. Secondly, theallocation to risky assets shows a complex relationship with the means-testedAge Pension that disappears once minimum withdrawal rules are enforced. As ageneral rule, when wealth decreases the proportion allocated to risky assetsincreases, due to the Age Pension working as a buffer against investmentlosses. Finally, couples can be more aggressive with risky allocations due totheir longer life expectancy compared with singles.

Angelini, M, Coupland, M, Schuck, S & Prescott, A 2016, 'Engaging Australian Students in Maths Learning', Reflections, vol. 41, no. 1.

Angeloski, A, Baker, AT, Bhadbhade, M & McDonagh, AM 2016, 'Bis(κ2S,Sʹ-di(isopropyl)dithiocarbamato)nickel(II): Anagostic C–H⋅⋅⋅Ni interactions and physical properties', Journal of Molecular Structure, vol. 1113, pp. 127-132.
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© 2016 Elsevier B.V. All rights reserved. The molecular structure of bis(κ2S,S′-di(isopropyl)dithiocarbamato)nickel(II) has been examined by single crystal X-ray diffraction. The data reveal a C-H·Ni anagostic interaction arising from the interaction of two non-equivalent molecules within the crystal. Thermal analysis data show that the complex decomposes at ∼330 °C. The structure of the resultant NiS material was examined using scanning electron microscopy and energy dispersive X-ray spectroscopy which revealed NiS nanowires.

Angeloski, A, Hook, JM, Bhadbhade, M, Baker, AT & McDonagh, AM 2016, 'Intramolecular H⋯S interactions in metal di-(isopropyl)dithiocarbamate complexes', CrystEngComm, vol. 18, no. 37, pp. 7070-7077.
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Intramolecular C–H⋯S interactions create restricted rotation of groups within di(isopropyl)dithiocarbate complexes.

Arantes de Carvalho, GG, Kondaveeti, S, Petri, DFS, Fioroto, AM, Albuquerque, LGR & Oliveira, PV 2016, 'Evaluation of calcium alginate beads for Ce, La and Nd preconcentration from groundwater prior to ICP OES analysis', Talanta, vol. 161, pp. 707-712.
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Archer, MS & Wallman, JF 2016, 'Context Effects in Forensic Entomology and Use of Sequential Unmasking in Casework', Journal of Forensic Sciences, vol. 61, no. 5, pp. 1270-1277.
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AbstractContext effects are pervasive in forensic science, and are being recognized by a growing number of disciplines as a threat to objectivity. Cognitive processes can be affected by extraneous context information, and many proactive scientists are therefore introducing context‐minimizing systems into their laboratories. Forensic entomologists are also subject to context effects, both in the processes they undertake (e.g., evidence collection) and decisions they make (e.g., whether an invertebrate taxon is found in a certain geographic area). We stratify the risk of bias into low, medium, and high for the decisions and processes undertaken by forensic entomologists, and propose that knowledge of the time the deceased was last seen alive is the most potentially biasing piece of information for forensic entomologists. Sequential unmasking is identified as the best system for minimizing context information, illustrated with the results of a casework trial (n = 19) using this approach in Victoria, Australia.

Arthington, AH, Dulvy, NK, Gladstone, W & Winfield, IJ 2016, 'Fish conservation in freshwater and marine realms: status, threats and management', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 26, no. 5, pp. 838-857.
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AbstractDespite the disparities in size and volume of marine and freshwater realms, a strikingly similar number of species is found in each – with 15 150 Actinopterygian fishes in fresh water and 14 740 in the marine realm. Their ecological and societal values are widely recognized yet many marine and freshwater fishes increasingly risk local, regional or global extinction.The prevailing threats in aquatic systems are habitat loss and degradation, invasive species, pollution, over‐exploitation and climate change. Unpredictable synergies with climate change greatly complicate the impacts of other stressors that threaten many marine and freshwater fishes.Isolated and fragmented habitats typically present the most challenging environments for small, specialized freshwater and marine fishes, whereas overfishing is by far the greatest threat to larger marine and freshwater species. Species that migrate within or between freshwater and marine realms may face high catchability in predictable migration bottlenecks, and degradation of breeding habitat, feeding habitat or the intervening migration corridors.Conservation reserves are vital to protect species‐rich habitats, important radiations, and threatened endemic species. Integration of processes that connect terrestrial, freshwater and marine protected areas promises more effective conservation outcomes than disconnected reserves. Diadromous species in particular require more attention in aquatic restoration and conservation planning across disparate government agencies.Human activities and stressors that increasingly threaten freshwater and marine fishes must be curbed to avoid a wave of extinctions. Freshwater recovery programmes range fr...

Asaad, S, Dickel, C, Langford, NK, Poletto, S, Bruno, A, Rol, MA, Deurloo, D & DiCarlo, L 2016, 'Independent, extensible control of same-frequency superconducting qubits by selective broadcasting', npj Quantum Information, vol. 2, no. 1, pp. 1-6.
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AbstractA critical ingredient for realising large-scale quantum information processors will be the ability to make economical use of qubit control hardware. We demonstrate an extensible strategy for reusing control hardware on same-frequency transmon qubits in a circuit QED chip with surface-code-compatible connectivity. A vector switch matrix enables selective broadcasting of input pulses to multiple transmons with individual tailoring of pulse quadratures for each, as required to minimise the effects of leakage on weakly anharmonic qubits. Using randomised benchmarking, we compare multiple broadcasting strategies that each pass the surface-code error threshold for single-qubit gates. In particular, we introduce a selective broadcasting control strategy using five pulse primitives, which allows independent, simultaneous Clifford gates on arbitrary numbers of qubits.

Asaad, S, Dickel, C, Langford, NK, Poletto, S, Bruno, A, Rol, MA, Deurloo, D & Dicarlo, L 2016, 'Independent, extensible control of same-frequency superconducting qubits by selective broadcasting(npj Quantum Information (2017) 3, 17001, 10.1038/npjqi.2017.1)', npj Quantum Information, vol. 2, no. 1.
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The original version of this Article contained an error in one of the calculations within the Results section. Although the authors note that this leakage rate is per Clifford, they actually quote the value per nanosecond: 'We extract per Clifford leakage rates ? of 4.1(2) × 10-6 (QT)and 1.3(4) × 10-6 (QB) by fitting the following simple model to the data'. Now reads: 'We extract per Clifford leakage rates k of 1.4(2) × 10-4 (QT) and 3.9(4) × 10-5 (QB) by fitting the following simple model to the data'. This error has now been corrected in the PDF and HTML versions of the Article.

Ashourloo, D, Matkan, AA, Huete, A, Aghighi, H & Mobasheri, MR 2016, 'Developing an Index for Detection and Identification of Disease Stages', IEEE Geoscience and Remote Sensing Letters, vol. 13, no. 6, pp. 851-855.
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Spectral data have been widely used to estimate the disease severity (DS) levels of different plants. However, such data have not been evaluated to estimate the disease stages of the plant. This study aimed at developing a spectral disease index (SDI) that is able to identify the stages of wheat leaf rust disease at various DS levels. To meet the aim of the study, the reflectance spectra (350-2500 nm) of infected leaves with different symptom fractions and DS levels were measured with a spectroradiometer. Then, pure spectra of the different disease symptoms at the leaf scale were analyzed, and a new function was developed to find the wavelengths most sensitive to disease symptom fraction. The reflectance spectra with highest sensitivity were found at 675 and 775 nm. Finally, the normalized difference of DS and the ratio ρ675/ρ775 was used as a new SDI to discriminate three different levels of the disease stage at the canopy level. The suggested SDI showed a promising performance to improve the detection disease stages in precision plant protection.

Baird, ME, Adams, MP, Babcock, RC, Oubelkheir, K, Mongin, M, Wild-Allen, KA, Skerratt, J, Robson, BJ, Petrou, K, Ralph, PJ, O'Brien, KR, Carter, AB, Jarvis, JC & Rasheed, MA 2016, 'A biophysical representation of seagrass growth for application in a complex shallow-water biogeochemical model', ECOLOGICAL MODELLING, vol. 325, pp. 13-27.
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Seagrasses are a critical component of the healthy functioning of many coastal marine ecosystems. Capturing the dynamics of seagrass communities requires both a detailed representation of processes such as seagrass nutrient uptake and photosynthesis, as well as models of light penetration, water column and sediment biogeochemical processes and other ecosystem characteristics that determine the environmental state. Here we develop a new two-state, 13-parameter seagrass model with the aim of providing sufficient detail to represent light and nutrient limitation, but simple enough to be coupled into a 60 state variable biogeochemical model. The novel formulation is built around a nitrogen-specific leaf area parameter, Ω, that is well-constrained and is used in calculating both the rate of photosynthesis and the fraction of the seafloor covered by seagrass, Aeff, where Aeff=1-exp(-ΩSGA) and SGA is the aboveground areal seagrass biomass. The model also contains terms for the uptake of nutrients from multiple layers of varying-porosity sediments, translocation of organic matter between leaves and roots, respiration and simple mortality terms. The model is applied to Gladstone Harbour, a macro-tidal sub-tropical estuary in northeast Australia, and is able to simulate realistic spatial seagrass distributions. A simplified form of the model is derived, which can be used to predict seagrass light-limited growth based on five measurable species-specific parameters (maximum growth rate, mortality rate, compensation irradiance, leaf blade angle and nitrogen-specific leaf area). The steady-state percent coverage of seagrass achieved at varying light levels and mortality intensity is calculated as a means of understanding the dynamics of the new seagrass model.

Baird, ME, Cherukuru, N, Jones, E, Margvelashvili, N, Mongin, M, Oubelkheir, K, Ralph, PJ, Rizwi, F, Robson, BJ, Schroeder, T, Skerratt, J, Steven, ADL & Wild-Allen, KA 2016, 'Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: Comparison with satellite data', ENVIRONMENTAL MODELLING & SOFTWARE, vol. 78, pp. 79-96.
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Baker, KG, Robinson, CM, Radford, DT, McInnes, AS, Evenhuis, C & Doblin, MA 2016, 'Thermal Performance Curves of Functional Traits Aid Understanding of Thermally Induced Changes in Diatom-Mediated Biogeochemical Fluxes', Frontiers in Marine Science, vol. 3, pp. 1-14.
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© 2016 Baker, Robinson, Radford, McInnes, Evenhuis and Doblin.How the functional traits (FTs) of phytoplankton change with temperature is important for understanding the impacts of ocean warming on phytoplankton mediated biogeochemical fluxes. This study quantifies the thermal performance curves (TPCs) of FTs in the cosmopolitan model diatom, Thalassiosira pseudonana, to advance understanding of trade-offs between physiological (photoacclimation, carbon fixation, nitrate, phosphate, and silicate uptake) and morphological traits (cell volume and frustule silicification). We show that each FT has substantial phenotypic plasticity and exhibits a unique TPC, varying in both shape and thermal optimum, and diverging from the growth response. The TPC for growth was symmetric with a thermal optimum (Topt) of 18°C. In comparison, the TPC for primary productivity was warm-skewed with a Topt around 21°C, whereas frustule silicification decreased linearly with increasing temperature. Together, this suggests that the optimal temperature for overall fitness is a balance of trade-offs in the underlying functional traits. Moreover, these results demonstrate that growth is not necessarily an accurate estimate of overall biogeochemical performance and that temperature change will likely influence elemental fluxes such as carbon and silicon. Finally, we show that temperature-driven changes in individual traits e.g., photoacclimation, can mimic responses experienced under other environmental stressors (high light) and so a multi-trait assessment is essential for accurate interpretation of the cellular impact of warming. This study also reveals that multi-trait analysis, in the context of TPCs, provides insight into the cellular physiology regulating the whole cell response and has the potential to provide better estimates of how diatom-mediated biogeochemical fluxes are likely to be impacted in the context of ocean warming. Analyzing the response of multiple traits more comprehensiv...

Baldwin, DS, Colloff, MJ, Mitrovic, SM, Bond, NR & Wolfenden, B 2016, 'Restoring dissolved organic carbon subsidies from floodplains to lowland river food webs: a role for environmental flows?', Marine and Freshwater Research, vol. 67, no. 9, pp. 1387-1387.
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Environmental flows are managed events in river systems designed to enhance the ecological condition of aquatic ecosystems. Although not traditionally seen as important in lowland rivers, there is mounting evidence that terrestrial subsidies can be an important energy source in aquatic metazoan food webs. We argue that the apparent lack of importance of terrestrial subsidies to many lowland river food webs may reflect an artefact resulting from historical anthropogenic changes to lowland river–floodplain ecosystems, including the loss of lateral connectivity between rivers and their floodplains, changes in floodplain land use and carbon stores, and loss of sites of transformation within the main channel. The loss of floodplain subsidies to the main river channel can be partially redressed using environmental flows; however, this will require mimicking important aspects of natural high-flow events that have hitherto been overlooked when targeting environmental flows to a limited suite of biota. We suggest that key biotic targets for environmental flow releases may not be achievable unless river–floodplain subsidies are sufficiently restored. Environmental flows can go some way to addressing this shortfall, but only if floodplain subsidies to river channels are explicitly included in the design and management of environmental flows.

Banihashemi, N, Robillard, R, Yang, J, Carpenter, JS, Hermens, DF, Naismith, SL, Terpening, Z, White, D, Scott, EM & Hickie, IB 2016, 'Quantifying the effect of body mass index, age, and depression severity on 24-h activity patterns in persons with a lifetime history of affective disorders', BMC Psychiatry, vol. 16, no. 1.
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Bao, W, Mondal, AK, Xu, J, Wang, C, Su, D & Wang, G 2016, '3D hybrid–porous carbon derived from carbonization of metal organic frameworks for high performance supercapacitors', Journal of Power Sources, vol. 325, pp. 286-291.
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Bao, W, Su, D, Zhang, W, Guo, X & Wang, G 2016, '3D Metal Carbide@Mesoporous Carbon Hybrid Architecture as a New Polysulfide Reservoir for Lithium‐Sulfur Batteries', Advanced Functional Materials, vol. 26, no. 47, pp. 8746-8756.
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3D metal carbide@mesoporous carbon hybrid architecture (Ti3C2Tx@Meso‐C, TX ≈ FxOy) is synthesised and applied as cathode material hosts for lithium‐sulfur batteries. Exfoliated‐metal carbide (Ti3C2Tx) nanosheets have high electronic conductivity and contain rich functional groups for effective trapping of polysulfides. Mesoporous carbon with a robust porous structure provides sufficient spaces for loading sulfur and effectively cushion the volumetric expansion of sulfur cathodes. Theoretical calculations have confirmed that metal carbide can absorb sulfur and polysulfides, therefore extending the cycling performance. The Ti3C2Tx@Meso‐C/S cathodes have achieved a high capacity of 1225.8 mAh g−1 and more than 300 cycles at the C/2 current rate. The Ti3C2Tx@Meso‐C hybrid architecture is a promising cathode host material for lithium‐sulfur batteries.

Barratt, J, Chan, D, Sandaradura, I, Malik, R, Spielman, D, Lee, R, Marriott, D, Harkness, J, Ellis, J & Stark, D 2016, 'Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen', PARASITOLOGY, vol. 143, no. 9, pp. 1087-1118.
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Angiostrongylus cantonensis is a metastrongyloid nematode found widely in the Asia-Pacific region, and the aetiological agent of angiostrongyliasis; a disease characterized by eosinophilic meningitis. Rattus rats are definitive hosts of A. cantonensis, while intermediate hosts include terrestrial and aquatic molluscs. Humans are dead-end hosts that usually become infected upon ingestion of infected molluscs. A presumptive diagnosis is often made based on clinical features, a history of mollusc consumption, eosinophilic pleocytosis in cerebral spinal fluid, and advanced imaging such as computed tomography. Serological tests are available for angiostrongyliasis, though many tests are still under development. While there is no treatment consensus, therapy often includes a combination of anthelmintics and corticosteroids. Angiostrongyliasis is relatively rare, but is often associated with morbidity and sometimes mortality. Recent reports suggest the parasites' range is increasing, leading to fatalities in regions previously considered Angiostrongylus-free, and sometimes, delayed diagnosis in newly invaded regions. Increased awareness of angiostrongyliasis would facilitate rapid diagnosis and improved clinical outcomes. This paper summarizes knowledge on the parasites' life cycle, clinical aspects and epidemiology. The molecular biology of Angiostrongylus spp. is also discussed. Attention is paid to the significance of angiostrongyliasis in Australia, given the recent severe cases reported from the Sydney region.

Barratt, J, Gough, R, Stark, D & Ellis, J 2016, 'Bulky Trichomonad Genomes: Encoding a Swiss Army Knife', Trends in Parasitology, vol. 32, no. 10, pp. 783-797.
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© 2016 Elsevier Ltd The trichomonads are a remarkably successful lineage of ancient, predominantly parasitic protozoa. Recent molecular analyses have revealed extensive duplication of certain genetic loci in trichomonads. Consequently, their genomes are exceptionally large compared to other parasitic protozoa. Retention of these large gene expansions across different trichomonad families raises the question: do these duplications afford an advantage? Many duplicated genes are linked to the parasitic lifestyle and some are regulated differently to their paralogues, suggesting they have acquired new functions. It is proposed that these large genomes encode a Swiss army knife of sorts, packed with a multitude of tools for use in many different circumstances. This may have bestowed trichomonads with the extraordinary versatility that has undoubtedly contributed to their success.

Beck, HJ, Feary, DA, Fowler, AM, Madin, EMP & Booth, DJ 2016, 'Temperate predators and seasonal water temperatures impact feeding of a range expanding tropical fish', MARINE BIOLOGY, vol. 163, no. 4.
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© 2016, Springer-Verlag Berlin Heidelberg. Range expansions of species due to climate change threaten the function and composition of marine ecosystems globally, yet factors constraining or facilitating this redistribution are poorly understood. Native predators may constrain prey shifting poleward through consumption, or by restricting their feeding activity. However, the extent that native predators impact range-expanders will likely be structured by physiological mismatches between these groups, associated with water temperatures. We examined how temperate predators and seasonal water temperature affected foraging of the planktivorous tropical reef fish, Abudefduf vaigiensis, within temperate southeastern Australian waters, an emerging new range. Foraging excursions of A. vaigiensis were compared between predator-rich marine reserves and predator-depauperate fished reefs during summer and winter (~18 and 22 °C water, respectively). A. vaigiensis foraged with shorter excursions in marine reserves than fished reefs and higher excursions during summer than winter. Effects of predation risk and water temperature on A. vaigiensis foraging were isolated in an aquarium experiment. Groups were held at 18 or 22 °C and visually exposed to a temperate predator, a predator control (temperate herbivore) and an empty tank. Foraging excursions and feeding rates were reduced when exposed to predators at 22 °C, but did not differ between predator and the predator control or empty tank at 18 °C. Results suggest temperate predators may restrict range expansions of A. vaigiensis by reducing its’ food intake during summer months. But winter water temperatures may limit feeding, independent of predation risk. Protection of predators from fishing should improve resistance of some marine ecosystems to impacts of range expanding prey.

Beck, HJ, Feary, DA, Nakamura, Y & Booth, DJ 2016, 'Wave-sheltered embayments are recruitment hotspots for tropical fishes on temperate reefs', MARINE ECOLOGY PROGRESS SERIES, vol. 546, pp. 197-212.
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© Inter-Research 2016. Poleward redistribution of species, facilitated by global warming, will be compromised if habitats at higher latitudes do not support the species' early life stages. For tropical reef fishes, reef structure may mediate colonisation of temperate regions; however, an understanding of key habitat requirements for colonisation is currently lacking. We show that density, diversity (taxonomic and trophic) and species richness of newly recruited tropical reef fishes were greater in embayed than exposed reefs in 2 mid-latitude temperate zones, where coastal waters are rapidly warming: southeastern Australia (30.5-33° S) and western Japan (32-33.5° N). Dietary generalists (e.g. planktivores and herbivores) and specialists (corallivores) associated more commonly with embayed reefs. Wave exposure was a stronger predictor of the density and richness of dietary generalists than water temperature, latitude, predatory fish densities, reef rugosities, benthos and distance to river mouths. Corallivores were strongly associated with branching corals, which were exclusive to highly sheltered reefs. We also explored habitat associations of 7 focal species within a coral reef, One Tree Island (OTI), Great Barrier Reef. Four species associated with wave - sheltered over exposed reef on OTI and temperate Australian reef. However, Abudefduf vaigiensis, Pomacentrus coelestis and Acanthurus triostegus associated more with wave-sheltered reef in temperate regions. We hypothesise that cool temperate waters promote greater sheltering of some warm-adapted, tropical fishes by impacting their swimming/physiological performance. Results suggest availability of embayed temperate reefs may influence where some tropical fishes colonise with warming waters, through impacting recruitment. Wave exposure of reefs should be considered when predicting geographic responses of tropical fishes to climate change.

Ben-Nissan, B, Macha, I, Cazalbou, S & Choi, AH 2016, 'Calcium Phosphate Nanocoatings and Nanocomposites, Part 2: Thin Films for Slow Drug Delivery and Osteomyelitis', Nanomedicine, vol. 11, no. 5, pp. 531-544.
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During the last two decades although many calcium phosphate based nanomaterials have been proposed for both drug delivery, and bone regeneration, their coating applications have been somehow slow due to the problems related to their complicated synthesis methods. In order to control the efficiency of local drug delivery of a biomaterial the critical pore sizes as well as good control of the chemical composition is pertinent. A variety of calcium phosphate based nanocoated composite drug delivery systems are currently being investigated. This review aims to give an update into the advancements of calcium phosphate nanocoatings and thin film nanolaminates. In particular recent research on PLA/hydroxyapatite composite thin films and coatings into the slow drug delivery for the possible treatment of osteomyelitis is covered.

Beringer, J, Hutley, LB, McHugh, I, Arndt, SK, Campbell, D, Cleugh, HA, Cleverly, J, Resco de Dios, V, Eamus, D, Evans, B, Ewenz, C, Grace, P, Griebel, A, Haverd, V, Hinko-Najera, N, Huete, A, Isaac, P, Kanniah, K, Leuning, R, Liddell, MJ, Macfarlane, C, Meyer, W, Moore, C, Pendall, E, Phillips, A, Phillips, RL, Prober, S, Restrepo-Coupe, N, Rutledge, S, Schroder, I, Silberstein, R, Southall, P, Sun, M, Tapper, NJ, van Gorsel, E, Vote, C, Walker, J & Wardlaw, T 2016, 'An introduction to the Australian and New Zealand flux tower network – OzFlux', Biogeosciences Discussions, vol. 13, pp. 5895-5916.
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Abstract. OzFlux is the regional Australian and New Zealand flux tower network that aims to provide a continental-scale national research facility to monitor and assess trends, and improve predictions, of Australia’s terrestrial biosphere and climate. This paper describes the evolution, design and current status of OzFlux as well as an overview of data processing. We analyse measurements from the Australian portion of the OzFlux network and found that the response of Australian biomes to climate was largely consistent with global studies but that Australian systems had a lower ecosystem water-use efficiency. Australian semi-arid/arid ecosystems are important because of their huge extent (70 %) and they have evolved with common moisture limitations. We also found that Australian ecosystems had similar radiation use efficiency per unit leaf area compared to global values that indicates a convergence toward a similar biochemical efficiency. The paper discusses the utility of the flux data and the synergies between flux, remote sensing and modelling. Lastly, the paper looks ahead at the future direction of the network and concludes that there has been a substantial contribution by OzFlux and considerable opportunities remain to further advance our understanding of ecosystem response to disturbances including drought, fire, land use and land cover change, land management and climate change that are relevant both nationally and internationally. It is suggested that a synergistic approach is required to address all of the spatial, ecological, human and cultural challenges of managing the delicately balanced ecosystems in Australia.

Beringer, J, Hutley, LB, McHugh, I, Arndt, SK, Campbell, D, Cleugh, HA, Cleverly, J, Resco de Dios, V, Eamus, D, Evans, B, Ewenz, C, Grace, P, Griebel, A, Haverd, V, Hinko-Najera, N, Huete, A, Isaac, P, Kanniah, K, Leuning, R, Liddell, MJ, Macfarlane, C, Meyer, W, Moore, C, Pendall, E, Phillips, A, Phillips, RL, Prober, SM, Restrepo-Coupe, N, Rutledge, S, Schroder, I, Silberstein, R, Southall, P, Yee, MS, Tapper, NJ, van Gorsel, E, Vote, C, Walker, J & Wardlaw, T 2016, 'An introduction to the Australian and New Zealand flux tower network - OzFlux', BIOGEOSCIENCES, vol. 13, no. 21, pp. 5895-5916.
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© Author(s) 2016. OzFlux is the regional Australian and New Zealand flux tower network that aims to provide a continental-scale national research facility to monitor and assess trends, and improve predictions, of Australia's terrestrial biosphere and climate. This paper describes the evolution, design, and current status of OzFlux as well as provides an overview of data processing. We analyse measurements from all sites within the Australian portion of the OzFlux network and two sites from New Zealand. The response of the Australian biomes to climate was largely consistent with global studies except that Australian systems had a lower ecosystem water-use efficiency. Australian semi-arid/arid ecosystems are important because of their huge extent (70 %) and they have evolved with common moisture limitations. We also found that Australian ecosystems had a similar radiation-use efficiency per unit leaf area compared to global values that indicates a convergence toward a similar biochemical efficiency. The two New Zealand sites represented extremes in productivity for a moist temperate climate zone, with the grazed dairy farm site having the highest GPP of any OzFlux site (2620 gC m-2 yr-1) and the natural raised peat bog site having a very low GPP (820 gC m-2 yr-1). The paper discusses the utility of the flux data and the synergies between flux, remote sensing, and modelling. Lastly, the paper looks ahead at the future direction of the network and concludes that there has been a substantial contribution by OzFlux, and considerable opportunities remain to further advance our understanding of ecosystem response to disturbances, including drought, fire, land-use and land-cover change, land management, and climate change, which are relevant both nationally and internationally. It is suggested that a synergistic approach is required to address all of the spatial, ecological, human, and cultural challenges of managing the delicately balanced ecosystems in Australasia.

Berry, IJ, Steele, JR, Padula, MP & Djordjevic, SP 2016, 'The application of terminomics for the identification of protein start sites and proteoforms in bacteria', PROTEOMICS, vol. 16, no. 2, pp. 257-272.
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Protein terminomics, or the study of amino acids sequences at the protein amino or carboxyl terminus has rapidly evolved as a proteomic discipline due to significant methodological improvements in the labelling and recovery of terminal peptides as well as the increased speed and sensitivity of current mass spectrometry instrumentation. The most significant beneficiaries of these developments include an increased awareness and understanding of complex proteolytic cascades that regulate key biological processes and in genome annotation. Most terminomics research to date has focused on gaining insight into important biological processes such as inflammation, wound healing and cancer. The application of terminomics to the study of important biological questions in prokaryotes is gaining traction. Here we review current applications and progress of terminomics in prokaryotes, discuss the significance of protease research in bacterial pathogenesis and protein maturation, and suggest novel applications of terminomics in the study of infectious disease.

Bertrand, PP, Polglaze, KE, Chen, H, Sandow, SL, Walduck, A, Jenkins, TA, Bertrand, RL, Lomax, AE & Liu, L 2016, 'Excitability and Synaptic Transmission in the Enteric Nervous System: Does Diet Play a Role?', ENTERIC NERVOUS SYSTEM: 30 YEARS LATER, vol. 891, pp. 201-211.
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Bhadra, A & Carroll, RJ 2016, 'Exact sampling of the unobserved covariates in Bayesian spline models for measurement error problems', Statistics and Computing, vol. 26, no. 4, pp. 827-840.
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© 2015, Springer Science+Business Media New York. In truncated polynomial spline or B-spline models where the covariates are measured with error, a fully Bayesian approach to model fitting requires the covariates and model parameters to be sampled at every Markov chain Monte Carlo iteration. Sampling the unobserved covariates poses a major computational problem and usually Gibbs sampling is not possible. This forces the practitioner to use a Metropolis–Hastings step which might suffer from unacceptable performance due to poor mixing and might require careful tuning. In this article we show for the cases of truncated polynomial spline or B-spline models of degree equal to one, the complete conditional distribution of the covariates measured with error is available explicitly as a mixture of double-truncated normals, thereby enabling a Gibbs sampling scheme. We demonstrate via a simulation study that our technique performs favorably in terms of computational efficiency and statistical performance. Our results indicate up to 62 and 54 % increase in mean integrated squared error efficiency when compared to existing alternatives while using truncated polynomial splines and B-splines respectively. Furthermore, there is evidence that the gain in efficiency increases with the measurement error variance, indicating the proposed method is a particularly valuable tool for challenging applications that present high measurement error. We conclude with a demonstration on a nutritional epidemiology data set from the NIH-AARP study and by pointing out some possible extensions of the current work.

Bibiloni‐Isaksson, J, Seymour, JR, Ingleton, T, van de Kamp, J, Bodrossy, L & Brown, MV 2016, 'Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia', Environmental Microbiology, vol. 18, no. 12, pp. 4485-4500.
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SummaryAerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml−1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter‐clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.

Billings, JL, Hare, DJ, Nurjono, M, Volitakis, I, Cherny, RA, Bush, AI, Adlard, PA & Finkelstein, DI 2016, 'Effects of Neonatal Iron Feeding and Chronic Clioquinol Administration on the Parkinsonian Human A53T Transgenic Mouse', ACS Chemical Neuroscience, vol. 7, no. 3, pp. 360-366.
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Bilton, K & Zaslawski, C 2016, 'Reliability of Manual Pulse Diagnosis Methods in Traditional East Asian Medicine: A Systematic Narrative Literature Review', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 22, no. 8, pp. 599-609.
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Bishop, DP, Clases, D, Fryer, F, Williams, E, Wilkins, S, Hare, DJ, Cole, N, Karst, U & Doble, PA 2016, 'Elemental bio-imaging using laser ablation-triple quadrupole-ICP-MS', Journal of Analytical Atomic Spectrometry, vol. 31, no. 1, pp. 197-202.
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Elemental bio-imaging using the technological advances of ICP-QQQ-MS.

Blackwell, GA, Hamidian, M & Hall, RM 2016, 'IncM Plasmid R1215 Is the Source of Chromosomally Located Regions Containing Multiple Antibiotic Resistance Genes in the Globally Disseminated Acinetobacter baumannii GC1 and GC2 Clones', mSphere, vol. 1, no. 3.
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Two lineages of extensively antibiotic-resistant A. baumannii currently plaguing modern medicine each acquired resistance to all of the original antibiotics (ampicillin, tetracycline, kanamycin, and sulfonamides) by the end of the 1970s and then became resistant to antibiotics from newer families after they were introduced in the 1980s. Here, we show that, in both of the dominant globally disseminated A. baumannii clones, a related set of antibiotic resistance genes was acquired together from the same resistance region that had already evolved in an IncM plasmid. In both cases, the action of IS 26 was important in this process, but homologous recombination was also involved. The findings highlight the fact that complex regions carrying several resistance genes can evolve in one location or organism and all or part of the evolved region can then move to other locations and other organisms, conferring resistance to several antibiotics in a single step.

Boakes, RA, Kendig, MD, Martire, SI & Rooney, KB 2016, 'Sweetening yoghurt with glucose, but not with saccharin, promotes weight gain and increased fat pad mass in rats', Appetite, vol. 105, pp. 114-128.
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Boakes, RA, Martire, SI, Rooney, KB & Kendig, MD 2016, 'Individual differences in saccharin acceptance predict rats' food intake', Physiology & Behavior, vol. 164, pp. 151-156.
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Booth, DJ 2016, 'Ability to home in small site‐attached coral reef fishes', Journal of Fish Biology, vol. 89, no. 2, pp. 1501-1506.
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The ability of two common, site‐attached coral‐reef fishes to return to their home corals after displacement was investigated in a series of field experiments at One Tree Island, southern Great Barrier Reef. The humbug Dascyllus aruanus was displaced up to 250 m, with 42% of individuals returning home, irrespective of body size, displacement, direction (up or across currents) and route complexity, while for the lemon damselfish Pomacentrus moluccensis 35% of individuals returned overall, with 33% from the greatest displacement, 100 m along a reef edge. Given that the home range of both species is <1 m2, over their 10+ year life span, the mechanisms and motivations for such homing ability are unclear but it may allow resilience if fishes are displaced by storm events, allowing rapid return to home corals.

Bordin, DCM, Alves, MNR, de Campos, EG & De Martinis, BS 2016, 'Disposable pipette tips extraction: Fundamentals, applications and state of the art', Journal of Separation Science, vol. 39, no. 6, pp. 1168-1172.
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Disposable pipette tips extraction consists of a solid‐phase extraction in which the sorbent is poorly dispersed in a pipette tip, which allows a quick and dynamic contact between the aspirated analyte from the sample and the solid phase. It is a technique used particularly in food and forensic analysis, since it requires a small amount of sample and solvent. This article highlights the principles, advantages and disadvantages of the disposable pipette tips extraction method and reviews recent applications.

Bos, KI, Herbig, A, Sahl, J, Waglechner, N, Fourment, M, Forrest, SA, Klunk, J, Schuenemann, VJ, Poinar, D, Kuch, M, Golding, GB, Dutour, O, Keim, P, Wagner, DM, Holmes, EC, Krause, J & Poinar, HN 2016, 'Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus', eLife, vol. 5, no. JANUARY2016.
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The 14th–18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague’s persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.

Bowman, S, Roffey, P, McNevin, D & Gahan, ME 2016, 'Evaluation of commercial DNA extraction methods for biosecurity applications', Australian Journal of Forensic Sciences, vol. 48, no. 4, pp. 407-420.
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Boysen, A, Palmisano, G, Krogh, TJ, Duggin, IG, Larsen, MR & Moller-Jensen, J 2016, 'A novel mass spectrometric strategy 'BEMAP' reveals Extensive O-linked protein glycosylation in Enterotoxigenic Escherichia coli', SCIENTIFIC REPORTS, vol. 6.
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© The Author(s) 2016. The attachment of sugars to proteins via side-chain oxygen atoms (O-linked glycosylation) is seen in all three domains of life. However, a lack of widely-applicable analytical tools has restricted the study of this process, particularly in bacteria. In E. coli, only four O-linked glycoproteins have previously been characterized. Here we present a glycoproteomics technique, termed BEMAP, which is based on the beta-elimination of O-linked glycans followed by Michael-addition of a phosphonic acid derivative, and subsequent titanium dioxide enrichment. This strategy allows site-specific mass-spectrometric identification of proteins with O-linked glycan modifications in a complex biological sample. Using BEMAP we identified cell surface-associated and membrane vesicle glycoproteins from Enterotoxigenic E. coli (ETEC) and non-pathogenic E. coli K-12. We identified 618 glycosylated Serine and Threonine residues mapping to 140 proteins in ETEC, including several known virulence factors, and 34 in E. coli K-12. The two strains had 32 glycoproteins in common. Remarkably, the majority of the ETEC glycoproteins were conserved in both strains but nevertheless were only glycosylated in the pathogen. Therefore, bacterial O-linked glycosylation is much more extensive than previously thought, and is especially important to the pathogen.

Branley, J, Bachmann, NL, Jelocnik, M, Myers, GSA & Polkinghorne, A 2016, 'Australian human and parrot Chlamydia psittaci strains cluster within the highly virulent 6BC clade of this important zoonotic pathogen', Scientific Reports, vol. 6, no. 1.
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AbstractChlamydia psittaci is an avian pathogen and zoonotic agent of atypical pneumonia. The most pathogenic C. psittaci strains cluster into the 6BC clade, predicted to have recently emerged globally. Exposure to infected parrots is a risk factor with limited evidence also of an indirect exposure risk. Genome sequencing was performed on six Australian human and a single avian C. psittaci strain isolated over a 9 year period. Only one of the five human patients had explicit psittacine contact. Genomics analyses revealed that the Australian C. psittaci strains are remarkably similar, clustering tightly within the C. psittaci 6BC clade suggested to have been disseminated by South America parrot importation. Molecular clock analysis using the newly sequenced C. psittaci genomes predicted the emergence of the 6BC clade occurring approximately 2,000 years ago. These findings reveal the potential for an Australian natural reservoir of C. psittaci 6BC strains. These strains can also be isolated from seriously ill patients without explicit psittacine contact. The apparent recent and global spread of C. psittaci 6BC strains raises important questions over how this happened. Further studies may reveal whether the dissemination of this important zoonotic pathogen is linked to Australian parrot importation rather than parrots from elsewhere.

Bray, K, Sandstrom, R, Elbadawi, C, Fischer, M, Schreck, M, Shimoni, O, Lobo, C, Toth, M & Aharonovich, I 2016, 'Localization of Narrowband Single Photon Emitters in Nanodiamonds', ACS Applied Materials & Interfaces, vol. 8, no. 11, pp. 7590-7594.
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© 2016 American Chemical Society. Diamond nanocrystals that host room temperature narrowband single photon emitters are highly sought after for applications in nanophotonics and bioimaging. However, current understanding of the origin of these emitters is extremely limited. In this work, we demonstrate that the narrowband emitters are point defects localized at extended morphological defects in individual nanodiamonds. In particular, we show that nanocrystals with defects such as twin boundaries and secondary nucleation sites exhibit narrowband emission that is absent from pristine individual nanocrystals grown under the same conditions. Critically, we prove that the narrowband emission lines vanish when extended defects are removed deterministically using highly localized electron beam induced etching. Our results enhance the current understanding of single photon emitters in diamond and are directly relevant to fabrication of novel quantum optics devices and sensors.

Brito, B, König, G, Cabanne, GS, Beascoechea, CP, Rodriguez, L & Perez, A 2016, 'Phylogeographic analysis of the 2000–2002 foot-and-mouth disease epidemic in Argentina', Infection, Genetics and Evolution, vol. 41, pp. 93-99.
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Brito, BP, Jori, F, Dwarka, R, Maree, FF, Heath, L & Perez, AM 2016, 'Transmission of Foot-and-Mouth Disease SAT2 Viruses at the Wildlife–Livestock Interface of Two Major Transfrontier Conservation Areas in Southern Africa', Frontiers in Microbiology, vol. 7.
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Brough, T, Ciobanu, L, Elder, M & Zetzsche, G 2016, 'Permutations of context-free, ET0L and indexed languages', Discrete Mathematics & Theoretical Computer Science. DMTCS., vol. 17, pp. 167-178.
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For a language $L$, we consider its cyclic closure, and more generally thelanguage $C^k(L)$, which consists of all words obtained by partitioning wordsfrom $L$ into $k$ factors and permuting them. We prove that the classes of ET0Land EDT0L languages are closed under the operators $C^k$. This both sharpensand generalises Brandst\'adt's result that if $L$ is context-free then $C^k(L)$is context-sensitive and not context-free in general for $k\geq 3$. We alsoshow that the cyclic closure of an indexed language is indexed.

Browne, EC, Parakh, S, Duncan, LF, Langford, SJ, Atkin, JD & Abbott, BM 2016, 'Efficacy of peptide nucleic acid and selected conjugates against specific cellular pathologies of amyotrophic lateral sclerosis', Bioorganic & Medicinal Chemistry, vol. 24, no. 7, pp. 1520-1527.
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Bruenisholz, E, Prakash, S, Ross, A, Morelato, M, O'Malley, T, Raymond, MA, Ribaux, O, Roux, CP & Walsh, S 2016, 'The Intelligent Use of Forensic Data: An Introduction to the Principles', Forensic Science Policy & Management: An International Journal, vol. 7, no. 1-2, pp. 21-29.
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For the past decade, the National Institute of Forensic Science (NIFS) has been involved in and committed to raising the awareness of forensic intelligence in Australia. In this context, a discussion paper was written and distributed across Australia and New Zealand covering forensic intelligence principles and offering a ‘quick reference’ guide. In addition, NIFS jointly facilitated a set of papers on forensic intelligence that was published in the Australian Journal of Forensic Sciences. The implementation of forensic intelligence requires substantial planning and adaptation within an organization. There must be commitment within an agency to refocus outcomes so that crime prevention and disruption become priorities along with the traditional focus on the court. This implies many changes including a shift from a single case focus to a multi-case focus and a breaking down of existing interdisciplinary silos. At a time of budget restrictions, the resources to implement these changes are often difficult to identify. However, established intelligence cells within forensic science facilities are realizing the benefits to be gained from this approach. The primary aim of this paper is to raise awareness on the principles and practice of forensic intelligence through the collation and integration of recently published findings and observations. It is intended to provide introductory principles to personnel of various levels and disciplines involved in law enforcement, including forensic scientists, police officers, and those involved in administering the criminal justice system.

Burke, CM & Darling, AE 2016, 'A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq', PeerJ, vol. 4, no. 9, pp. e2492-e2492.
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BackgroundThe bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision.ResultsWe describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection.ConclusionsThis method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.

Büttner, TFS, Poulton, CG, Steel, MJ, Hudson, DD & Eggleton, BJ 2016, 'Phase-locking in cascaded stimulated Brillouin scattering', New Journal of Physics, vol. 18, no. 2, pp. 025003-025003.
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C. Walsh, J, N. Angstmann, C, V. McGann, A, I. Henry, B, G. Duggin, I & M. G. Curmi, P 2016, 'Patterning of the MinD cell division protein in cells of arbitrary shape can be predicted using a heuristic dispersion relation', AIMS Biophysics, vol. 3, no. 1, pp. 119-145.
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© 2016, Paul M. G. Curmi, et al. Many important cellular processes require the accurate positioning of subcellular structures. Underpinning many of these are protein systems that spontaneously generate spatiotemporal patterns. In some cases, these systems can be described by non-linear reaction-diffusion equations, however, a full description of such equations is rarely available. A well-studied patterning system is the Min protein system that underpins the positioning of the FtsZ contractile ring during cell division in Escherichia coli. Using a coordinate-free linear stability analysis, the reaction terms can be separated from the geometry of a cell. The reaction terms produce a dispersion relation that can be used to predict patterning on any cell shape and size. Applying linear stability analysis to an accurate mathematical model of the Min system shows that while it correctly predicts the onset of patterning, the dispersion relation fails to predict oscillations and quantitative mode transitions. However, we show that data from full solutions of the Min model can be used to generate a heuristic dispersion relation. We show that this heuristic dispersion relation can be used to approximate the Min protein patterning obtained by full simulations of the non-linear reaction-diffusion equations. Moreover, it also predicts Min patterning obtained from experiments where the shapes of E. coli cells have been deformed into rectangles or arbitrary shapes. Using this procedure, it should be possible to generate heuristic dispersion relations from protein patterning data or simulations for any patterning process and subsequently use these to predict patterning for arbitrary cell shapes.

Cai, M, Zhou, B, Tian, Y, Zhou, J, Xu, S & Zhang, J 2016, 'Broadband mid-infrared 2.8μm emission in Ho3+/Yb3+-codoped germanate glasses', Journal of Luminescence, vol. 171, pp. 143-148.
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This work reports the mid-infrared emission properties around 2.85 μm in Ho3+/Yb3+ codoped germanate glasses. The glass not only possesses considerably low OH− absorption coefficient (0.24 cm−1), but also exhibits low phonon energy (790 cm−1). A large spontaneous transition probability (36.66 s−1) corresponding to the Ho3+:5I6→5I7 transition has been calculated based on the Judd–Ofelt theory. Besides, a broad 2.85 μm fluorescence has been successfully observed and a reasonably model has been proposed to unravel the origin of the broadening emission band. Moreover, the peak emission cross sections of the glass is as high as 9.2×10−21 cm2, and the maximum gain per unit length at 2.85 μm could be as high as 4.3 dB/cm. Results indicate that the prepared germanate glass is a promising candidate for 2.85 μm mid-infrared laser materials applications.

Callahan, DL, Hare, DJ, Bishop, DP, Doble, PA & Roessner, U 2016, 'Elemental imaging of leaves from the metal hyperaccumulating plant Noccaea caerulescens shows different spatial distribution of Ni, Zn and Cd', RSC Advances, vol. 6, no. 3, pp. 2337-2344.
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Elemental imaging using laser ablation inductively coupled plasma mass spectrometry was performed on whole leaves of the hyperaccumulating plantNoccaea caerulescensafter treatments with either Ni, Zn or Cd.

Camacho-Morales, R, Rahmani, M, Kruk, S, Wang, L, Xu, L, Smirnova, DA, Solntsev, AS, Miroshnichenko, A, Tan, HH, Karouta, F, Naureen, S, Vora, K, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 2016, 'Nonlinear Generation of Vector Beams From AlGaAs Nanoantennas', Nano Letters, vol. 16, no. 11, pp. 7191-7197.
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© 2016 American Chemical Society. The quest for nanoscale light sources with designer radiation patterns and polarization has motivated the development of nanoantennas that interact strongly with the incoming light and are able to transform its frequency, radiation, and polarization patterns. Here, we demonstrate dielectric AlGaAs nanoantennas for efficient second harmonic generation, enabling the control of both directionality and polarization of nonlinear emission. This is enabled by specialized III-V semiconductor nanofabrication of high-quality AlGaAs nanostructures embedded in optically transparent low-index material, thus allowing for simultaneous forward and backward nonlinear emission. We show that the nanodisk AlGaAs antennas can emit second harmonic in preferential direction with a backward-to-forward ratio of up to five and can also generate complex vector polarization beams, including beams with radial polarization.

Camlin, NJ, Sobinoff, AP, Sutherland, JM, Beckett, EL, Jarnicki, AG, Vanders, RL, Hansbro, PM, McLaughlin, EA & Holt, JE 2016, 'Maternal Smoke Exposure Impairs the Long-Term Fertility of Female Offspring in a Murine Model1', Biology of Reproduction, vol. 94, no. 2, p. 39.
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The theory of fetal origins of adult disease was first proposed in 1989, and in the decades since, a wide range of other diseases from obesity to asthma have been found to originate in early development. Because mammalian oocyte development begins in fetal life it has been suggested that environmental and lifestyle factors of the mother could directly impact the fertility of subsequent generations. Cigarette smoke is a known ovotoxicant in active smokers, yet disturbingly 13% of Australian and 12% of US women continue to smoke throughout pregnancy. The focus of our investigation was to characterize the adverse effects of smoking on ovary and oocyte quality in female offspring exposed in utero. Pregnant mice were nasally exposed to cigarette smoke for 12 wk throughout pregnancy/lactation, and ovary and oocyte quality of the F1 (maternal smoke exposed) generation was examined. Neonatal ovaries displayed abnormal somatic cell proliferation and increased apoptosis, leading to a reduction in follicle numbers. Further investigation found that altered somatic cell proliferation and reduced follicle number continued into adulthood; however, apoptosis did not. This reduction in follicles resulted in decreased oocyte numbers, with these oocytes found to have elevated levels of oxidative stress, altered metaphase II spindle, and reduced sperm-egg interaction. These ovarian and oocyte changes ultimately lead to subfertility, with maternal smoke-exposed animals having smaller litters and also taking longer to conceive. In conclusion, our results demonstrate that in utero and lactational exposure to cigarette smoke can have long-lasting effects on the fertility of the next generation of females.

Camp, EF, Hobbs, J-PA, De Brauwer, M, Dumbrell, AJ & Smith, DJ 2016, 'Cohabitation promotes high diversity of clownfishes in the Coral Triangle', Proceedings of the Royal Society B: Biological Sciences, vol. 283, no. 1827, pp. 20160277-20160277.
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Global marine biodiversity peaks within the Coral Triangle, and understanding how such high diversity is maintained is a central question in marine ecology. We investigated broad-scale patterns in the diversity of clownfishes and their host sea anemones by conducting 981 belt-transects at 20 locations throughout the Indo-Pacific. Of the 1508 clownfishes encountered, 377 fish occurred in interspecific cohabiting groups and cohabitation was almost entirely restricted to the Coral Triangle. Neither the diversity nor density of host anemone or clownfish species alone influenced rates of interspecific cohabitation. Rather cohabitation occurred in areas where the number of clownfish species exceeds the number of host anemone species. In the Coral Triangle, cohabiting individuals were observed to finely partition their host anemone, with the subordinate species inhabiting the periphery. Furthermore, aggression did not increase in interspecific cohabiting groups, instead dominant species were accepting of subordinate species. Various combinations of clownfish species were observed cohabiting (independent of body size, phylogenetic relatedness, evolutionary age, dentition, level of specialization) in a range of anemone species, thereby ensuring that each clownfish species had dominant reproductive individuals in some cohabiting groups. Clownfishes are obligate commensals, thus cohabitation is an important process in maintaining biodiversity in high diversity systems because it supports the persistence of many species when host availability is limiting. Cohabitation is a likely explanation for high species richness in other obligate commensals within the Coral Triangle, and highlights the importance of protecting these habitats in order to conserve unique marine biodiversity.

Camp, EF, Smith, DJ, Evenhuis, C, Enochs, I, Manzello, D, Woodcock, S & Suggett, DJ 2016, 'Acclimatization to high-variance habitats does not enhance physiological tolerance of two key Caribbean corals to future temperature and pH', Proceedings of the Royal Society B: Biological Sciences, vol. 283, no. 1831, pp. 20160442-20160442.
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Corals are acclimatized to populate dynamic habitats that neighbour coral reefs. Habitats such as seagrass beds exhibit broad diel changes in temperature and pH that routinely expose corals to conditions predicted for reefs over the next 50–100 years. However, whether such acclimatization effectively enhances physiological tolerance to, and hence provides refuge against, future climate scenarios remains unknown. Also, whether corals living in low-variance habitats can tolerate present-day high-variance conditions remains untested. We experimentally examined how pH and temperature predicted for the year 2100 affects the growth and physiology of two dominant Caribbean corals ( Acropora palmata and Porites astreoides ) native to habitats with intrinsically low (outer-reef terrace, LV) and/or high (neighbouring seagrass, HV) environmental variance. Under present-day temperature and pH, growth and metabolic rates (calcification, respiration and photosynthesis) were unchanged for HV versus LV populations. Superimposing future climate scenarios onto the HV and LV conditions did not result in any enhanced tolerance to colonies native to HV. Calcification rates were always lower for elevated temperature and/or reduced pH. Together, these results suggest that seagrass habitats may not serve as refugia against climate change if the magnitude of future temperature and pH changes is equivalent to neighbouring reef habitats.

Camp, EF, Suggett, DJ, Gendron, G, Jompa, J, Manfrino, C & Smith, DJ 2016, 'Mangrove and Seagrass Beds Provide Different Biogeochemical Services for Corals Threatened by Climate Change', Frontiers in Marine Science, vol. 3, no. APR, pp. 1-16.
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© 2016 Camp, Suggett, Gendron, Jompa, Manfrino and Smith. Rapidly rising atmospheric CO2 concentrations are driving acidification in parallel with warming of the oceans. Future ocean acidification scenarios have the potential to impact coral growth and associated reef function, although reports suggest such affects could be reduced in adjacent seagrass habitats as a result of physio-chemical buffering. To-date, it remains unknown whether these habitats can actually support the metabolic function of a diverse range of corals. Similarly, whether mangroves provide the same ecological buffering service remains unclear. We examine whether reef-associated habitat sites (seagrass and mangroves) can act as potential refugia to future climate change by maintaining favorable chemical conditions (elevated pH and aragonite saturation state relative to the open-ocean), but by also assessing whether the metabolic function (photosynthesis, respiration and calcification) of important reef-building corals are sustained. We investigated three sites in the Atlantic, Indian, and Pacific Oceans and consistently observed that seagrass beds experience an overall elevation in mean pH (8.15 ± 0.01) relative to the adjacent outer-reef (8.12 ± 0.03), but with periods of high and low pH. Corals in the seagrass habitats either sustained calcification or experienced an average reduction of 17.0 ± 6.1% relative to the outer-reef. In contrast, mangrove habitats were characterized by a low mean pH (8.04 ± 0.01) and a relatively moderate pH range. Corals within mangrove-dominated habitats were thus pre-conditioned to low pH but with significant suppression to calcification (70.0 ± 7.3% reduction relative to the outer-reef). Both habitats also experienced more variable temperatures (diel range up to 2.5°C) relative to the outer-reef (diel range less than 0.7°C), which did not correspond with changes in calcification rates. Here we report, for the first time, the biological costs for cora...

Capistrano, S, Zakarya, R, Chen, H & Oliver, B 2016, 'Biomass Smoke Exposure Enhances Rhinovirus-Induced Inflammation in Primary Lung Fibroblasts', International Journal of Molecular Sciences, vol. 17, no. 9, pp. 1403-1403.
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Biomass smoke is one of the major air pollutants and contributors of household air pollution worldwide. More than 3 billion people use biomass fuels for cooking and heating, while other sources of exposure are from the occurrence of bushfires and occupational conditions. Persistent biomass smoke exposure has been associated with acute lower respiratory infection (ALRI) as a major environmental risk factor. Children under the age of five years are the most susceptible in developing severe ALRI, which accounts for 940,000 deaths globally. Around 90% of cases are attributed to viral infections, such as influenza, adenovirus, and rhinovirus. Although several epidemiological studies have generated substantial evidence of the association of biomass smoke and respiratory infections, the underlying mechanism is still unknown. Using an in vitro model, primary human lung fibroblasts were stimulated with biomass smoke extract (BME), specifically investigating hardwood and softwood types, and human rhinovirus-16 for 24 h. Production of pro-inflammatory mediators, such as IL-6 and IL-8, were measured via ELISA. Firstly, we found that hardwood and softwood smoke extract (1%) up-regulate IL-6 and IL-8 release (p ≤ 0.05). In addition, human rhinovirus-16 further increased biomass smoke-induced IL-8 in fibroblasts, in comparison to the two stimulatory agents alone. We also investigated the effect of biomass smoke on viral susceptibility by measuring viral load, and found no significant changes between BME exposed and non-exposed infected fibroblasts. Activated signaling pathways for IL-6 and IL-8 production by BME stimulation were examined using signaling pathway inhibitors. p38 MAPK inhibitor SB239063 significantly attenuated IL-6 and IL-8 release the most (p ≤ 0.05). This study demonstrated that biomass smoke can modulate rhinovirus-induced inflammation during infection, which can alter the severity of the disease. The mechanism by which biomass smoke exposure...

Cardoso, BR, Busse, AL, Hare, DJ, Cominetti, C, Horst, MA, McColl, G, Magaldi, RM, Jacob-Filho, W & Cozzolino, SMF 2016, 'Pro198Leu polymorphism affects the selenium status and GPx activity in response to Brazil nut intake', Food & Function, vol. 7, no. 2, pp. 825-833.
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Selenoproteins play important roles in antioxidant mechanisms, but it is hypothesised that single polymorphism nucleotides (SNPs) may affect their function.

Carney, RL, Seymour, JR, Westhorpe, D & Mitrovic, SM 2016, 'Lotic bacterioplankton and phytoplankton community changes under dissolved organic-carbon amendment: evidence for competition for nutrients', Marine and Freshwater Research, vol. 67, no. 9, pp. 1362-1362.
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During periods of low river discharge, bacterial growth is typically limited by dissolved organic carbon (DOC) and is tightly regulated by phytoplankton production. However, import of allochthonous DOC into rivers by freshwater inflows may diminish bacterial reliance on phytoplankton-produced carbon, leading to competition for nitrogen (N) and phosphorus (P). To investigate phytoplankton–bacterial competition in response to allochthonous inputs, we conducted a mesocosm experiment, comparing microbial responses to the following two manipulation treatments: (1) addition of N and P, and (2) addition of a DOC and N and P. Measurement of chlorophyll-a estimated phytoplankton biomass and microscopic counts were performed to discriminate community change. Bacterial abundance was tracked using flow cytometry and community assemblages were characterised using automated ribosomal intergenic spacer analyses and 16S rRNA-amplicon sequencing. We found that bacterial abundance increased in the leachate addition, whereas chlorophyll-a was reduced and the bacterial community shifted to one dominated by heterotrophic genera, and autotrophic microbes including Synechococcus and Cyclotella increased significantly in the nutrient treatment. These observations indicated that DOC and nutrient inputs can lead to shifts in the competitive dynamics between bacteria and phytoplankton, reducing phytoplankton biomass, which may potentially shift the major pathway of carbon to higher trophic organisms, from the phytoplankton grazer chain to the microbial food web.

Carter, DA, Blair, SE, Cokcetin, NN, Bouzo, D, Brooks, P, Schothauer, R & Harry, EJ 2016, 'Therapeutic Manuka Honey: No Longer So Alternative', Frontiers in Microbiology, vol. 7, no. APR.
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© 2016 Carter, Blair, Cokcetin, Bouzo, Brooks, Schothauer and Harry. Medicinal honey research is undergoing a substantial renaissance. From a folklore remedy largely dismissed by mainstream medicine as 'alternative', we now see increased interest by scientists, clinical practitioners and the general public in the therapeutic uses of honey. There are a number of drivers of this interest: First, the rise in antibiotic resistance by many bacterial pathogens has prompted interest in developing and using novel antibacterials; second, an increasing number of reliable studies and case reports have demonstrated that certain honeys are very effective wound treatments; third, therapeutic honey commands a premium price, and the honey industry is actively promoting studies that will allow it to capitalize on this; and finally, the very complex and rather unpredictable nature of honey provides an attractive challenge for laboratory scientists. In this paper we review manuka honey research, from observational studies on its antimicrobial effects through to current experimental and mechanistic work that aims to take honey into mainstream medicine. We outline current gaps and remaining controversies in our knowledge of how honey acts, and suggest new studies that could make honey a no longer 'alternative' alternative.

Carter, DJ, Brown, J & Rahmani, A 2016, 'Reading the High Court at a Distance: Topic Modelling the Legal Subject Matter and Judicial Activity of the High Court of Australia, 1903–2015', Carter, DJ, Brown, J & Rahmani, A 2016, 'Reading the High Court at a Distance: Topic Modelling the Legal Subject Matter And Judicial Activity of the High Court of Australia, 1903–2015', University of New South Wales Law Journal, vol. 39, no. 4, pp. 1300-1354.
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In this article we apply the method of quantitative textual analysis known as ‘topic modelling’ to a significant Australian legal text corpus: that of judgments of the High Court of Australia from 1903 to 2015. The High Court of Australia has been a perennial topic for study and analysis. It is the highest court in the Australian judicial hierarchy and the site of many of the most significant contests of legal doctrine and practice in Australian history. We find that the topic models generated by this research enable the development of a range of unique, novel and robust observations of the High Court’s judicial workload and the shifting make-up of its legal subject matter over time. Moreover, this article reveals the feasibility and value of topic modelling as a method for the study of legal texts and practices that might fruitfully complement other methods of legal scholarship.

Castorina, A, Loreto, C, Vespasiani, G, Giunta, S, Musumeci, G, Castorina, S, Basic, D & Sansalone, S 2016, 'Increased aquaporin 1 expression in the tunica albuginea of Peyronie's disease patients: an in vivo pilot study.', Histol Histopathol, vol. 31, no. 11, pp. 1241-1249.
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Peyronie's disease (PD) is a localized disorder of the connective tissue of the tunica albuginea (TA) whose etiology has not been elucidated. Although several studies have implicated genetic susceptibility and/or mechanical trauma as triggering events for PD, the underlying molecular mechanisms remain largely unknown. Aquaporin 1 (AQP1) is a water channel protein potentially implicated in connective tissue resistance to mechanical stress, acting primarily by increasing tension within the collagen network. Although it represents a potentially attractive molecular target in PD, to date no studies had ever addressed whether AQP1 is detectable and/or differentially expressed in the TA of these patients. Herein the present study, through immunohistochemical and biochemical approaches, we were able to detect AQP1 expression in the TA of control and PD affected patients. We demonstrated that AQP1-like immunoreactivity and expression are significantly increased in plaques of PD patients Vs controls, implying that AQP1 overexpression might be the consequence of a localized maladaptive response of the connective tissue to repeated mechanical trauma. In summary, these data support the idea that AQP1 might represent a potentially useful biomarker of mechanical injury in the TA and a promising target for the treatment of PD.

Cawley, A, Pasin, D, Ganbat, N, Ennis, L, Smart, C, Greer, C, Keledjian, J, Fu, S & Chen, A 2016, 'The potential for complementary targeted/non-targeted screening of novel psychoactive substances in equine urine using liquid chromatography-high resolution accurate mass spectrometry', Analytical Methods, vol. 8, no. 8, pp. 1789-1797.
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The use of LC-HRAM spectrometry to identify ‘unknown’ compounds by non-targeted screening provides a potential advantage for forensic toxicology.

Cawley, AT, Blakey, K, Waller, CC, McLeod, MD, Boyd, S, Heather, A, McGrath, KC, Handelsman, DJ & Willis, AC 2016, 'Detection and metabolic investigations of a novel designer steroid: 3‐chloro‐17α‐methyl‐5α‐androstan‐17β‐ol', Drug Testing and Analysis, vol. 8, no. 7, pp. 621-632.
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In 2012, seized capsules containing white powder were analyzed to show the presence of unknown steroid‐related compounds. Subsequent gas chromatography–mass spectrometry (GC‐MS) and nuclear magnetic resonance (NMR) investigations identified a mixture of 3α‐ and 3β‐ isomers of the novel compound; 3‐chloro‐17α‐methyl‐5α‐androstan‐17β‐ol. Synthesis of authentic reference materials followed by comparison of NMR, GC‐MS and gas chromatography‐tandem mass spectrometry (GC‐MS/MS) data confirmed the finding of a new ‘designer’ steroid. Furthermore, in vitro androgen bioassays showed potent activity highlighting the potential for doping using this steroid. Due to the potential toxicity of the halogenated steroid, in vitro metabolic investigations of 3α‐chloro‐17α‐methyl‐5α‐androstan‐17β‐ol using equine and human S9 liver fractions were performed. For equine, GC‐MS/MS analysis identified the diagnostic 3α‐chloro‐17α‐methyl‐5α‐androstane‐16α,17β‐diol metabolite. For human, the 17α‐methyl‐5α‐androstane‐3α,17β‐diol metabolite was found. Results from these studies were used to verify the ability of GC‐MS/MS precursor‐ion scanning techniques to support untargeted detection strategies for designer steroids in anti‐doping analyses. Copyright © 2015 John Wiley & Sons, Ltd.

Chan, D, Barratt, J, Roberts, T, Phillips, O, Šlapeta, J, Ryan, U, Marriott, D, Harkness, J, Ellis, J & Stark, D 2016, 'Detection of Dientamoeba fragilis in animal faeces using species specific real time PCR assay', Veterinary Parasitology, vol. 227, pp. 42-47.
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© 2016 Elsevier B.V. Dientamoeba fragilis is a potentially pathogenic, enteric, protozoan parasite with a worldwide distribution. While clinical case reports and prevalence studies appear regularly in the scientific literature, little attention has been paid to this parasite's biology, life cycle, host range, and possible transmission routes. Overall, these aspects of Dientamoeba biology remain poorly understood at best. In this study, a total of 420 animal samples, collected from Australia, were surveyed for the presence of Dientamoeba fragilis using PCR. Several PCR assays were evaluated for sensitivity and specificity. Two previously published PCR methods demonstrated cross reactivity with other trichomonads commonly found in animal samples. Only one assay exhibited excellent specificity. Using this assay D. fragilis was detected from one dog and one cat sample. This is the first report of D. fragilis from these animals and highlights the role companion animals may play in D. fragilis transmission. This study demonstrated that some published D. fragilis molecular assays cross react with other closely related trichomonads and consequently are not suitable for animal prevalence studies.

Chan, L & Platen, E 2016, 'Pricing of long dated equity-linked life insurance contracts', STOCHASTIC ANALYSIS AND APPLICATIONS, vol. 34, no. 2, pp. 339-355.
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This article adopts an approach to pricing of equity-linked life insurance contracts, which only requires the existence of the numéraire portfolio. An equity-linked life insurance contract is equivalent to a sum of the guaranteed amount and the value of an option on the equity index with some mortality risk attached. The numéraire portfolio equals the growth optimal portfolio and is used as numéraire or benchmark, where the real-world probability measure is taken as pricing measure. To obtain tractable solutions the short rate is modelled as a quadratic form of some Gaussian factor processes. Furthermore, the dynamics of the mortality rate is modelled as a threshold life table. The dynamics of the discounted equity market index or benchmark is modelled by a time transformed squared Bessel process. The equity-linked life insurance contracts are evaluated analytically.

Chan, YL, Saad, S, Al‐Odat, I, Zaky, AA, Oliver, B, Pollock, C, Li, W, Jones, NM & Chen, H 2016, 'Impact of maternal cigarette smoke exposure on brain and kidney health outcomes in female offspring', Clinical and Experimental Pharmacology and Physiology, vol. 43, no. 12, pp. 1168-1176.
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SummaryIncreased oxidative stress in the brain can lead to increased sympathetic tone that may further induce kidney dysfunction. Previously we have shown that maternal cigarette smoke exposure (SE) leads to significantly increased oxidative stress and inflammation in both brain and kidney, as well as reduced brain and kidney mitochondrial activity. This is closely associated with significant kidney underdevelopment and abnormal function in adulthood in the male offspring. This study aimed to investigate the impact of maternal SE on brain and kidney health in the female offspring. In this study, the mouse dams were exposed to two cigarettes, twice daily for 6 weeks prior to gestation, during pregnancy and lactation. Brains and kidneys from the female offspring were collected at 20 days (P20) and 13 weeks (W13) and were subject to further analysis. We found that mRNA expression of brain inflammatory markers interleukin‐1 receptor and Toll‐like receptor 4 were significantly increased in the SE offspring at both P20 and W13. Their brain mitochondrial activity markers were however increased at W13 with increased antioxidant activity. Kidney development and function in the female SE offspring were not different from the control offspring. We concluded that although brain inflammatory markers were upregulated in the SE female offspring, they were protected from some of the indicators of brain oxidative stress, such as endogenous antioxidant and mitochondrial dysfunction, as well as abnormal kidney development and function in adulthood.

Chan, YL, Saad, S, Pollock, C, Oliver, B, Al-Odat, I, Zaky, AA, Jones, N & Chen, H 2016, 'Impact of maternal cigarette smoke exposure on brain inflammation and oxidative stress in male mice offspring', Scientific Reports, vol. 6, no. 1.
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AbstractMaternal cigarette smoke exposure (SE) during gestation can cause lifelong adverse effects in the offspring’s brain. Several factors may contribute including inflammation, oxidative stress and hypoxia, whose changes in the developing brain are unknown. Female Balb/c mice were exposed to cigarette smoke prior to mating, during gestation and lactation. Male offspring were studied at postnatal day (P) 1, P20 and 13 weeks (W13). SE dams had reduced inflammatory mediators (IL-1β, IL-6 and toll like receptor (TLR)4 mRNA), antioxidant (manganese superoxide dismutase (MnSOD)) and increased mitochondrial activities (OXPHOS-I, III and V) and protein damage marker nitrotyrosine. Brain hypoxia-inducible factor (HIF)1α and its upstream signalling molecule early growth response factor (EGR)1 were not changed in the SE dams. In the SE offspring, brain IL-1R, IL-6 and TLR4 mRNA were increased at W13. The translocase of outer mitochondrial membrane and MnSOD were reduced at W13 with higher nitrotyrosine staining. HIF-1α was also increased at W13, although EGR1 was only reduced at P1. In conclusion, maternal SE increased markers of hypoxia and oxidative stress with mitochondrial dysfunction and cell damage in both dams and offspring and upregulated inflammatory markers in offspring, which may render SE dams and their offspring vulnerable to additional brain insults.

Charoensuk, T, Sirisathitkul, C, Boonyang, U, Macha, IJ, Santos, J, Grossin, D & Ben-Nissan, B 2016, 'In vitro bioactivity and stem cells attachment of three-dimensionally ordered macroporous bioactive glass incorporating iron oxides', JOURNAL OF NON-CRYSTALLINE SOLIDS, vol. 452, pp. 62-73.
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Chartrand, KM, Bryant, CV, Carter, AB, Ralph, PJ & Rasheed, MA 2016, 'Light Thresholds to Prevent Dredging Impacts on the Great Barrier Reef Seagrass, Zostera muelleri ssp. capricorni', Frontiers in Marine Science, vol. 3, no. JUL, pp. 1-17.
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© 2016 Chartrand, Bryant, Carter, Ralph and Rasheed. Coastal seagrass habitats are at risk from a range of anthropogenic activities that modify the natural light environment, including dredging activities associated with coastal and port developments. On Australia's east coast, the tropical seagrass Zostera muelleri ssp. capricorni dominates intertidal mudbanks in sheltered embayments which are also preferred locations for harbors and port facilities. Dredging to establish and maintain shipping channels in these areas can degrade water quality and diminish light conditions that are required for seagrass growth. Based on this potential conflict, we simulated in-situ light attenuation events to measure effects on Z. muelleri ssp. capricorni condition. Semi-annual in situ shading studies conducted over 3 years were used to quantify the impact of prolonged light reduction on seagrass morphometrics (biomass, percent cover, and shoot density). Experimental manipulations were complimented with an assessment of 46 months of light history and concurrent natural seagrass change at the study site in Gladstone Harbour. There was a clear light-dependent effect on seagrass morphometrics during seagrass growing seasons, but no effect during senescent periods. Significant seagrass declines occurred between 4 and 8 weeks after shading during the growing seasons with light maintained in the range of 4-5 mol photons m-2 d-1. Sensitivity to shading declined when applied in 2-week intervals (fortnightly) rather than continuous over the same period. Field observations were correlated to manipulative experiments to derive an applied threshold of 6 mol photons m-2 d-1 which formed the basis of a reactive light-based management strategy which has been successfully implemented to ensure positive ecological outcomes for seagrass during a large-scale dredging program.

Chatterjee, N, Chen, Y-H, Maas, P & Carroll, RJ 2016, 'Constrained Maximum Likelihood Estimation for Model Calibration Using Summary-Level Information From External Big Data Sources', Journal of the American Statistical Association, vol. 111, no. 513, pp. 107-117.
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© 2016 American Statistical Association. Information from various public and private data sources of extremely large sample sizes are now increasingly available for research purposes. Statistical methods are needed for using information from such big data sources while analyzing data from individual studies that may collect more detailed information required for addressing specific hypotheses of interest. In this article, we consider the problem of building regression models based on individual-level data from an “internal” study while using summary-level information, such as information on parameters for reduced models, from an “external” big data source. We identify a set of very general constraints that link internal and external models. These constraints are used to develop a framework for semiparametric maximum likelihood inference that allows the distribution of covariates to be estimated using either the internal sample or an external reference sample. We develop extensions for handling complex stratified sampling designs, such as case-control sampling, for the internal study. Asymptotic theory and variance estimators are developed for each case. We use simulation studies and a real data application to assess the performance of the proposed methods in contrast to the generalized regression calibration methodology that is popular in the sample survey literature. Supplementary materials for this article are available online.

Chavez-Dozal, AA, Nourabadi, N, Erken, M, McDougald, D & Nishiguchi, MK 2016, 'Comparative analysis of quantitative methodologies for Vibrionaceae biofilms', Folia Microbiologica, vol. 61, no. 6, pp. 449-453.
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© 2016, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. Multiple symbiotic and free-living Vibrio spp. grow as a form of microbial community known as a biofilm. In the laboratory, methods to quantify Vibrio biofilm mass include crystal violet staining, direct colony-forming unit (CFU) counting, dry biofilm cell mass measurement, and observation of development of wrinkled colonies. Another approach for bacterial biofilms also involves the use of tetrazolium (XTT) assays (used widely in studies of fungi) that are an appropriate measure of metabolic activity and vitality of cells within the biofilm matrix. This study systematically tested five techniques, among which the XTT assay and wrinkled colony measurement provided the most reproducible, accurate, and efficient methods for the quantitative estimation of Vibrionaceae biofilms.

Chen, C, Cleverly, J, Zhang, L, Yu, Q & Eamus, D 2016, 'Modelling Seasonal and Inter-annual Variations in Carbon and Water Fluxes in an Arid-Zone Acacia Savanna Woodland, 1981-2012', ECOSYSTEMS, vol. 19, no. 4, pp. 625-644.
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© 2016, Springer Science+Business Media New York. Changes in climatic characteristics such as seasonal and inter-annual variability may affect ecosystem structure and function, hence alter carbon and water budgets of ecosystems. Studies of modelling combined with field experiments can provide essential information to investigate interactions between carbon and water cycles and climate. Here we present a first attempt to investigate the long-term climate controls on seasonal patterns and inter-annual variations in water and carbon exchanges in an arid-zone savanna-woodland ecosystem using a detailed mechanistic soil–plant–atmosphere model (SPA), driven by leaf area index (LAI) simulated by an ecohydrological model (WAVES) and observed climate data during 1981–2012. The SPA was tested against almost 3 years of eddy covariance flux measurements in terms of gross primary productivity (GPP) and evapotranspiration (ET). The model was able to explain 80 and 71% of the variability of observed daily GPP and ET, respectively. Long-term simulations showed that carbon accumulation rates and ET ranged from 20.6 g C m−2 mon−1 in the late dry season to 45.8 g C m−2 mon−1 in the late wet season, respectively, primarily driven by seasonal variations in LAI and soil moisture. Large climate variations resulted in large seasonal variation in ecosystem water-use efficiency (eWUE). Simulated annual GPP varied between 146.4 and 604.7 g C m−2 y−1. Variations in annual ET coincided with that of GPP, ranging from 110.2 to 625.8 mm y−1. Annual variations in GPP and ET were driven by the annual variations in precipitation and vapour pressure deficit (VPD) but not temperature. The linear coupling of simulated annual GPP and ET resulted in eWUE having relatively small year-to-year variation.

Chen, H, Chan, YL, Nguyen, LT, Mao, Y, de Rosa, A, Beh, IT, Chee, C, Oliver, B, Herok, G, Saad, S & Gorrie, C 2016, 'Moderate traumatic brain injury is linked to acute behaviour deficits and long term mitochondrial alterations', Clinical and Experimental Pharmacology and Physiology, vol. 43, no. 11, pp. 1107-1114.
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SummaryTraumatic brain injury (TBI) remains one of the leading causes of death and disability worldwide. Mild TBI may lead to neuropsychiatric sequelae, including memory loss and motor impairment. Mitochondrial dysfunction and oxidative stress have a contributory role in several neurological disorders; however, their association with mitophagy in mild TBI is unclear. TBI was induced in female Sprague Dawley (SD) rats using a New York University Impactor (10 g, impactor head 2.5 mm diameter, weight drop 50 mm) and compared to sham surgery controls. The novel object recognition and error ladder tests were performed at 24 hours and for 6 weeks post injury, and the brains were examined histologically to confirm the extent of injury. Mitochondria manganese superoxide dismutase (MnSOD) and the oxidative phosphorylation (OXPHOS) complexes I‐V (CI‐CV), as well as mitophagy markers, dynamin related protein 1 (DRP‐1), LC3A/B and PTEN‐induced putative kinase 1 (PINK‐1), were measured in the penumbra by western blot. At 24 hours sham rats performed as expected on a novel object recognition test while TB...

Chen, H, Kelly, M, Hayes, C, van Reyk, D & Herok, G 2016, 'The use of simulation as a novel experiential learning module in undergraduate science pathophysiology education', ADVANCES IN PHYSIOLOGY EDUCATION, vol. 40, no. 3, pp. 335-341.
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© 2016 The American Physiological Society. Teaching of pathophysiology concepts is a core feature in health professional programs, but it can be challenging in undergraduate medical/biomedical science education, which is often highly theoretical when delivered by lectures and pen-and-paper tutorials. Authentic case studies allow students to apply their theoretical knowledge but still require good imagination on the part of the students. Lecture content can be reinforced through practical learning experiences in clinical environments. In this study, we report a new approach using clinical simulation within a Human Pathophysiology course to enable undergraduate science students to see 'pathophysiology in action' in a clinical setting. Students role played health professionals, and, in these roles, they were able to interact with each other and the manikin 'patient,' take a medical history, perform a physical examination and consider relevant treatments. Evaluation of students' experiences suggests that using clinical simulation to deliver case studies is more effective than traditional paper-based case studies by encouraging active learning and improving the understanding of physiological concepts.

Chen, J, Loyeung, B, Zaslawski, C, Liang, F-R & Li, W-H 2016, 'Comparison of traditional Chinese medicine education between mainland China and Australia—a case study', Journal of Integrative Medicine, vol. 14, no. 4, pp. 291-296.
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OBJECTIVE: To analyze and compare the curriculum and delivery of a Chinese and Australian university-level Chinese medicine program. METHODS: A review of PubMed and the Chinese National Knowledge Infrastructure for relevant educational papers was undertaken. Online and paper documents available at the University of Technology Sydney (UTS) and the Chengdu University of Traditional Chinese Medicine (CDUTCM) were read and analyzed. In addition, in-depth interviews with academics from the two universities were conducted during 2014 to 2015. RESULTS: The two Chinese medicine programs share the common goal of providing health services to the local community, but differ in some aspects when the curricula are compared. Areas such as student profile, curriculum structure, teaching approaches and education quality assurance were found to be different. The UTS program adopts a 'flipped learning' approach with the use of educational technology aiming at improving learning outcomes. On the other hand, the CDUTCM has better clinical facilities and specialist physician resources. CONCLUSION: A better understanding of the different curricula and approaches to Chinese medicine education will facilitate student learning and educational outcomes.

Chen, P, Zhong, Z, Jia, H, Zhou, J, Han, J, Liu, X & Qiu, J 2016, 'Magnetic field enhanced upconversion luminescence and magnetic–optical hysteresis behaviors in NaYF₄: Yb, Ho nanoparticles', RSC Advances, vol. 6, no. 9, pp. 7391-7395.
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A magnetic field induces the enhancement of upconversion luminescence and magnetic–optical hysteresis behaviors in NaYF₄: 20% Yb, 1% Ho nanoparticles.

Chen, S, Ao, Z, Sun, B, Xie, X & Wang, G 2016, 'Porous carbon nanocages encapsulated with tin nanoparticles for high performance sodium-ion batteries', Energy Storage Materials, vol. 5, pp. 180-190.
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© 2016 Sodium-ion batteries (SIBs) are recognized as an alternative to lithium ion batteries due to the abundance of sodium and potentially low cost of the whole battery system. One of the major challenges facing SIBs is to develop suitable anode materials with high capacity and long cycling life. Herein, we report the synthesis of porous carbon nanocage-Sn (PCNCs-Sn) nanocomposites as anodes of SIBs, demonstrating a high capacity of 828 mAh g−1 at 40 mA g−1. The electrodes also exhibited good rate capabilities (up to 3C) and superior cycling performances (1000 cycles). Post-mortem analyses verified the efficient volume change restriction by carbon nanocages and the well-preserved porous structure. Theoretical calculations indicated that the pulverization of bare Sn electrodes could be ascribed to strong bonds formed between amorphous carbon and the discharge product (Na15Sn4), which also deteriorated the conductivity. In contrast, the relatively weak interaction between Na15Sn4 and graphitic carbon can maintain superior conductivity and structural stability for better cycling performance.

Chew, SC, Kundukad, B, Teh, WK, Doyle, P, Yang, L, Rice, SA & Kjelleberg, S 2016, 'Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers', Soft Matter, vol. 12, no. 23, pp. 5224-5232.
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Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments.

Choi, S, Tran, TT, Elbadawi, C, Lobo, C, Wang, X, Juodkazis, S, Seniutinas, G, Toth, M & Aharonovich, I 2016, 'Engineering and Localization of Quantum Emitters in Large Hexagonal Boron Nitride Layers', ACS APPLIED MATERIALS & INTERFACES, vol. 8, no. 43, pp. 29642-29648.
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Hexagonal boron nitride is a wide-band-gap van der Waals material that has recently emerged as a promising platform for quantum photonics experiments. In this work, we study the formation and localization of narrowband quantum emitters in large flakes (up to tens of micrometers wide) of hexagonal boron nitride. The emitters can be activated in as-grown hexagonal boron nitride by electron irradiation or high-temperature annealing, and the emitter formation probability can be increased by ion implantation or focused laser irradiation of the as-grown material. Interestingly, we show that the emitters are always localized at the edges of the flakes, unlike most luminescent point defects in three-dimensional materials. Our results constitute an important step on the roadmap of deploying hexagonal boron nitride in nanophotonics applications.

Choi, V, Cobbin, D & Walsh, S 2016, 'Revisiting the Zhen Jiu Jia Yi Jing: Differential Diagnostic Indications Related to the LI Channel Acupoint Sequence', Medical Acupuncture, vol. 28, no. 3, pp. 148-155.
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Background: Huang-Fu Mi’s Jia Yi Jing (JYJ) is regarded as the earliest text (282 AD) on differential diagnosis and clinical acumoxa therapy in Chinese Medicine (CM). Objective: Within this Classical framework, this study examined CM clinical indications for the 20 Large Intestine (LI) channel points for evidence of possible sequence-associated patterns. Materials and Methods: The JYJ detailed the systematic definition and grouping of all acupoints termed ‘‘Ruling Points’’ (RPs) in relation to their unique patterns of signs and symptoms (‘‘RP indications’’), rather than as channel-specific lists. The JYJ includes comprehensive descriptions for RP indications for hundreds of clinical patterns for all channel acupoints, systematically categorized across six differential diagnostic books (Seven to Twelve). Two editions of the Zhen Jiu Jia Yi Jing (ZJJYJ) were scrutinized to identify all RPs for the LI channel sequence: the Song Dynasty Chinese edition (1077) and the English translation The Systematic Classic of Acupuncture and Moxibustion (1994) translated by Yang and Chace. RP indications for each acupoint were coded by ZJJYJ diagnostic Book and Chapter Part and examined for relationships between sequence position and diagnostic category of individual RP indications. Results: While no single category of CM indications based on the RP diagnostic system, was common to all 19 points, there were at least seven patterns involving clusters of RP indications associated with sequence posi-tions. Most important were the first 7 acupoints together with LI 11. These contributed 49 of the 61 RPs channel points, with indications drawn from all six diagnostic Books. Overall, the RP indications for the channel focused primarily on the head and neck, as well as on generalized fever and upper-limb pain and weakness. The most frequent diagnostic indications for the channel came from diagnostic Book Twelve (head and neck) with 24 RPs being identified for 12 LI acupoints. Conclusions:...

Chou, J, Ito, T, Otsuka, M, Ben-Nissan, B & Milthorpe, B 2016, 'The effectiveness of the controlled release of simvastatin from β-TCP macrosphere in the treatment of OVX mice', Journal of Tissue Engineering and Regenerative Medicine, vol. 10, no. 3, pp. E195-E203.
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Simvastatin, a cholesterol treatment drug, has been shown to stimulate bone regeneration. As such, there has been an increase interest in the development of suitable materials and systems for the delivery of simvastatin. Without the appropriate dosage of simvastatin, the therapeutic effects on bone growth will be significantly reduced. Furthermore, similar to many pharmaceutical compounds, at high concentration simvastatin can cause various adverse side-effects. Given the associated side-effects with the usage of simvastatin, the development of suitable controlled drug release system is pertinent. Calcium phosphate in particularly beta-tricalcium phosphate (β-TCP) has been extensively studied and used as a carrier material for drug delivery system. In this study, Foraminifera exoskeletons were used as calcium carbonate precursor materials, which were hydrothermally converted to β-TCP as a carrier material for simvastatin. Natural marine exoskeletons posses interconnected and uniformly porous network capable of improving drug loading and release rate. To prolong the release of simvastatin, an apatite coating was made around the β-TCP sample and in vitro release studies in simulated body fluid (SBF) showed a significant decrease in release rate. Osteoporotic mice were used to examine the compare therapeutic effectiveness of β-TCP, β-TCP with simvastatin, apatite-coated β-TCP with simvastatin and direct injection of simvastatin near the right femur of the mice. Localized and systemic effect were compared with the femur of the non-implanted side (left) and showed that β-TCP with or without simvastatin was able to induce significant bone formation over 6 weeks. Mechanical analysis showed that apatite-coated β-TCP with simvastatin produced significantly stronger bones compared with other experimental groups. This study shows that natural exoskeletons with the appropriate structure can be successfully used as a drug delivery system for simvastatin and can its release ca...

Chou, J, Komuro, M, Hao, J, Kuroda, S, Hattori, Y, Ben‐Nissan, B, Milthorpe, B & Otsuka, M 2016, 'Bioresorbable zinc hydroxyapatite guided bone regeneration membrane for bone regeneration', Clinical Oral Implants Research, vol. 27, no. 3, pp. 354-360.
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AbstractObjectivesThe aim of this study was to investigate the bone regenerative properties of a heat treated cross‐linkedGBRmembrane with zinc hydroxyapatite powders in the rat calvarial defect model over a 6‐week period.Material and MethodsIn vitrophysio‐chemical characterization involved X‐ray diffraction analysis, surface topology by scanning electron microscopy, and zinc release studies in physiological buffers. Bilateral rat calvarial defects were used to compare the Zn‐HAp membranes against the commercially available collagen membranes and the unfilled defect group through radiological and histological evaluation.ResultsThe synthesized Zn‐MEM(100 μm thick) showed no zinc ions released in the phosphate buffer solution (PBS) buffer, but zinc was observed under acidic conditions. At 6 weeks, both the micro‐CTand histological analyses revealed that the Zn‐MEMgroup yielded significantly greater bone formation with 80 ± 2% of bone filled, as compared with 60 ± 5% in the collagen membrane and 40 ± 2% in the unfilled control group.ConclusionThis study demonstrated the use of heat treatment as an alternative method to cross‐linking the Zn‐MEMto be applied as aGBRmembrane. Its synthesis and ...

Chowdhury, PR, DeMaere, M, Chapman, T, Worden, P, Charles, IG, Darling, AE & Djordjevic, SP 2016, 'Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease', BMC MICROBIOLOGY, vol. 16, no. 1.
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© 2016 Roy Chowdhury et al. Background: Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfer and express clinically relevant levels of toxins has reinforced the need to characterise them genetically. In addition, further studies that examine the pathogenic potential of toxin-negative strains of C. difficile and the frequency by which toxin-negative strains may acquire the PaLoc are needed. Results: We undertook a comparative genomic analysis of five Australian toxin-negative isolates of C. difficile that lack tcdA, tcdB and both binary toxin genes cdtA and cdtB that were recovered from humans and farm animals with symptoms of gastrointestinal disease. Our analyses show that the five C. difficile isolates cluster closely with virulent toxigenic strains of C. difficile belonging to the same sequence type (ST) and have virulence gene profiles akin to those in toxigenic strains. Furthermore, phage acquisition appears to have played a key role in the evolution of C. difficile. Conclusions: Our results are consistent with the C. difficile global population structure comprising six clades each containing both toxin-positive and toxin-negative strains. Our data also suggests that toxin-negative strains of C. difficile encode a repertoire of putative virulence factors that are similar to those found in toxigenic strains of C. difficile, raising the possibility that acquisition of PaLoc by toxin-negative strains poses a thre...

Christensen, S, Grøftehauge, MK, Byriel, K, Huston, WM, Furlong, E, Heras, B, Martin, JL & McMahon, RM 2016, 'Structural and Biochemical Characterization of Chlamydia trachomatis DsbA Reveals a Cysteine-Rich and Weakly Oxidising Oxidoreductase', PLOS ONE, vol. 11, no. 12, pp. e0168485-e0168485.
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The Gram negative bacteria Chlamydia trachomatis is an obligate intracellular human pathogen that can cause pelvic inflammatory disease, infertility and blinding trachoma. C. trachomatis encodes a homolog of the dithiol oxidoreductase DsbA. Bacterial DsbA proteins introduce disulfide bonds to folding proteins providing structural bracing for secreted virulence factors, consequently these proteins are potential targets for antimicrobial drugs. Despite sharing functional and structural characteristics, the DsbA enzymes studied to date vary widely in their redox character. In this study we show that the truncated soluble form of the predicted membrane anchored protein C. trachomatis DsbA (CtDsbA) has oxidase activity and redox properties broadly similar to other characterized DsbA proteins. However CtDsbA is distinguished from other DsbAs by having six cysteines, including a second disulfide bond, and an unusual dipeptide sequence in its catalytic motif (Cys-Ser-Ala-Cys). We report the 2.7 Å crystal structure of CtDsbA revealing a typical DsbA fold, which is most similar to that of DsbA-II type proteins. Consistent with this, the catalytic surface of CtDsbA is negatively charged and lacks the hydrophobic groove found in EcDsbA and DsbAs from other enterobacteriaceae. Biochemical characterization of CtDsbA reveals it to be weakly oxidizing compared to other DsbAs and with only a mildly destabilizing active site disulfide bond. Analysis of the crystal structure suggests that this redox character is consistent with a lack of contributing factors to stabilize the active site nucleophilic thiolate relative to more oxidizing DsbA proteins.

Ciccone, N, West, D, Cream, A, Cartwright, J, Rai, T, Granger, A, Hankey, GJ & Godecke, E 2016, 'Constraint-induced aphasia therapy (CIAT): a randomised controlled trial in very early stroke rehabilitation', Aphasiology, vol. 30, no. 5, pp. 566-584.
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© 2015 Taylor & Francis. Background: Communication outcomes following stroke are improved when treatments for aphasia are administered early, within the first 3 months after stroke, and provided for more than 2 hours per week. However, uncertainty remains about the optimal type of aphasia therapy. Aims: We compared constraint-induced aphasia therapy (CIAT) with individual, impairment-based intervention, both administered early and daily after acute stroke. Methods&Procedures: This prospective, single-blinded, randomised, controlled trial recruited participants with mild to severe aphasia within 10 days of an acute stroke from acute/subacute Perth metropolitan hospitals (n = 20). Participants were allocated by computer-generated block randomisation method to either the CIAT (n = 12) or individual, impairment-based intervention group (n = 8) delivered at the same intensity (45–60 min, 5 days a week) for 20 sessions over 5 weeks (15–20 hours total). The primary outcome, measured after completing the intervention, was the Aphasia Quotient (AQ) from the Western Aphasia Battery. Secondary outcomes were the AQ at 12 and 26 weeks post stroke, a Discourse Analysis (DA) score and the Stroke and Aphasia Quality of Life Scale (SAQoL), measured at therapy completion, 12 and 26 weeks post stroke. There was a 10% (n = 2) dropout at the primary end point, both participants were in the CIAT group. The estimates for each treatment group were compared using repeated measures ANOVAs. Data from the 26-week follow-up assessment are presented, however, were not included in the between-group comparisons due to the low number of data points in each group. Outcomes & Results: Within groups analyses comparing performance at baseline, therapy completion, and 12 weeks post stroke revealed a statistically significant treatment effect for the AQ (p < .001), DA (p = .002), and SAQoL (p < .001). Between groups analysis found there was no significant difference between the CIAT and indi...

Cinner, JE, Huchery, C, MacNeil, MA, Graham, NAJ, McClanahan, TR, Maina, J, Maire, E, Kittinger, JN, Hicks, CC, Mora, C, Allison, EH, D'Agata, S, Hoey, A, Feary, DA, Crowder, L, Williams, ID, Kulbicki, M, Vigliola, L, Wantiez, L, Edgar, G, Stuart-Smith, RD, Sandin, SA, Green, AL, Hardt, MJ, Beger, M, Friedlander, A, Campbell, SJ, Holmes, KE, Wilson, SK, Brokovich, E, Brooks, AJ, Cruz-Motta, JJ, Booth, DJ, Chabanet, P, Gough, C, Tupper, M, Ferse, SCA, Sumaila, UR & Mouillot, D 2016, 'Bright spots among the world's coral reefs', NATURE, vol. 535, no. 7612, pp. 416-+.
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© 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Ongoing declines in the structure and function of the world's coral reefs require novel approaches to sustain these ecosystems and the millions of people who depend on them. A presently unexplored approach that draws on theory and practice in human health and rural development is to systematically identify and learn from the 'outliers' - places where ecosystems are substantially better ('bright spots') or worse ('dark spots') than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental conditions. We identify 15 bright spots and 35 dark spots among our global survey of coral reefs, defined as sites that have biomass levels more than two standard deviations from expectations. Importantly, bright spots are not simply comprised of remote areas with low fishing pressure; they include localities where human populations and use of ecosystem resources is high, potentially providing insights into how communities have successfully confronted strong drivers of change. Conversely, dark spots are not necessarily the sites with the lowest absolute biomass and even include some remote, uninhabited locations often considered near pristine. We surveyed local experts about social, institutional, and environmental conditions at these sites to reveal that bright spots are characterized by strong sociocultural institutions such as customary taboos and marine tenure, high levels of local engagement in management, high dependence on marine resources, and beneficial environmental conditions such as deep-water refuges. Alternatively, dark spots are characterized by intensive capture and storage technology and a recent history of environm...

Clarke, HJ, Howe, ENW, Wu, X, Sommer, F, Yano, M, Light, ME, Kubik, S & Gale, PA 2016, 'Transmembrane Fluoride Transport: Direct Measurement and Selectivity Studies', Journal of the American Chemical Society, vol. 138, no. 50, pp. 16515-16522.
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Cleverly, J, Eamus, D, Coupe, NR, Chen, C, Maes, WH, Li, L, Faux, R, Santini, NS, Rumman, R, Yu, Q & Huete, A 2016, 'Soil moisture controls on phenology and productivity in a semi-arid critical zone', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 568, pp. 1227-1237.
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© 2016 Elsevier B.V. The Earth's Critical Zone, where physical, chemical and biological systems interact, extends from the top of the canopy to the underlying bedrock. In this study, we investigated soil moisture controls on phenology and productivity of an Acacia woodland in semi-arid central Australia. Situated on an extensive sand plain with negligible runoff and drainage, the carry-over of soil moisture content (θ) in the rhizosphere enabled the delay of phenology and productivity across seasons, until conditions were favourable for transpiration of that water to prevent overheating in the canopy. Storage of soil moisture near the surface (in the top few metres) was promoted by a siliceous hardpan. Pulsed recharge of θ above the hardpan was rapid and depended upon precipitation amount: 150mm storm-1 resulted in saturation of θ above the hardpan (i.e., formation of a temporary, discontinuous perched aquifer above the hardpan in unconsolidated soil) and immediate carbon uptake by the vegetation. During dry and inter-storm periods, we inferred the presence of hydraulic lift from soil storage above the hardpan to the surface due to (i) regular daily drawdown of θ in the reservoir that accumulates above the hardpan in the absence of drainage and evapotranspiration; (ii) the dimorphic root distribution wherein most roots were found in dry soil near the surface, but with significant root just above the hardpan; and (iii) synchronisation of phenology amongst trees and grasses in the dry season. We propose that hydraulic redistribution provides a small amount of moisture that maintains functioning of the shallow roots during long periods when the surface soil layer was dry, thereby enabling Mulga to maintain physiological activity without diminishing phenological and physiological responses to precipitation when conditions were favourable to promote canopy cooling.

Cleverly, J, Eamus, D, Luo, Q, Coupe, NR, Kljun, N, Ma, X, Ewenz, C, Li, L, Yu, Q & Huete, A 2016, 'The importance of interacting climate modes on Australia's contribution to global carbon cycle extremes', SCIENTIFIC REPORTS, vol. 6.
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The global carbon cycle is highly sensitive to climate-driven fluctuations of precipitation, especially in the Southern Hemisphere. This was clearly manifested by a 20% increase of the global terrestrial C sink in 2011 during the strongest sustained La Niña since 1917. However, inconsistencies exist between El Niño/La Niña (ENSO) cycles and precipitation in the historical record; for example, significant ENSO-precipitation correlations were present in only 31% of the last 100 years, and often absent in wet years. To resolve these inconsistencies, we used an advanced temporal scaling method for identifying interactions amongst three key climate modes (El Niño, the Indian Ocean dipole, and the southern annular mode). When these climate modes synchronised (1999-2012), drought and extreme precipitation were observed across Australia. The interaction amongst these climate modes, more than the effect of any single mode, was associated with large fluctuations in precipitation and productivity. The long-term exposure of vegetation to this arid environment has favoured a resilient flora capable of large fluctuations in photosynthetic productivity and explains why Australia was a major contributor not only to the 2011 global C sink anomaly but also to global reductions in photosynthetic C uptake during the previous decade of drought.

Cleverly, J, Eamus, D, Van Gorsel, E, Chen, C, Rumman, R, Luo, Q, Coupe, NR, Li, L, Kljun, N, Faux, R, Yu, Q & Huete, A 2016, 'Productivity and evapotranspiration of two contrasting semiarid ecosystems following the 2011 global carbon land sink anomaly', AGRICULTURAL AND FOREST METEOROLOGY, vol. 220, pp. 151-159.
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© 2016 Elsevier B.V. Global carbon balances are increasingly affected by large fluctuations in productivity occurring throughout semiarid regions. Recent analyses found a large C uptake anomaly in 2011 in arid and semiarid regions of the southern hemisphere. Consequently, we compared C and water fluxes of two distinct woody ecosystems (a Mulga (Acacia) woodland and a Corymbia savanna) between August 2012 and August 2014 in semiarid central Australia, demonstrating that the 2011 anomaly was short-lived in both ecosystems. The Mulga woodland was approximately C neutral but with periods of significant uptake within both years. The extreme drought tolerance of Acacia is presumed to have contributed to this. By contrast, the Corymbia savanna was a very large net C source (130 and 200gCm-2yr-1 in average and below average rainfall years, respectively), which is likely to have been a consequence of the degradation of standing, senescent biomass that was a legacy of high productivity during the 2011 anomaly. The magnitude and temporal patterns in ecosystem water-use efficiencies (WUE), derived from eddy covariance data, differed across the two sites, which may reflect differences in the relative contributions of respiration to net C fluxes across the two ecosystems. In contrast, differences in leaf-scale measures of WUE, derived from 13C stable isotope analyses, were apparent at small spatial scales and may reflect the different rooting strategies of Corymbia and Acacia trees within the Corymbia savanna. Restrictions on root growth and infiltration by a siliceous hardpan located below Acacia, whether in the Mulga woodland or in small Mulga patches of the Corymbia savanna, impedes drainage of water to depth, thereby producing a reservoir for soil moisture storage under Acacia while acting as a barrier to access of groundwater by Corymbia trees in Mulga patches, but not in the open Corymbia savanna.

Clifton, LA, Ciesielski, F, Skoda, MWA, Paracini, N, Holt, SA & Lakey, JH 2016, 'The Effect of Lipopolysaccharide Core Oligosaccharide Size on the Electrostatic Binding of Antimicrobial Proteins to Models of the Gram Negative Bacterial Outer Membrane', Langmuir, vol. 32, no. 14, pp. 3485-3494.
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Cokcetin, NN, Pappalardo, M, Campbell, LT, Brooks, P, Carter, DA, Blair, SE & Harry, EJ 2016, 'The Antibacterial Activity of Australian Leptospermum Honey Correlates with Methylglyoxal Levels', PLOS ONE, vol. 11, no. 12, pp. e0167780-e0167780.
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© 2016 Cokcetin 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. Most commercially available therapeutic honey is derived from flowering Leptospermum scoparium (manuka) plants from New Zealand. Australia has more than 80 Leptospermum species, and limited research to date has found at least some produce honey with high nonperoxide antibacterial activity (NPA) similar to New Zealand manuka, suggesting Australia may have a ready supply of medical-grade honey. The activity of manuka honey is largely due to the presence of methylglyoxal (MGO), which is produced non-enzymatically from dihydroxyacetone (DHA) present in manuka nectar. The aims of the current study were to chemically quantify the compounds contributing to antibacterial activity in a collection of Australian Leptospermum honeys, to assess the relationship between MGO and NPA in these samples, and to determine whether NPA changes during honey storage. Eighty different Leptospermum honey samples were analysed, and therapeutically useful NPA was seen in samples derived from species including L. liversidgei and L. polygalifolium. Exceptionally high levels of up to 1100 mg/kg MGO were present in L. polygalifolium honey samples sourced from the Northern Rivers region in NSW and Byfield, QLD, with considerable diversity among samples. There was a strong positive relationship between NPA and MGO concentration, and DHA was present in all of the active honey samples, indicating a potential for ongoing conversion to MGO. NPA was stable, with most samples showing little change following seven years of storage in the dark at 4°C. This study demonstrates the potential for Australian Leptospermum honey as a wound care product, and argues for an extension of this analysis to other Leptospermum species.

Cole, AJ, Dwight, T, Gill, AJ, Dickson, K-A, Zhu, Y, Clarkson, A, Gard, GB, Maidens, J, Valmadre, S, Clifton-Bligh, R & Marsh, DJ 2016, 'Assessing mutant p53 in primary high-grade serous ovarian cancer using immunohistochemistry and massively parallel sequencing', Scientific Reports, vol. 6, no. 1.
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AbstractThe tumour suppressor p53 is mutated in cancer, including over 96% of high-grade serous ovarian cancer (HGSOC). Mutations cause loss of wild-type p53 function due to either gain of abnormal function of mutant p53 (mutp53), or absent to low mutp53. Massively parallel sequencing (MPS) enables increased accuracy of detection of somatic variants in heterogeneous tumours. We used MPS and immunohistochemistry (IHC) to characterise HGSOCs for TP53 mutation and p53 expression. TP53 mutation was identified in 94% (68/72) of HGSOCs, 62% of which were missense. Missense mutations demonstrated high p53 by IHC, as did 35% (9/26) of non-missense mutations. Low p53 was seen by IHC in 62% of HGSOC associated with non-missense mutations. Most wild-type TP53 tumours (75%, 6/8) displayed intermediate p53 levels. The overall sensitivity of detecting a TP53 mutation based on classification as ‘Low’, ‘Intermediate’ or ‘High’ for p53 IHC was 99%, with a specificity of 75%. We suggest p53 IHC can be used as a surrogate marker of TP53 mutation in HGSOC; however, this will result in misclassification of a proportion of TP53 wild-type and mutant tumours. Therapeutic targeting of mutp53 will require knowledge of both TP53 mutations and mutp53 expression.

Cole, VJ, Parker, LM, O’Connor, SJ, O’Connor, WA, Scanes, E, Byrne, M & Ross, PM 2016, 'Effects of multiple climate change stressors: ocean acidification interacts with warming, hyposalinity, and low food supply on the larvae of the brooding flat oyster Ostrea angasi', Marine Biology, vol. 163, no. 5.
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Ocean acidification, rising temperatures, and increased intensity of rain events are occurring due to climate change. Individually, each of these stressors has the potential to influence the growth and survival of many marine organisms, particularly during early development. Together the interactive and multiple impacts of elevated pCO2, temperature, and salinity may be exacerbated by a lack of food. Life history traits are important in determining the response of organisms to climate change. Larvae that develop within a brood chamber, such as the flat oyster, Ostrea angasi, may be pre-exposed to living a higher CO2 environment. This study determined the pH of the fluid surrounding the gills of adult oysters where larvae are brooded and investigated the interactive effects of the multiple climate-related stressors: ocean acidification, warming, hyposalinity, and reduced food availability, on development of O. angasi larvae. The fluid surrounding the larvae was of pH 7.88 ± 0.04, lower than that of surrounding sea water, and was significantly reduced (to pH 7.46 ± 0.05) when oysters remained closed as occurs in nature during periods of stress caused by low salinity. Elevated pCO2 [853–1194 µatm (pHNBS 7.79)] resulted in larvae being 3 % smaller, but it had no effect on the timing of progression through developmental stages, percentage of abnormalities, or survival of larvae. Exposure to elevated pCO2 together with increased temperature (+4 °C) or reduced salinity (20) had a negative effect on the time to the eyed larval stage and with an increase in the percentage of abnormal larvae. Unexpectedly, larvae did not meet their higher metabolic requirements to survive under elevated pCO2 by eating more. In a sublethal effect of elevated pCO2, larval feeding was impaired. We found that O. angasi larva were relatively resilient to elevated pCO2, a trait that may be due to the acclimatisation of hypercapnic conditions in the brood cavity or because they are rele...

Colley, B, Dederer, V, Carnell, M, Kjelleberg, S, Rice, SA & Klebensberger, J 2016, 'SiaA/D Interconnects c-di-GMP and RsmA Signaling to Coordinate Cellular Aggregation of Pseudomonas aeruginosa in Response to Environmental Conditions', Frontiers in Microbiology, vol. 7.
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Colwell, DB, El-Hassan, N & Kwon, OK 2016, 'Variance Minimizing Strategies for Stochastic Processes with Applications to Tracking Stock Indices', International Review of Finance.
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This paper extends the notion of variance optimal hedging of contingent claims under the incomplete market setting to the hedging of entire processes and applies the results to the problem of tracking stock indices. Sufficient conditions under which this is possible are given, along with the corresponding variance minimizing strategy. The performances of tracking error variance (TEV) minimizing, locally risk minimizing, and variance minimizing strategies in tracking stock indices are investigated using both simulated and historical market data. In particular, it is shown using S&P500 data over the period 2000 and 2015 that the TEV of the variance minimizing strategy is statistically lower than other strategies at the 95% confidence level for 6-month holding periods.

Combes, V, Latham, SL, Wen, B, Allison, AC & Grau, GER 2016, 'DIANNEXIN DOWN-MODULATES TNF-INDUCED ENDOTHELIAL MICROPARTICLE RELEASE BY BLOCKING MEMBRANE BUDDING PROCESS', International Journal of Innovative Medicine and Health Science, vol. 7, pp. 1-11.
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BACKGROUND: Microparticles are now recognised as true biological effectors with a role in immunopathology through their ability to disseminate functional properties. Diannexin, a homodimer of annexin V, binds to PS with a higher affinity and longer blood half-life than the monomer, inhibits prothrombinase complex activity thereby diminishing coagulation and reperfusion injury mediators and prevent microvesicle-mediated material transfer. Our aim was to determine if Diannexin could modulate microparticle production by endothelial cells by interacting with the phosphatidylserine exposure occurring during the release of these vesicles. RESULTS: In this study we showed that fluorescently labelled Diannexin binds to calcimycin-activated endothelial cells but not to resting cells. After overnight incubation, Diannexin enters cells and their released MP carry Diannexin. Some Diannexin seems to be processed via early endosomes and later is found in lysosomes. Both unlabelled Diannexin and fluorescent Diannexin inhibit MP release from TNF-activated endothelial cells. However, Diannexin treatment does not prevent endothelial activation by TNF. In addition, the inhibitory effect of Diannexin on MP release could be observed when cells were pre-, concomitantly or post-treated with cytokines. Scanning electron microscopy showed differences in the numbers and types of protuberances at the cell surface when cells were treated or not with Diannexin. Finally, there is no apparent congruency between fluorescent Diannexin labelling and surface protuberances as shown by correlative microscopy. CONCLUSIONS: Altogether these data suggest that Diannexin can inhibit endothelial vesiculation by binding PS present either at the cell surface or at the level of the inner leaflet of the plasma membrane.

Constantine, M, Liew, CK, Lo, V, Macmillan, A, Cranfield, CG, Sunde, M, Whan, R, Graham, RM & Martinac, B 2016, 'Heterologously-expressed and Liposome-reconstituted Human Transient Receptor Potential Melastatin 4 Channel (TRPM4) is a Functional Tetramer', SCIENTIFIC REPORTS, vol. 6.
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Corporal-Lodangco, IL, Leslie, LM & Lamb, PJ 2016, 'Impacts of ENSO on Philippine Tropical Cyclone Activity', Journal of Climate, vol. 29, no. 5, pp. 1877-1897.
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Abstract This study investigates the El Niño–Southern Oscillation (ENSO) contribution to Philippine tropical cyclone (TC) variability, for a range of quarterly TC metrics. Philippine TC activity is found to depend on both ENSO quarter and phase. TC counts during El Niño phases differ significantly from neutral phases in all quarters, whereas neutral and La Niña phases differ only in January–March and July–September. Differences in landfalls between neutral and El Niño phases are significant in January–March and October–December and in January–March for neutral and La Niña phases. El Niño and La Niña landfalls are significantly different in April–June and October–December. Philippine neutral and El Niño TC genesis cover broader longitude–latitude ranges with similar long tracks, originating farther east in the western North Pacific. In El Niño phases, the mean eastward displacement of genesis locations and more recurving TCs reduce Philippine TC frequencies. Proximity of La Niña TC genesis to the Philippines and straight-moving tracks in April–June and October–December increase TC frequencies and landfalls. Neutral and El Niño accumulated cyclone energy (ACE) values are above average, except in April–June of El Niño phases. Above-average quarterly ACE in neutral years is due to increased TC frequencies, days, and intensities, whereas above-average El Niño ACE in July–September is due to increased TC days and intensities. Below-average La Niña ACE results from fewer TCs and shorter life cycles. Longer TC durations produce slightly above-average TC days in July–September El Niño phases. Fewer TCs than neutral years, as well as shorter TC durations, imply less TC days in La Niña phases. However, above-average TC days occur in October–December as a result of higher TC frequencies.

Cramb, SM, Mengersen, KL, Lambert, PC, Ryan, LM & Baade, PD 2016, 'A flexible parametric approach to examining spatial variation in relative survival', Statistics in Medicine, vol. 35, no. 29, pp. 5448-5463.
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Most of the few published models used to obtain small‐area estimates of relative survival are based on a generalized linear model with piecewise constant hazards under a Bayesian formulation. Limitations of these models include the need to artificially split the time scale, restricted ability to include continuous covariates, and limited predictive capacity. Here, an alternative Bayesian approach is proposed: a spatial flexible parametric relative survival model. This overcomes previous limitations by combining the benefits of flexible parametric models: the smooth, well‐fitting baseline hazard functions and predictive ability, with the Bayesian benefits of robust and reliable small‐area estimates. Both spatially structured and unstructured frailty components are included. Spatial smoothing is conducted using the intrinsic conditional autoregressive prior. The model was applied to breast, colorectal, and lung cancer data from the Queensland Cancer Registry across 478 geographical areas. Advantages of this approach include the ease of including more realistic complexity, the feasibility of using individual‐level input data, and the capacity to conduct overall, cause‐specific, and relative survival analysis within the same framework. Spatial flexible parametric survival models have great potential for exploring small‐area survival inequalities, and we hope to stimulate further use of these models within wider contexts. Copyright © 2016 John Wiley & Sons, Ltd.

Cranfield, CG, Berry, T, Holt, SA, Hossain, KR, Le Brun, AP, Carne, S, Al Khamici, H, Coster, H, Valenzuela, SM & Cornell, B 2016, 'Evidence of the Key Role of H3O+ in Phospholipid Membrane Morphology', LANGMUIR, vol. 32, no. 41, pp. 10725-10734.
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© 2016 American Chemical Society. This study explains the importance of the phosphate moiety and H3O+ in controlling the ionic flux through phospholipid membranes. We show that despite an increase in the H3O+ concentration when the pH is decreased, the level of ionic conduction through phospholipid bilayers is reduced. By modifying the lipid structure, we show the dominant determinant of membrane conduction is the hydrogen bonding between the phosphate oxygens on adjacent phospholipids. The modulation of conduction with pH is proposed to arise from the varying H3O+ concentrations altering the molecular area per lipid and modifying the geometry of conductive defects already present in the membrane. Given the geometrical constraints that control the lipid phase structure of membranes, these area changes predict that organisms evolving in environments with different pHs will select for different phospholipid chain lengths, as is found for organisms near highly acidic volcanic vents (short chains) or in highly alkaline salt lakes (long chains). The stabilizing effect of the hydration shells around phosphate groups also accounts for the prevalence of phospholipids across biology. Measurement of ion permeation through lipid bilayers was made tractable using sparsely tethered bilayer lipid membranes with swept frequency electrical impedance spectroscopy and ramped dc amperometry. Additional evidence of the effect of a change in pH on lipid packing density is obtained from neutron reflectometry data of tethered membranes containing perdeuterated lipids.

Curtis, EM, Gollan, J, Murray, BR & Leigh, A 2016, 'Native microhabitats better predict tolerance to warming than latitudinal macro‐climatic variables in arid‐zone plants', Journal of Biogeography, vol. 43, no. 6, pp. 1156-1165.
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AbstractAimUnderstanding species ability to withstand heat stress is paramount for predicting their response to increasing temperatures and decreasing rainfall. Arid systems are subject to climatic extremes, where plants, being immobile, live on the frontline of climate change. Our aim was to investigate whether: (1) warming tolerance [WT = the difference between a species physiological thermal damage threshold (T50) and the maximum temperature within its distribution (Thab)] for desert plants is higher at high latitudes, as has been shown for terrestrial ectotherms, and (2) if T50 of desert plants better corresponds with broad climatic indicators or species native microhabitats.LocationThe Australian Arid Lands Botanic Garden, Port Augusta, South Australia.MethodsUsing chlorophyll fluorescence techniques, we measured T50 for 42 Australian arid plant species native to different microhabitats based on water availability. WT was calculated (T50−Thab) and each metric was compared against microhabitat and broad‐scale climatic variables for each species.ResultsT50 was unrelated to macro‐scale climate or latitude, whereas WT increased for species whose distributions extend into higher latitudes,...

Cwiklinski, K, O'Neill, SM, Donnelly, S & Dalton, JP 2016, 'A prospective view of animal and human Fasciolosis', PARASITE IMMUNOLOGY, vol. 38, no. 9, pp. 558-568.
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© 2016 The Authors. Parasite Immunology Published by John Wiley & Sons Ltd. Fasciolosis, a food-borne trematodiasis, results following infection with the parasites, Fasciola hepatica and Fasciola gigantica. These trematodes greatly affect the global agricultural community, infecting millions of ruminants worldwide and causing annual economic losses in excess of US $3 billion. Fasciolosis, an important zoonosis, is classified by WHO as a neglected tropical disease with an estimated 17 million people infected and a further 180 million people at risk of infection. The significant impact on agriculture and human health together with the increasing demand for animal-derived food products to support global population growth demonstrate that fasciolosis is a major One Health problem. This review details the problematic issues surrounding fasciolosis control, including drug resistance, lack of diagnosis and the threat that hybridization of the Fasciola species poses to future animal and human health. We discuss how these parasites may mediate their long-term survival through regulation and modulation of the host immune system, by altering the host immune homeostasis and/or by influencing the intestinal microbiome particularly in respect to concurrent infections with other pathogens. Large genome, transcriptome and proteomic data sets are now available to support an integrated One Health approach to develop novel diagnostic and control strategies for both animal and human disease.

Czibula, OG, Gu, H, Hwang, F-J, Kovalyov, MY & Zinder, Y 2016, 'Bi-criteria sequencing of courses and formation of classes for a bottleneck classroom', COMPUTERS & OPERATIONS RESEARCH, vol. 65, pp. 53-63.
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© 2015 Elsevier Ltd. Abstract In this paper, the problem of class formation and sequencing for multiple courses subject to a bottleneck classroom with an ordered bi-criteria objective is studied. The problem can be modelled as a single-machine batch scheduling problem with incompatible job families and parallel job processing in batches, where the batch size is family-dependent. For the minimisation of the number of tardy jobs, the strong NP-hardness is proven. For the performance measure of the maximum cost, we consider single criterion and bi-criteria cases. We present an O(ⁿ²logn) algorithm, n is the number of jobs, for both cases. An Integer Programming model as well as Simulated Annealing and Genetic Algorithm matheuristics to solve a fairly general case of the bi-criteria problem is presented and computationally tested.

Dai, Y, Ji, Z, Wang, C, Hu, X & Wang, G 2016, 'Microcantilever biosensors', Progress in Chemistry, vol. 28, no. 5, pp. 697-710.
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Microcantilever biosensors based on atomic force microscope have the advantages of label-free, rapid, real-time, and high sensitivity detection features. Therefore, microcantilever biosensors can be applied in the fields of biomedicine, environmental monitoring, food production and military defenses. Microcantilever biosensors have become the focus of scientific research. In this paper, we review the working principle, excitation method and detection mechanism of microcantilever biosensors. Preview reviews about the microcantilever biosensors mainly focuse on the progress of applications, but lack of comprehensive and systematic introduction on detection methods. Herein, we not only systematically analyze eight detection methods, but also introduce several typical sizes, appearance and 'heat mode' of microcantilever biosensors. So far, these have not been reported in literatures. In order to realize specific detection and improve sensitivity of microcantilever sensors, we summarize the surface modification methods of microcantilever sensors and review the latest applications of microcantilever biosensors. Furthermore, we introduce a new kind of self-actuating and self-sensing microcantilever biosensors. The prospective of microcantilever biosensors is also discussed in this paper.

Daley, DO, Skoglund, U & Söderström, B 2016, 'FtsZ does not initiate membrane constriction at the onset of division', Scientific Reports, vol. 6, no. 1, p. 33138.
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AbstractThe source of constriction required for division of a bacterial cell remains enigmatic. FtsZ is widely believed to be a key player, because in vitro experiments indicate that it can deform liposomes when membrane tethered. However in vivo evidence for such a role has remained elusive as it has been challenging to distinguish the contribution of FtsZ from that of peptidoglycan-ingrowth. To differentiate between these two possibilities we studied the early stages of division in Escherichia coli, when FtsZ is present at the division site but peptidoglycan synthesizing enzymes such as FtsI and FtsN are not. Our approach was to use correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) to monitor the localization of fluorescently labeled FtsZ, FtsI or FtsN correlated with the septal ultra-structural geometry in the same cell. We noted that the presence of FtsZ at the division septum is not sufficient to deform membranes. This observation suggests that, although FtsZ can provide a constrictive force, the force is not substantial at the onset of division. Conversely, the presence of FtsN always correlated with membrane invagination, indicating that allosteric activation of peptidoglycan ingrowth is the trigger for constriction of the cell envelope during cell division in E. coli.

Dana, S, Herdean, A, Lundin, B & Spetea, C 2016, 'Retracted: Each of the chloroplast potassium efflux antiporters affects photosynthesis and growth of fully developed Arabidopsis rosettes under short‐day photoperiod', Physiologia Plantarum, vol. 158, no. 4, pp. 483-491.
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In Arabidopsis thaliana, the chloroplast harbors three potassium efflux antiporters (KEAs), namely KEA1 and KEA2 in the inner envelope and KEA3 in the thylakoid membrane. They may play redundant physiological roles as in our previous analyses of young developing Arabidopsis rosettes under long‐day photoperiod (16 h light per day), chloroplast kea single mutants resembled the wild‐type plants, whereas kea1kea2 and kea1kea2kea3 mutants were impaired in chloroplast development and photosynthesis resulting in stunted growth. Here, we aimed to study whether chloroplast KEAs play redundant roles in chloroplast function of older Arabidopsis plants with fully developed rosettes grown under short‐day photoperiod (8 h light per day). Under these conditions, we found defects in photosynthesis and growth in the chloroplast kea single mutants, and most dramatic defects in the kea1kea2 double mutant. The mechanism behind these defects in the single mutants involves reduction in the electron transport rate (kea1 and kea3), and stomata conductance (kea1, kea2 and kea3), which in turn affect CO2 fixation rates. The kea1kea2 mutant, in addition to these alterations, displayed reduced levels of photosynthetic machinery. Taken together, our data suggest that, in...

Davey, PA, Pernice, M, Sablok, G, Larkum, A, Lee, HT, Golicz, A, Edwards, D, Dolferus, R & Ralph, P 2016, 'The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses', FUNCTIONAL & INTEGRATIVE GENOMICS, vol. 16, no. 5, pp. 465-480.
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Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

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 2016, 'A database of marine phytoplankton abundance, biomass and species composition in Australian waters', Scientific Data, vol. 3, no. 1.
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AbstractThere have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.

Dayananda, B, Gray, S, Pike, D & Webb, JK 2016, 'Communal nesting under climate change: fitness consequences of higher incubation temperatures for a nocturnal lizard', Global Change Biology, vol. 22, no. 7, pp. 2405-2414.
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AbstractCommunal nesting lizards may be vulnerable to climate warming, particularly if air temperatures regulate nest temperatures. In southeastern Australia, velvet geckos Oedura lesueurii lay eggs communally inside rock crevices. We investigated whether increases in air temperatures could elevate nest temperatures, and if so, how this could influence hatching phenotypes, survival, and population dynamics. In natural nests, maximum daily air temperature influenced mean and maximum daily nest temperatures, implying that nest temperatures will increase under climate warming. To determine whether hotter nests influence hatchling phenotypes, we incubated eggs under two fluctuating temperature regimes to mimic current ‘cold’ nests (mean = 23.2 °C, range 10–33 °C) and future ‘hot’ nests (27.0 °C, 14–37 °C). ‘Hot’ incubation temperatures produced smaller hatchlings than did cold temperature incubation. We released individually marked hatchlings into the wild in 2014 and 2015, and monitored their survival over 10 months. In 2014 and 2015, hot‐incubated hatchlings had higher annual mortality (99%, 97%) than cold‐incubated (11%, 58%) or wild‐born hatchlings (78%, 22%). To determine future trajectories of velvet gecko populations under climate warming, we ran population viability analyses in Vortex and varied annual rates of hatchling mortality within the range 78– 96%. Hatchling mortality strongly influenced the probability of extinction and the mean time to extinction. When hatchling mortality was >86%, populations had a higher probability of extinction (PE: range 0.52– 1.0) with mean times to extinction of 18–44 years. Whether future changes in hatchling survival translate into reduced population viability will depend on the ability of females to modify their nest‐site choices. Over the period 1992–2015, females used the same communal ne...

De Brauwer, M, Camp, E, Jompa, J & Smith, DJ 2016, 'High levels of heterospecific cohabitation among anemonefishes in Hoga Island, Indonesia', Marine Biodiversity, vol. 46, no. 1, pp. 19-20.
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Anemonefishes have an obligate association with host sea anemones and normally occur in conspecific groups. Occasionally, heterospecific social groups are observed (Fautin and Allen 1997). Here, we report the highest documented frequency of heterospecific cohabitation in the world. Observations on coral reefs around Hoga Island (Southwest Sulawesi, Indonesia) were conducted on the reef crest and slope habitats (3–15 m depth) during July and August 2014, and cohabitation was recorded in the sea anemones Entacmaea quadricolor, Heteractis crispa and Stichodactyla mertensii. Surveys revealed that 55 out of 106 surveyed sea anemones (52 %) were occupied by more than one species of anenomefish; all other observed sea anemones were occupied by only one. The following combinations of anemonefishes were observed: Amphiprion clarkii (adult)—Premnas biaculeatus (juvenile) (1.8 %), A. melanopus (ad.)—P. biaculeatus (juv.) (3.6 %), A. perideraion (ad.)—A. clarkii (juv.) (7.3 %), A. clarkii (ad.)—A. perideraion (juv.) (85.5 %), A. sandaracinos (ad.)—A. clarkii (juv.) (1.8 %) (Fig. 1).

De Silva, KSB, Keast, VJ & Cortie, MB 2016, 'Effect of Al additions on the optical properties of Au alpha-phase', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 679, pp. 225-230.
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Dean, S, Zaslawski, C, Roche, M & Adams, J 2016, '“Talk to them”: Teaching communication skills to students of Traditional Chinese Medicine', Journal of Nursing Education and Practice, vol. 6, no. 12, pp. 49-56.
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Objective: To explore students’ perceptions of the efficacy and value of teaching communication skills in a health professional course for Traditional Chinese Medicine (TCM). Methods: Individual surveys were used to evaluate students’ self-assessment of their communication skills pre and post a communication subject in a four-year degree course in a Bachelor of Health Science in TCM at a large metropolitan university in Australia. Quantitative and qualitative data were collected. Results: Findings indicate that students recognise the need for good communication skills training as part of their professional training and self-reported that their communication skills improved following a semester of study of a communication subject. Conclusions: One of the primary components driving increasing demand for complementary and alternative medicine (CAM), which includes TCM, is that consumers place a high value on effective communication and quality engagement with their CAM provider. Communication skills are often seen as the cornerstone of good health care practice, patient recovery and practitioner job satisfaction. Implementing a focused communication skills component in health professional educational programs, including those for TCM, is therefore essential. Further research is needed to explore the retention of these skills throughout health professionals’ degree programs and after graduation and clinical experience, to evaluate the effectiveness and sustainability of personal communication skills education. Practice implications: Communication skills training should be incorporated into health care profession curricula, early in the program and integrated with clinical exposure.

DeMaere, MZ & Darling, AE 2016, 'Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)', PeerJ, vol. 4, no. 11, pp. e2676-e2676.
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BackgroundChromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised.MethodsWe developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure.ResultsWhen all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance.DiscussionPreviously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considere...

Deng, X, Chen, Y, Cheng, Z, Deng, K, Ma, P, Hou, Z, Liu, B, Huang, S, Jin, D & Lin, J 2016, 'Rational design of a comprehensive cancer therapy platform using temperature-sensitive polymer grafted hollow gold nanospheres: simultaneous chemo/photothermal/photodynamic therapy triggered by a 650 nm laser with enhanced anti-tumor efficacy', Nanoscale, vol. 8, no. 12, pp. 6837-6850.
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© The Royal Society of Chemistry 2016. Combining multi-model treatments within one single system has attracted great interest for the purpose of synergistic therapy. In this paper, hollow gold nanospheres (HAuNs) coated with a temperature-sensitive polymer, poly(oligo(ethylene oxide) methacrylate-co-2-(2-methoxyethoxy)ethyl methacrylate) (p(OEGMA-co-MEMA)), co-loaded with DOX and a photosensitizer Chlorin e6 (Ce6) were successfully synthesized. As high as 58% DOX and 6% Ce6 by weight could be loaded onto the HAuNs-p(OEGMA-co-MEMA) nanocomposites. The grafting polymer brushes outside the HAuNs play the role of 'gate molecules' for controlled drug release by 650 nm laser radiation owing to the temperature-sensitive property of the polymer and the photothermal effect of HAuNs. The HAuNs-p(OEGMA-co-MEMA)-Ce6-DOX nanocomposites with 650 nm laser radiation show effective inhibition of cancer cells in vitro and enhanced anti-tumor efficacy in vivo. In contrast, control groups without laser radiation show little cytotoxicity. The nanocomposite demonstrates a way of 'killing three birds with one stone', that is, chemotherapy, photothermal and photodynamic therapy are triggered simultaneously by the 650 nm laser stimulation. Therefore, the nanocomposites show the great advantages of multi-modal synergistic effects for cancer therapy by a remote-controlled laser stimulus.

Deplazes, E, Davies, J, Bonvin, AMJJ, King, GF & Mark, AE 2016, 'Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a', Journal of Chemical Information and Modeling, vol. 56, no. 1, pp. 127-138.
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Deplazes, E, Henriques, ST, Smith, JJ, King, GF, Craik, DJ, Mark, AE & Schroeder, CI 2016, 'Membrane-binding properties of gating modifier and pore-blocking toxins: Membrane interaction is not a prerequisite for modification of channel gating', Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1858, no. 4, pp. 872-882.
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Dhouib, R, Othman, DSMP, Lin, V, Lai, XJ, Wijesinghe, HGS, Essilfie, A-T, Davis, A, Nasreen, M, Bernhardt, PV, Hansbro, PM, McEwan, AG & Kappler, U 2016, 'A Novel, Molybdenum-Containing Methionine Sulfoxide Reductase Supports Survival of Haemophilus influenzae in an In vivo Model of Infection', Frontiers in Microbiology, vol. 7, no. NOV.
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© 2016 Dhouib, Othman, Lin, Lai, Wijesinghe, Essilfie, Davis, Nasreen, Bernhardt, Hansbro, McEwan and Kappler. Haemophilus influenzae is a host adapted human mucosal pathogen involved in a variety of acute and chronic respiratory tract infections, including chronic obstructive pulmonary disease and asthma, all of which rely on its ability to efficiently establish continuing interactions with the host. Here we report the characterization of a novel molybdenum enzyme, TorZ/MtsZ that supports interactions of H. influenzae with host cells during growth in oxygen-limited environments. Strains lacking TorZ/MtsZ showed a reduced ability to survive in contact with epithelial cells as shown by immunofluorescence microscopy and adherence/invasion assays. This included a reduction in the ability of the strain to invade human epithelial cells, a trait that could be linked to the persistence of H. influenzae. The observation that in a murine model of H. influenzae infection, strains lacking TorZ/MtsZ were almost undetectable after 72 h of infection, while ~3.6 × 103 CFU/mL of the wild type strain were measured under the same conditions is consistent with this view. To understand how TorZ/MtsZ mediates this effect we purified and characterized the enzyme, and were able to show that it is an S- and N-oxide reductase with a stereospecificity for S-sulfoxides. The enzyme converts two physiologically relevant sulfoxides, biotin sulfoxide and methionine sulfoxide (MetSO), with the kinetic parameters suggesting that MetSO is the natural substrate of this enzyme. TorZ/MtsZ was unable to repair sulfoxides in oxidized Calmodulin, suggesting that a role in cell metabolism/energy generation and not protein repair is the key function of this enzyme. Phylogenetic analyses showed that H. influenzae TorZ/MtsZ is only distantly related to the Escherichia coli TorZ TMAO reductase, but instead is a representative of a new, previously uncharacterized clade of molybdenum enzyme that is ...

Di, A, Xue, Y, Yang, X, Leys, J, Guang, J, Mei, L, Wang, J, She, L, Hu, Y, He, X, Che, Y & Fan, C 2016, 'Dust Aerosol Optical Depth Retrieval and Dust Storm Detection for Xinjiang Region Using Indian National Satellite Observations', Remote Sensing, vol. 8, no. 9, pp. 702-702.
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The Xinjiang Uyghur Autonomous Region (Xinjiang) is located near the western border of China. Xinjiang has a high frequency of dust storms, especially in late winter and early spring. Geostationary satellite remote sensing offers an ideal way to monitor the regional distribution and intensity of dust storms, which can impact the regional climate. In this study observations from the Indian National Satellite (INSAT) 3D are used for dust storm detection in Xinjiang because of the frequent 30-min observations with six bands. An analysis of the optical properties of dust and its quantitative relationship with dust storms in Xinjiang is presented for dust events in April 2014. The Aerosol Optical Depth (AOD) derived using six predefined aerosol types shows great potential to identify dust events. Cross validation between INSAT-3D retrieved AOD and MODIS AOD shows a high coefficient of determination (R2 = 0.92). Ground validation using AERONET (Aerosol Robotic Network) AOD also shows a good correlation with R2 of 0.77. We combined the apparent reflectance (top-of-atmospheric reflectance) of visible and shortwave infrared bands, brightness temperature of infrared bands and retrieved AOD into a new Enhanced Dust Index (EDI). EDI reveals not only dust extent but also the intensity. EDI performed very well in measuring the intensity of dust storms between 22 and 24 April 2014. A visual comparison between EDI and Feng Yun-2E (FY-2E) Infrared Difference Dust Index (IDDI) also shows a high level of similarity. A good linear correlation (R2 of 0.78) between EDI and visibility on the ground demonstrates good performance of EDI in estimating dust intensity. A simple threshold method was found to have a good performance in delineating the extent of the dust plumes but inadequate for providing information on dust plume intensity.

Dickson, K-A, Cole, AJ, Gill, AJ, Clarkson, A, Gard, GB, Chou, A, Kennedy, CJ, Henderson, BR, Fereday, S, Traficante, N, Alsop, K, Bowtell, DD, deFazio, A, Clifton-Bligh, R & Marsh, DJ 2016, 'The RING finger domain E3 ubiquitin ligases BRCA1 and the RNF20/RNF40 complex in global loss of the chromatin mark histone H2B monoubiquitination (H2Bub1) in cell line models and primary high-grade serous ovarian cancer', Human Molecular Genetics, vol. 25, no. 24, pp. ddw362-ddw362.
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Dilusha Cooray, MC, Sandanayake, S, Li, F, Langford, SJ, Bond, AM & Zhang, J 2016, 'Efficient Enzymatic Oxidation of Glucose Mediated by Ferrocene Covalently Attached to Polyethylenimine Stabilized Gold Nanoparticles', Electroanalysis, vol. 28, no. 11, pp. 2728-2736.
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AbstractBioanodes for fuel cell applications require highly efficient oxidation reactions to achieve a sufficiently large current density. In this study, gold nanoparticles have been synthesized using branched polyethylenimine (bPEI), a well‐known polymer that forms a hydrogel in water, as the stabilizer. Primary amine groups available in bPEI provide active sites for further conjugation with ferrocene propionic acid via the 1‐Ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide coupling reaction, with the enzyme glucose oxidase, using glutaraldehyde as linkers. This composite material was then used for the fabrication of glucose oxidase electrodes by drop casting of aqueous solutions onto glassy carbon electrodes. The three‐dimensional structure offered by the new hydrogel facilitates communication between the enzyme and the electrode through the redox mediator ferrocene. This allows the glucose oxidase electrode to exhibit excellent activity towards electrocatalytic oxidation of glucose in phosphate buffer solutions at pH 7 with a maximum current density of approximately 800 μA cm−2, one of the highest values reported so far for redox hydrogel based glucose oxidase electrodes. Over a wide glucose concentration range, the enzyme response follows that predicted by the Michaelis‐Menten equation with a Michaelis constant of 8.4 mM. In the sensing context, this electrode also exhibits a wide linear dynamic glucose concentration range of 0.5–10 mM with a limit of detection of 0.04 mM.

Doblin, MA & van Sebille, E 2016, 'Drift in ocean currents impacts intergenerational microbial exposure to temperature', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 113, no. 20, pp. 5700-5705.
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Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Doblin, MA, Petrou, K, Sinutok, S, Seymour, JR, Messer, LF, Brown, MV, Norman, L, Everett, JD, McInnes, AS, Ralph, PJ, Thompson, PA & Hassler, CS 2016, 'Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current', PEERJ, vol. 4, no. 4.
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© 2016 Doblin et al. The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC) region to sample microbes in a cyclonic (cold-core) eddy (CCE) and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2-10 times greater Shannon index) in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67%) by larger micro-plankton (≥ 20μm), as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN- A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a 'greening' effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si) and iron amendment, whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially mitigate the negative conse...

Donelson, JM, Wong, M, Booth, DJ & Munday, PL 2016, 'Transgenerational plasticity of reproduction depends on rate of warming across generations', Evolutionary Applications, vol. 9, no. 9, pp. 1072-1081.
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AbstractPredicting the impacts of climate change to biological systems requires an understanding of the ability for species to acclimate to the projected environmental change through phenotypic plasticity. Determining the effects of higher temperatures on individual performance is made more complex by the potential for environmental conditions experienced in previous and current generations to independently affect phenotypic responses to high temperatures. We used a model coral reef fish (Acanthochromis polyacanthus) to investigate the influence of thermal conditions experienced by two generations on reproductive output and the quality of offspring produced by adults. We found that more gradual warming over two generations, +1.5°C in the first generation and then +3.0°C in the second generation, resulted in greater plasticity of reproductive attributes, compared to fish that experienced the same increase in one generation. Reproduction ceased at the projected future summer temperature (31.5°C) when fish experienced +3.0°C for two generations. Additionally, we found that transgenerational plasticity to +1.5°C induced full restoration of thermally affected reproductive and offspring attributes, which was not possible with developmental plasticity alone. Our results suggest that transgenerational effects differ depending on the absolute thermal change and in which life stage the thermal change is experienced.

Donovan, C, Bourke, JE & Vlahos, R 2016, 'Targeting the IL-33/IL-13 Axis for Respiratory Viral Infections', Trends in Pharmacological Sciences, vol. 37, no. 4, pp. 252-261.
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© 2016 Elsevier Ltd. Lung diseases, such as asthma and chronic obstructive pulmonary disease (COPD), are highly prevalent worldwide. One of the major factors that limits the efficacy of current medication in these patients are viral infections, leading to exacerbations of symptoms and decreased quality of life. Current pharmacological strategies targeting virus-induced lung disease are problematic due to antiviral resistance and the requirement for strain-specific vaccination. Thus, new therapeutic strategies are urgently required. In this Opinion article, we provide state-of-the-art evidence from humans and preclinical animal models implicating the interleukin (IL)-33/IL-13 axis in virus-induced lung disease. Thus, targeting the IL-33/IL-13 axis may be a feasible way to overcome the limitations of current therapy used to treat virus-induced exacerbations of lung disease.

Donovan, C, Seow, HJ, Bourke, JE & Vlahos, R 2016, 'Influenza A virus infection and cigarette smoke impair bronchodilator responsiveness to β-adrenoceptor agonists in mouse lung', Clinical Science, vol. 130, no. 10, pp. 829-837.
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β2-adrenoceptor agonists are the mainstay therapy for patients with asthma but their effectiveness in cigarette smoke (CS)-induced lung disease such as chronic obstructive pulmonary disease (COPD) is limited. In addition, bronchodilator efficacy of β2-adrenoceptor agonists is decreased during acute exacerbations of COPD (AECOPD), caused by respiratory viruses including influenza A. Therefore, the aim of the present study was to assess the effects of the β2-adrenoceptor agonist salbutamol (SALB) on small airway reactivity using mouse precision cut lung slices (PCLS) prepared from CS-exposed mice and from CS-exposed mice treated with influenza A virus (Mem71, H3N1). CS exposure alone reduced SALB potency and efficacy associated with decreased β2-adrenoceptor mRNA expression, and increased tumour necrosis factor α (TNFα) and interleukin-1β (IL-1β) expression. This impaired relaxation was restored by day 12 in the absence of further CS exposure. In PCLS prepared after Mem71 infection alone, responses to SALB were transient and were not well maintained. CS exposure prior to Mem71 infection almost completely abolished relaxation, although β2-adrenoceptor and TNFα and IL-1β expression were unaltered. The present study has shown decreased sensitivity to SALB after CS or a combination of CS and Mem71 occurs by different mechanisms. In addition, the PCLS technique and our models of CS and influenza infection provide a novel setting for assessment of alternative bronchodilators.

Dooley, AH, Hare, KE & Roginskaya, M 2016, 'On $L^p$-improving measures', Revista Matemática Iberoamericana, vol. 32, no. 4, pp. 1211-1226.
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We give criteria for establishing that a measure is L^p -improving. Many Riesz product measures and Cantor measures satisfy this criteria, as well as certain Markov measures.

Dossou, KB, Poulton, CG & Botten, LC 2016, 'Effective impedance modeling of metamaterial structures', Journal of the Optical Society of America A, vol. 33, no. 3, pp. 361-361.
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© 2016 Optical Society of America. We present methods for retrieving the effective impedance of metamaterials from the Fresnel reflection coefficients at the interface between two semi-infinite media. The derivation involves the projection of rigorous modal expansions onto the dominant modes of the two semi-infinite media. It is shown that the effective impedance can also be written as a ratio of averaged field quantities. Thus, a number of effective impedance formulas, previously obtained by field averaging techniques, can also be derived from the scattering-based formalism by an appropriate choice of projection. Within the effective medium limit, it is observed that a simple semianalytic modeling technique based on the effective impedance can be used to reliably compute the reflection coefficients of metamaterials over a wide range of incidence angles. We use this technique to model planar metamaterial waveguides or surface modes.

Doumit, M, Belessis, Y, Stelzer-Braid, S, Mallitt, K-A, Rawlinson, W & Jaffe, A 2016, 'Diagnostic accuracy and distress associated with oropharyngeal suction in cystic fibrosis', Journal of Cystic Fibrosis, vol. 15, no. 4, pp. 473-478.
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Dowd, A, Geisler, M, Zhu, S, Wood, ML & Cortie, MB 2016, 'Role of multipolar plasmon resonances during surface-enhanced Raman spectroscopy on Au micro-patches', RSC Advances, vol. 6, no. 116, pp. 115284-115289.
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Large more reproducibly fabricated microstructures can also provide significant Raman signal enhancementviausually neglected multipolar plasmon resonances.

Du, K & Platen, E 2016, 'BENCHMARKED RISK MINIMIZATION', Mathematical Finance, vol. 26, no. 3, pp. 617-637.
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AbstractThis paper discusses the problem of hedging not perfectly replicable contingent claims using the numéraire portfolio. The proposed concept of benchmarked risk minimization leads beyond the classical no‐arbitrage paradigm. It provides in incomplete markets a generalization of the pricing under classical risk minimization, pioneered by Föllmer, Sondermann, and Schweizer. The latter relies on a quadratic criterion, requests square integrability of claims and gains processes, and relies on the existence of an equivalent risk‐neutral probability measure. Benchmarked risk minimization avoids these restrictive assumptions and provides symmetry with respect to all primary securities. It employs the real‐world probability measure and the numéraire portfolio to identify the minimal possible price for a contingent claim. Furthermore, the resulting benchmarked (i.e., numéraire portfolio denominated) profit and loss is only driven by uncertainty that is orthogonal to benchmarked‐traded uncertainty, and forms a local martingale that starts at zero. Consequently, sufficiently different benchmarked profits and losses, when pooled, become asymptotically negligible through diversification. This property makes benchmarked risk minimization the least expensive method for pricing and hedging diversified pools of not fully replicable benchmarked contingent claims. In addition, when hedging it incorporates evolving information about nonhedgeable uncertainty, which is ignored under classical risk minimization.

Duan, X, Ao, Z, Li, D, Sun, H, Zhou, L, Suvorova, A, Saunders, M, Wang, G & Wang, S 2016, 'Surface-tailored nanodiamonds as excellent metal-free catalysts for organic oxidation', Carbon, vol. 103, pp. 404-411.
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Duan, X, Ao, Z, Zhou, L, Sun, H, Wang, G & Wang, S 2016, 'Occurrence of radical and nonradical pathways from carbocatalysts for aqueous and nonaqueous catalytic oxidation', Applied Catalysis B: Environmental, vol. 188, pp. 98-105.
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© 2016 Elsevier B.V. Metal-free activation of superoxides provides an efficient and environmentally benign strategy for heterogeneous catalytic oxidation. In this study, nanocarbons with varying carbon-conjugation structures and functional groups were investigated for peroxymonosulfate (PMS) activation. It was discovered that radical and nonradical oxidations could occur on different carbocatalysts depending on the carbon structure. Radical oxidation occurs exclusively on MWCNTs and CMK-3, similar to a metal oxide, MnO2. Both radical and nonradical oxidations are very pronounced in nanodiamond (AND-900)/PMS whilst nonradical oxidation is dominated in reduced graphene oxide (rGO-900)/PMS. Density functional theory (DFT) calculations were employed to explore the PMS adsorption and OO bond activation on the different carbon configurations for an in-depth probe of the activation mechanism. The intact sp2-conjugated π system in MWCNTs and electron-rich ketonic groups (as Lewis basic sites) in CMK-3 can stimulate PMS dissociation to generate SO4- and OH, similar to metal-based catalysts. However, the defective edges at the boundary of carbon network are able to facilitate the organic degradation without generation of the reactive radicals, which is well supported by both experiments and the DFT calculation. The emerging nonradical oxidation induced by the carbocatalysis is superior to the radical oxidation on most metal oxides for effective degradation of various organics. The influences of solution pH, various anions (H2PO42-, HCO3- and Cl-) and background organic matters (humic acid) on the nonradical oxidation were further evaluated. The nonradical oxidation on carbocatalysts can be utilized as a green and effective oxidation strategy for aqueous environmental remediation and nonaqueous phase oxidation.

Duan, X, Sun, H, Ao, Z, Zhou, L, Wang, G & Wang, S 2016, 'Unveiling the active sites of graphene-catalyzed peroxymonosulfate activation', Carbon, vol. 107, pp. 371-378.
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Dubossarsky, E, Friedman, JH, Ormerod, JT & Wand, MP 2016, 'Wavelet-based gradient boosting', Statistics and Computing, vol. 26, no. 1-2, pp. 93-105.
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© 2014, Springer Science+Business Media New York. A new data science tool named wavelet-based gradient boosting is proposed and tested. The approach is special case of componentwise linear least squares gradient boosting, and involves wavelet functions of the original predictors. Wavelet-based gradient boosting takes advantages of the approximate $$\ell _1$$ℓ1 penalization induced by gradient boosting to give appropriate penalized additive fits. The method is readily implemented in R and produces parsimonious and interpretable regression fits and classifiers.

Duchêne, S, Holt, KE, Weill, F-X, Le Hello, S, Hawkey, J, Edwards, DJ, Fourment, M & Holmes, EC 2016, 'Genome-scale rates of evolutionary change in bacteria', Microbial Genomics, vol. 2, no. 11, p. e000094.
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Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host–pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with ‘ancient DNA’ data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10−5 to 10−8 nucleotide substitutions per site year−1. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

Eamus, D, Huete, A, Cleverly, J, Nolan, RH, Ma, X, Tarin, T & Santini, NS 2016, 'Mulga, a major tropical dry open forest of Australia: recent insights to carbon and water fluxes', Environmental Research Letters, vol. 11, no. 12, pp. 125011-125011.
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© 2016 IOP Publishing Ltd. Mulga, comprised of a complex of closely related Acacia spp., grades from a low open forest to tall shrublands in tropical and sub-tropical arid and semi-arid regions of Australia and experiences warm-to-hot annual temperatures and a pronounced dry season. This short synthesis of current knowledge briefly outlines the causes of the extreme variability in rainfall characteristic of much of central Australia, and then discusses the patterns and drivers of variability in carbon and water fluxes of a central Australian low open Mulga forest. Variation in phenology and the impact of differences in the amount and timing of precipitation on vegetation function are then discussed. We use field observations, with particular emphasis on eddy covariance data, coupled with modelling and remote sensing products to interpret inter-seasonal and inter-annual patterns in the behaviour of this ecosystem. We show that Mulga can vary between periods of near carbon neutrality to periods of being a significant sink or source for carbon, depending on both the amount and timing of rainfall. Further, we demonstrate that Mulga contributed significantly to the 2011 global land sink anomaly, a result ascribed to the exceptional rainfall of 2010/2011. Finally, we compare and contrast the hydraulic traits of three tree species growing close to the Mulga and show how each species uses different combinations of trait strategies (for example, sapwood density, xylem vessel implosion resistance, phenological guild, access to groundwater and Huber value) to co-exist in this semi-arid environment. Understanding the inter-annual variability in functional behaviour of this important arid-zone biome and mechanisms underlying species co-existence will increase our ability to predict trajectories of carbon and water balances for future changing climates.

Ekren, N, Gunduz, O, Celik, S, Ayata, B, Sahin, YM, Chou, J, Ben-Nissan, B, Salman, S, Gökçe, H & Oktar, FN 2016, 'Production of Apatite from Snail Shells for Biomedical Engineering Applications', Key Engineering Materials, vol. 696, pp. 51-56.
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Bioceramics is very important application for dental and orthopedic procedures. Beside all these normal procedures traffic accidents are requiring increasing number of graft, prostheses and orthosis applications. Bioceramics can be produced from local and natural sources with various methods. Those can be produced from various bone structures through calcination (at high temperatures) or with diluted hydrochloric acid (HCl) application & freeze drying. Beside these methods calcite and aragonite structures like from sea shells and egg shells bioceramic production can be realized through mechanochemical processing via a simple hot-plate or ultrasonic equipment. A fresh water snail shell (Zebra Nerite Snail - Neritinanatalensis) was prepared as bioceramic production source. The resulting hydroxyapatite (HA) powders were obtained without any impurities. At two varying temperature of 865 and 885 °C the snail shells was transformed to HA bioceramics. Scanning electron microscopy (SEM), X-ray diffraction (XRD) and differential thermal analysis (TG/DTA) were evaluated.

Elbadawi, C, Tran, TT, Kolíbal, M, Šikola, T, Scott, J, Cai, Q, Li, LH, Taniguchi, T, Watanabe, K, Toth, M, Aharonovich, I & Lobo, C 2016, 'Electron beam directed etching of hexagonal boron nitride', Nanoscale, vol. 8, no. 36, pp. 16182-16186.
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High resolution directed electron beam etching of hBN using water as the precursor gas.

Elder, M & Rogers, C 2016, 'On a theorem of Avez', Journal of Group Theory, vol. 22, no. 3.
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For each symmetric, aperiodic probability measure $\mu$ on a finitelygenerated group $G$, we define a subset $A_{\mu}$ consisting of group elements$g$ for which the limit of the ratio ${\mu^{\ast n}(g)}/{\mu^{\ast n}(e)}$tends to $1$. We prove that $A_\mu$ is a subgroup, is amenable, contains everyfinite normal subgroup, and $G=A_\mu$ if and only if $G$ is amenable. Fornon-amenable groups we show that $A_\mu$ is not always a normal subgroup, andcan depend on the measure. We formulate some conjectures relating $A_\mu$ tothe amenable radical.

Elder, M & Rogers, C 2016, 'Sub-dominant cogrowth behaviour and the viability of deciding amenability numerically', Experimental Mathematics, vol. 28, no. 1, pp. 67-80.
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We critically analyse a recent numerical method due to the first author,Rechnitzer and van Rensburg, which attempts to detect amenability ornon-amenability in a finitely generated group by numerically estimating itsasymptotic cogrowth rate. We identify two potential sources of error. We thenpropose a modification of the method that enables it to easily computesurprisingly accurate estimates for initial terms of the cogrowth sequence.

Evans, E, Costrino, C, do Lago, CL, Garcia, CD, Roux, C & Blanes, L 2016, 'Determination of Inorganic Ion Profiles of Illicit Drugs by Capillary Electrophoresis', Journal of Forensic Sciences, vol. 61, no. 6, pp. 1610-1614.
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AbstractA portable capillary electrophoresis instrument with dual capacitively coupled contactless conductivity detection (C4D) was used to determine the inorganic ionic profiles of three pharmaceutical samples and precursors of two illicit drugs (contemporary samples of methylone and para‐methoxymethamphetamine). The LODs ranged from 0.10 μmol/L to 1.25 μmol/L for the 10 selected cations, and from 0.13 μmol/L to 1.03 μmol/L for the eight selected anions. All separations were performed in less than 6 min with migration times and peak area RSD values ranging from 2 to 7%. The results demonstrate the potential of the analysis of inorganic ionic species to aid in the identification and/or differentiation of unknown tablets, and real samples found in illicit drug manufacture scenarios. From the resulting ionic fingerprint, the unknown tablets and samples can be further classified.

Farooq, MU, Butt, S, Gao, K, Sun, X, Pang, X, Khan, SU, Xu, W, Mohmed, F, Mahmood, A & Mahmood, N 2016, 'Enhanced thermoelectric efficiency of Cu2−Se–Cu2S composite by incorporating Cu2S nanoparticles', Ceramics International, vol. 42, no. 7, pp. 8395-8401.
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Farooq, MU, Butt, S, Gao, K, Sun, X, Pang, X, Mahmood, A, Mahmood, W, Khan, SU & Mahmood, N 2016, 'Pronounced effect of ZnTe nanoinclusions on thermoelectric properties of Cu2−x Se chalcogenides', Science China Materials, vol. 59, no. 2, pp. 135-143.
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Farrell, H, O'Connor, W, Seebacher, F, Harwood, DT & Murray, S 2016, 'MOLECULAR DETECTION OF THE SXTA GENE FROM SAXITOXIN-PRODUCING ALEXANDRIUM MINUTUM IN COMMERCIAL OYSTERS', JOURNAL OF SHELLFISH RESEARCH, vol. 35, no. 1, pp. 169-177.
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The production of toxic secondary metabolites by marine phytoplankton and their accumulation in molluscs and fish has ecosystem-wide and human health impacts.

Farrell, H, Zammit, A, Manning, J, Shadbolt, C, Szabo, L, Harwood, DT, McNabb, P, Turahui, JA & van den Berg, DJ 2016, 'Clinical diagnosis and chemical confirmation of ciguatera fish poisoning in New South Wales, Australia.', Commun Dis Intell Q Rep, vol. 40, no. 1, pp. E1-E6.
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Ciguatera fish poisoning is common in tropical and sub-tropical areas and larger fish (> 10 kg) are more susceptible to toxin accumulation with age. Although the coastal climate of northern New South Wales is considered sub-tropical, prior to 2014 there has only been 1 documented outbreak of ciguatera fish poisoning from fish caught in the region. During February and March 2014, 2 outbreaks of ciguatera fish poisoning involved 4 and 9 individuals, respectively, both following consumption of Spanish mackerel from northern New South Wales coastal waters (Evans Head and Scotts Head). Affected individuals suffered a combination of gastrointestinal and neurological symptoms requiring hospital treatment. At least 1 individual was symptomatic up to 7 months later. Liquid chromatography-tandem mass spectrometry detected the compound Pacific ciguatoxin-1B at levels up to 1.0 µg kg(-1) in fish tissue from both outbreaks. During April 2015, another outbreak of ciguatera fish poisoning was reported in 4 individuals. The fish implicated in the outbreak was caught further south than the 2014 outbreaks (South West Rocks). Fish tissue was unavailable for analysis; however, symptoms were consistent with ciguatera fish poisoning. To our knowledge, these cases are the southernmost confirmed sources of ciguatera fish poisoning in Australia. Educational outreach to the fishing community, in particular recreational fishers was undertaken after the Evans Head outbreak. This highlighted the outbreak, species of fish involved and the range of symptoms associated with ciguatera fish poisoning. Further assessment of the potential for ciguatoxins to occur in previously unaffected locations need to be considered in terms of food safety.

Feng, S, Tan, CH, Cohen, Y & Rice, SA 2016, 'Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members', Environmental Microbiology, vol. 18, no. 11, pp. 3923-3931.
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SummaryIt is reported here that a predatory bacterium belonging to the Genus Bdellovibrio, was isolated from activated sludge at the Ulu Pandan Water Reclamation Plant, Singapore. 16S rDNA gene sequencing analysis revealed that this isolate was 99% identical to ‘Bdellovibrio bacteriovorus strain Tiberius’ and hence is designated as ‘Bdellovibrio bacteriovorus UP’. Using a novel approach based on fluorescence in situ hybridization (FISH), a prey cell density‐dependent growth pattern of B. bacteriovorus UP was established. B. bacteriovorus UP preyed upon a broad range of bacterial species (60 species) isolated from the activated sludge. Except for Ochrobactrum anthropi, all Gram‐negative species were sensitive to predation by B. bacteriovorus UP irrespective of the mode of growth (planktonic or biofilm). Similarly, the predation‐sensitive species were not protected by the predation‐resistant species, O. anthropi, as determined in multiple dual‐species planktonic and biofilm consortia. Given the broad prey spectrum, B. bacteriovorus UP may impact functional community members, which are largely members of the Proteobacteria. Thus, these results provide an important insight to the role of predatory bacteria in shaping of community structure and function in both natural and engineered ecosystems.

Finkelstein, DI, Hare, DJ, Billings, JL, Sedjahtera, A, Nurjono, M, Arthofer, E, George, S, Culvenor, JG, Bush, AI & Adlard, PA 2016, 'Clioquinol Improves Cognitive, Motor Function, and Microanatomy of the Alpha-Synuclein hA53T Transgenic Mice', ACS Chemical Neuroscience, vol. 7, no. 1, pp. 119-129.
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The abnormal accumulation of alpha-synuclein (α-syn) has been linked to a number of neurodegenerative disorders, the most noteworthy of which is Parkinson's disease. Alpha-synuclein itself is not toxic and fulfills various physiological roles in the central nervous system. However, specific types of aggregates have been shown to be toxic, and metals have been linked to the assembly of these toxic aggregates. In this paper, we have characterized a transgenic mouse that overexpresses the A53T mutation of human α-syn, specifically assessing cognition, motor performance, and subtle anatomical markers that have all been observed in synucleinopathies in humans. We hypothesized that treatment with the moderate-affinity metal chelator, clioquinol (CQ), would reduce the interaction between metals and α-syn to subsequently improve the phenotype of the A53T animal model. We showed that CQ prevents an iron-synuclein interaction, the formation of urea-soluble α-syn aggregates, α-syn-related substantia nigra pars compacta cell loss, reduction in dendritic spine density of hippocampal and caudate putamen medium spiny neurons, and the decline in motor and cognitive function. In conclusion, our data suggests that CQ is capable of mitigating the pathological metal/α-syn interactions, suggesting that the modulation of metal ions warrants further study as a therapeutic approach for the synucleinopathies.

Fisher, C, Botten, LC, Poulton, CG, McPhedran, RC & de Sterke, CM 2016, 'End-fire coupling efficiencies of surface plasmons for silver, gold, and plasmonic nitride compounds', Journal of the Optical Society of America B, vol. 33, no. 6, pp. 1044-1044.
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Flemming, H-C, Wingender, J, Szewzyk, U, Steinberg, P, Rice, SA & Kjelleberg, S 2016, 'Biofilms: an emergent form of bacterial life', Nature Reviews Microbiology, vol. 14, no. 9, pp. 563-575.
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© 2016 Macmillan Publishers Limited, part of Springer Nature. Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms-such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials-all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

FLETCHER-LARTEY, SM, ANDRESEN, D, VAN HAL, S, MERIF, J, STARK, D, RAWLINSON, W, HARKNESS, J & ELLIS, J 2016, 'Comparison of enteric protozoan infections in four Australian hospitals: variable tests and variable results', Parasitology Open, vol. 2, no. e13, pp. 1-8.
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SUMMARYThere is limited evidence of the prevalence of enteric protozoon infections in developed settings. We estimated the prevalence of enteric protozoa and evaluated the outcome of testing algorithms used in hospital settings in Sydney, Australia. This retrospective study assessed microbiological data from four public clinical laboratories. Pooled data from the four hospitals revealed the most common enteric protozoon detected wasBlastocystisspp. in an average of 5·4% of cases, followed byGiardia intestinalis(1·1%) andDientamoeba fragilis(0·8%). Protozoon detection rates between hospitals were significantly different and could be based on multiple factors. The modified iron haematoxylin staining method, consistently detected higher rates ofBlastocystisspp., andG. intestinalisin comparison with microscopy of wet preparations, as well as higher rates ofG. intestinalisandCryptosporidiumwhen compared with enzyme immunoassay. The study concludes that there are multiple factors that contribute to the variability in protozoa detection rates in metropolitan hospitals, including widespread variability in the testing protocols for enteric protozoa, individual and population characteristics. A gold standard approach for diagnosis of enteric protozoa is recommended. Molecular diagnostic methods such as polymerase chain reaction would provide consistency across laboratories and yield more reliable estimates of the actual prevalence of enteric protozoa.

Forbes, SL, Troobnikoff, AN, Ueland, M, Nizio, KD & Perrault, KA 2016, 'Profiling the decomposition odour at the grave surface before and after probing', FORENSIC SCIENCE INTERNATIONAL, vol. 259, pp. 193-199.
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© 2016 Elsevier Ireland Ltd. Human remains detection (HRD) dogs are recognised as a valuable and non-invasive search method for remains concealed in many different environments, including clandestine graves. However, the search for buried remains can be a challenging task as minimal odour may be available at the grave surface for detection by the dogs. Handlers often use a soil probe during these searches in an attempt to increase the amount of odour available for detection, but soil probing is considered an invasive search technique. The aim of this study was to determine whether the soil probe assists with increasing the abundance of volatile organic compounds (VOCs) available at the grave surface. A proof-of-concept method was developed using porcine remains to collect VOCs within the grave without disturbing the burial environment, and to compare their abundance at the grave surface before and after probing. Detection and identification of the VOC profiles required the use of comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) due to its superior sensitivity and selectivity for decomposition odour profiling. The abundance of decomposition VOCs was consistently higher within the grave environment compared to the grave surface, except when the grave surface had been disturbed, confirming the reduced availability of odour at the grave surface. Although probing appeared to increase the abundance of VOCs at the grave surface on many of the sampling days, there were no clear trends identified across the study and no direct relationships with the environmental variables measured. Typically, the decomposition VOCs that were most prevalent in the grave soil were the same VOCs detected at the grave surface, whereas the trace VOCs detected in these environments varied throughout the post-burial period. This study highlighted that probing the soil can assist with releasing decomposition VOCs but is likely correlated...

Fourment, M & Holmes, EC 2016, 'Seqotron: a user-friendly sequence editor for Mac OS X', BMC Research Notes, vol. 9, no. 1, pp. 1-4.
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Accurate multiple sequence alignment is central to bioinformatics and molecular evolutionary analyses. Although sophisticated sequence alignment programs are available, manual adjustments are often required to improve alignment quality. Unfortunately, few programs offer a simple and intuitive way to edit sequence alignments.We present Seqotron, a sequence editor that reads and writes files in a wide variety of sequence formats. Sequences can be easily aligned and manually edited using the mouse and keyboard. The program also allows the user to estimate both phylogenetic trees and distance matrices.Seqotron will benefit researchers who need to manipulate and align complex sequence data. Seqotron is a Mac OS X compatible open source project and is available from Github https://github.com/4ment/seqotron/.

Fowler, AM, Smith, SM, Booth, DJ & Stewart, J 2016, 'Partial migration of grey mullet (Mugil cephalus) on Australia’s east coast revealed by otolith chemistry', Marine Environmental Research, vol. 119, pp. 238-244.
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© 2016 Partial migration affects the ecology and evolution of animal populations, and is an important consideration for the management of harvested species, yet the phenomenon is understudied in fish. We provide the first insights into partially diadromous migration of grey mullet (Mugil cephalus) in Australia by examining the otolith chemistry of old individuals (aged 7–10 years) from two regions on the east coast. Strontium and Barium concentrations were measured across the otolith using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and indicated considerable diversity in migratory histories among individuals. Only 15% of individuals made repeated movements from estuaries to the marine environment, consistent with the annual spawning run in the region. The remainder either made irregular movements between salinity environments (70%), or resided in estuaries or fresh water for their entire life following the early juvenile stage (15%). The patterns are consistent with ‘skipped spawning’ partial migration, where a proportion of the mature population forgoes spawning each year. If confirmed, the behavior may afford the east coast population of M. cephalus some resilience to fishing pressure on the annual spawning run.

Fronzi, M, Daly, W & Nolan, M 2016, 'Reactivity of metal oxide nanocluster modified rutile and anatase TiO2: Oxygen vacancy formation and CO2 interaction', Applied Catalysis A: General, vol. 521, pp. 240-249.
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Fronzi, M, Iwaszuk, A, Lucid, A & Nolan, M 2016, 'Metal oxide nanocluster-modified TiO₂as solar activated photocatalyst materials', Journal of Physics: Condensed Matter, vol. 28, no. 7, pp. 074006-074006.
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Fung, J & Zinder, Y 2016, 'Permutation schedules for a two-machine flow shop with storage', OPERATIONS RESEARCH LETTERS, vol. 44, no. 2, pp. 153-157.
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© 2015 Elsevier B.V. All rights reserved. This paper considers a two-machine flow shop problem with a buffer, arising in various applications, and addresses a fundamental question of the existence of an optimal permutation schedule. The paper proves that the problem of recognising whether an instance has an optimal permutation schedule is NP-complete in the strong sense, and estimates the deviation from the optimal makespan as a result of the restriction to permutation schedules only.

Gadau, M, Zhang, S-P, Yip, H-Y, Yeung, W-F, Bian, Z-X, Lu, A-P & Zaslawski, C 2016, 'Pattern Differentiation of Lateral Elbow Pain in Traditional Chinese Medicine: A Systematic Review', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 22, no. 11, pp. 921-935.
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Gail, MH, Wu, J, Wang, M, Yaun, S, Cook, NR, Eliassen, AH, McCullough, ML, Yu, K, Zeleniuch‐Jacquotte, A, Smith‐Warner, SA, Ziegler, RG & Carroll, RJ 2016, 'Calibration and seasonal adjustment for matched case–control studies of vitamin D and cancer', Statistics in Medicine, vol. 35, no. 13, pp. 2133-2148.
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Vitamin D measurements are influenced by seasonal variation and specific assay used. Motivated by multicenter studies of associations of vitamin D with cancer, we formulated an analytic framework for matched case–control data that accounts for seasonal variation and calibrates to a reference assay. Calibration data were obtained from controls sampled within decile strata of the uncalibrated vitamin D values. Seasonal sine–cosine series were fit to control data. Practical findings included the following: (1) failure to adjust for season and calibrate increased variance, bias, and mean square error and (2) analysis of continuous vitamin D requires a variance adjustment for variation in the calibration estimate. An advantage of the continuous linear risk model is that results are independent of the reference date for seasonal adjustment. (3) For categorical risk models, procedures based on categorizing the seasonally adjusted and calibrated vitamin D have near nominal operating characteristics; estimates of log odds ratios are not robust to choice of seasonal reference date, however. Thus, public health recommendations based on categories of vitamin D should also define the time of year to which they refer. This work supports the use of simple methods for calibration and seasonal adjustment and is informing analytic approaches for the multicenter Vitamin D Pooling Project for Breast and Colorectal Cancer. Published 2016. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Gale, PA, Howe, ENW & Wu, X 2016, 'Anion Receptor Chemistry', Chem, vol. 1, no. 3, pp. 351-422.
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Ganio, K, James, SA, Hare, DJ, Roberts, BR & McColl, G 2016, 'Accurate biometal quantification per individual Caenorhabditis elegans', The Analyst, vol. 141, no. 4, pp. 1434-1439.
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A comparison of complementary methods to quantify biometals per individual for analytical biochemical studies using microscopic model organisms.

Gardner, SG, Nielsen, DA, Laczka, O, Shimmon, R, Beltran, VH, Ralph, PJ & Petrou, K 2016, 'Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 283, no. 1824, pp. 1-9.
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© 2016 The Author(s) Published by the Royal Society. All rights reserved. Corals are among the most active producers of dimethylsulfoniopropionate (DMSP), a key molecule in marine sulfur cycling, yet the specific physiological role of DMSP in corals remains elusive. Here, we examine the oxidative stress response of three coral species (Acropora millepora, Stylophora pistillata and Pocillopora damicornis) and explore the antioxidant role of DMSP and its breakdown products under short-termhyposalinity stress. Symbiont photosynthetic activity declined with hyposalinity exposure in all three reef-building corals. This corresponded with the upregulation of superoxide dismutase and glutathione in the animal host of all three species. For the symbiont component, there were differences in antioxidant regulation, demonstrating differential responses to oxidative stress between the Symbiodinium subclades. Of the three coral species investigated, only A. millepora provided any evidence of the role of DMSP in the oxidative stress response. Our study reveals variability in antioxidant regulation in corals and highlights the influence life-history traits, and the subcladal differences can have on coral physiology.Our data expand on the emerging understanding of the role of DMSP in coral stress regulation and emphasizes the importance of exploring both the host and symbiont responses for defining the threshold of the coral holobiont to hyposalinity stress.

Garg, M, Lata, K & Satija, S 2016, 'Cytotoxic potential of few Indian fruit peels through 3-(4,5-dimethylthiazol-yl)-2,5-diphenyltetrazolium bromide assay on HepG2 cells', Indian Journal of Pharmacology, vol. 48, no. 1, pp. 64-64.
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Garren, M, Son, K, Tout, J, Seymour, JR & Stocker, R 2016, 'Temperature-induced behavioral switches in a bacterial coral pathogen', The ISME Journal, vol. 10, no. 6, pp. 1363-1372.
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Abstract Evidence to date indicates that elevated seawater temperatures increase the occurrence of coral disease, which is frequently microbial in origin. Microbial behaviors such as motility and chemotaxis are often implicated in coral colonization and infection, yet little is known about the effect of warming temperatures on these behaviors. Here we present data demonstrating that increasing water temperatures induce two behavioral switches in the coral pathogen Vibrio coralliilyticus that considerably augment the bacterium’s performance in tracking the chemical signals of its coral host, Pocillopora damicornis. Coupling field-based heat-stress manipulations with laboratory-based observations in microfluidic devices, we recorded the swimming behavior of thousands of individual pathogen cells at different temperatures, associated with current and future climate scenarios. When temperature reached ⩾23 °C, we found that the pathogen’s chemotactic ability toward coral mucus increased by &gt;60%, denoting an enhanced capability to track host-derived chemical cues. Raising the temperature further, to 30 °C, increased the pathogen’s chemokinetic ability by &gt;57%, denoting an enhanced capability of cells to accelerate in favorable, mucus-rich chemical conditions. This work demonstrates that increasing temperature can have strong, multifarious effects that enhance the motile behaviors and host-seeking efficiency of a marine bacterial pathogen.

Ge, L, Habiel, DM, Hansbro, PM, Kim, RY, Gharib, SA, Edelman, JD, Königshoff, M, Parimon, T, Brauer, R, Huang, Y, Allen, J, Jiang, D, Kurkciyan, AA, Mizuno, T, Stripp, BR, Noble, PW, Hogaboam, CM & Chen, P 2016, 'miR-323a-3p regulates lung fibrosis by targeting multiple profibrotic pathways', JCI Insight, vol. 1, no. 20, p. e90301.
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Maladaptive epithelial repair from chronic injury is a common feature in fibrotic diseases, which in turn activates a pathogenic fibroblast response that produces excessive matrix deposition. Dysregulated microRNAs (miRs) can regulate expression of multiple genes and fundamentally alter cellular phenotypes during fibrosis. Although several miRs have been shown to be associated with lung fibrosis, the mechanisms by which miRs modulate epithelial behavior in lung fibrosis are lacking. Here, we identified miR-323a-3p to be downregulated in the epithelium of lungs with bronchiolitis obliterans syndrome (BOS) after lung transplantation, idiopathic pulmonary fibrosis (IPF), and murine bleomycin-induced fibrosis. Antagomirs for miR-323a-3p augment, and mimics suppress, murine lung fibrosis after bleomycin injury, indicating that this miR may govern profibrotic signals. We demonstrate that miR-323a-3p attenuates TGF-α and TGF-β signaling by directly targeting key adaptors in these important fibrogenic pathways. Moreover, miR-323a-3p lowers caspase-3 expression, thereby limiting programmed cell death from inducers of apoptosis and ER stress. Finally, we find that epithelial expression of miR-323a-3p modulates inhibitory crosstalk with fibroblasts. These studies demonstrate that miR-323a-3p has a central role in lung fibrosis that spans across murine and human disease, and downregulated expression by the lung epithelium releases inhibition of various profibrotic pathways to promote fibroproliferation.

Geiss, R, Sergeyev, A, Hartung, H, Solntsev, AS, Sukhorukov, AA, Grange, R, Schrempel, F, Kley, E-B, Tünnermann, A & Pertsch, T 2016, 'Fabrication of free-standing lithium niobate nanowaveguides down to 50 nm in width', Nanotechnology, vol. 27, no. 6, pp. 065301-065301.
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© 2016 IOP Publishing Ltd. Nonlinear optical nanoscale waveguides are a compact and powerful platform for efficient wavelength conversion. The free-standing waveguide geometry opens a range of applications in microscopy for local delivery of light, where in situ wavelength conversion helps to overcome various wavelength-dependent issues, such as biological tissue damage. In this paper, we present an original patterning method for high-precision fabrication of free-standing nanoscale waveguides based on lithium niobate, a material with a strong second-order nonlinearity and a broad transparency window covering the visible and mid-infrared wavelength ranges. The fabrication process combines electron-beam lithography with ion-beam enhanced etching and produces nanowaveguides with lengths from 5 to 50 μm, widths from 50 to 1000 nm and heights from 50 to 500 nm, each with a precision of few nanometers. The fabricated nanowaveguides are tested in an optical characterization experiment showing efficient second-harmonic generation.

Gentle, AR & Smith, GB 2016, 'Is enhanced radiative cooling of solar cell modules worth pursuing?', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 150, pp. 39-42.
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© 2016 Elsevier B.V. All rights reserved. Recent suggestions that worthwhile additional cooling of 1.0-1.5 °C below what glass covers in solar cell modules already achieve, hence raised power output, will occur via enhanced thermal radiation to the sky with special nanostructures, is examined. Rigorous thermal models indicate these observations require a much lower hemispherical emittance (EH) for the benchmarks of silica and glass covers near 0.75. If the currently accepted value for EH of glass of 0.84 applied even EH=1.0 would provide inadequate extra cooling. An accurate angular emittance profile for glass does predict this lower EH. Complete models include solar heating, heating by atmospheric radiation, cooling by convection and side/base losses. Unfortunately any large lift in radiative output from raised EH at normal cell temperatures is mostly annulled by the accompanying fall in convective cooling. The link of EH to angular IR response points the way to novel coating approaches which may achieve the desired cooling gains. This has wider implications for buildings and other solar technologies. Direct power gains from accompanying anti-reflectance add value.

Gentle, AR, Yambem, SD, Burn, PL, Meredith, P & Smith, GB 2016, 'AZO/Ag/AZO anode for resonant cavity red, blue, and yellow organic light emitting diodes', JOURNAL OF APPLIED PHYSICS, vol. 119, no. 24.
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© 2016 Author(s). Indium tin oxide (ITO) is the transparent electrode of choice for organic light-emitting diodes (OLEDs). Replacing ITO for cost and performance reasons is a major drive across optoelectronics. In this work, we show that changing the transparent electrode on red, blue, and yellow OLEDs from ITO to a multilayer buffered aluminium zinc oxide/silver/aluminium zinc oxide (AZO/Ag/AZO) substantially enhances total output intensity, with better control of colour, its constancy, and intensity over the full exit hemisphere. The thin Ag containing layer induces a resonant cavity optical response of the complete device. This is tuned to the emission spectra of the emissive material while minimizing internally trapped light. A complete set of spectral intensity data is presented across the full exit hemisphere for each electrode type and each OLED colour. Emission zone modelling of output spectra at a wide range of exit angles to the normal was in excellent agreement with the experimental data and hence could, in principle, be used to check and adjust production settings. These multilayer transparent electrodes show significant potential for both eliminating indium from OLEDs and spectrally shaping the emission.

Geronimo, FRB, Barter, PJ, Rye, KA, Heather, AK, Shearston, KD & Rodgers, KJ 2016, 'Plaque stabilizing effects of apolipoprotein A-IV', Atherosclerosis, vol. 251, pp. 39-46.
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BACKGROUND AND AIMS: Apolipoprotein (apo) A-IV, the third most abundant HDL-associated protein, is atheroprotective and shares similar properties as apoA-I. We have reported previously that apoA-I, the most abundant apolipoprotein in HDL, inhibits plaque disruption in a mouse model. We aimed at examining the effects of apoA-IV on markers of plaque stability in vivo. METHODS: Plaques within brachiocephalic arteries of 16-week old apoE-knockout C57BL/6 mice were examined for changes in composition after 10 weeks on a high-fat diet (HFD). The animals received twice-weekly injections of human lipid-free apoA-IV (1 mg/kg, n = 31) or PBS (n = 32) during the 9th and 10th weeks of the HFD. RESULTS: In the apoA-IV treated mice, there were significantly fewer hemorrhagic plaque disruptions (9/31 vs. 18/32, p < 0.05), thicker fibrous caps, smaller lipid cores, a lower macrophage:SMC ratio, less MMP-9 protein, more collagen, and fewer proliferating cells. In the plaques of mice given apoA-IV, MCP-1, VCAM-1, and inducible NOS were also significantly lower. Based on the percentage of cleaved PARP-positive and TUNEL-positive plaque nuclei, apoA-IV reduced apoptosis. in HMDMs, apoA-IV reduced MMP-9 mRNA expression by half, doubled mRNA levels of TIMP1 and decreased MMP-9 activity. CONCLUSIONS: ApoA-IV treatment is associated with a more stable plaque phenotype and a reduced incidence of acute disruptions in this mouse model.

Ghazilou, A, Shokri, MR & Gladstone, W 2016, 'Animal v. plant‐based bait: does the bait type affect census of fish assemblages and trophic groups by baited remote underwater video (BRUV) systems?', Journal of Fish Biology, vol. 88, no. 5, pp. 1731-1745.
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Coral reef fish communities were sampled at the Nayband Marine Park, Iran, using baited remote underwater video stations (BRUVSs) which incorporated animal (i.e. frigate tuna Auxis thazard and beef liver), or plant‐based baits (i.e. raw dough and raw dough‐turmeric powder mix). The A. thazard was found to record significantly (P < 0·05) higher species richness and number of carnivorous fishes than plant‐based baits, while abundance of herbivores was maximum in raw dough‐turmeric powder mix trials. There was also a significant difference in trophic composition of fish assemblages surveyed by animal‐ and plant‐based baits which seemed to be due to variations in attraction patterns of carnivores and herbivores occurring at the earlier phases of each BRUV deployments. Meanwhile, the assemblage structure was comparable among fish assemblages sampled by different bait treatments, indicating that species‐level responses to each bait type may be more complicated. In essence, the efficiency of mixed baits should also be examined in future studies.

Ghazilou, A, Shokri, MR & Gladstone, W 2016, 'Application of baited remote underwater video stations to assess benthic coverage in the Persian Gulf', Marine Pollution Bulletin, vol. 105, no. 2, pp. 606-612.
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Ghazilou, A, Shokri, MR & Gladstone, W 2016, 'Coral reef fish assemblages along a disturbance gradient in the northern Persian Gulf: A seasonal perspective', Marine Pollution Bulletin, vol. 105, no. 2, pp. 599-605.
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Gholami, A & Maddahfar, M 2016, 'Synthesis and characterization of barium molybdate nanostructures with the aid of amino acids and investigation of its photocatalytic degradation of methyl orange', Journal of Materials Science: Materials in Electronics, vol. 27, no. 7, pp. 6773-6778.
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Gholami, A & Maddahfar, M 2016, 'Synthesis and characterization of novel samarium-doped CuAl2O4 and its photocatalytic performance through the modified sol–gel method', Journal of Materials Science: Materials in Electronics, vol. 27, no. 4, pp. 3341-3346.
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Glastras, SJ, Chen, H, McGrath, RT, Zaky, AA, Gill, AJ, Pollock, CA & Saad, S 2016, 'Effect of GLP-1 Receptor Activation on Offspring Kidney Health in a Rat Model of Maternal Obesity', Scientific Reports, vol. 6, no. 1.
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AbstractMaternal obesity is associated with an increased risk of chronic disease in offspring, including type 2 diabetes (T2D). Exendin-4 (Exd-4) activates the glucagon like peptide-1 (GLP-1) receptor thereby decreasing serum glucose levels and body weight. In addition, Exd-4 has been shown to reduce renal and cardiac complications in experimental models of T2D. We hypothesized that treatment with Exd-4 would ameliorate the detrimental effects of maternal and diet-induced obesity on renal characteristics in offspring. Female Sprague-Dawley rats were fed either normal or high-fat diet (HFD) for 6 weeks prior to pregnancy, during pregnancy and lactation, and their offspring were weaned to normal or HFD. The offspring were randomized to Exd-4 or placebo from weaning and their kidneys harvested at Week 9. We found that the kidneys of offspring from obese mothers, regardless of postnatal diet, had significantly increased markers of inflammation, oxidative stress and fibrosis. Exd-4 ameliorated the negative renal effects of maternal obesity and in particular, reduced renal inflammation, oxidative stress and fibrosis. In conclusion, maternal obesity has persisting effects on renal structure in the offspring. GLP-1 analogues are potentially useful for protecting against the deleterious effects of maternal obesity on renal physiology in offspring.

Glastras, SJ, Tsang, M, Teh, R, Chen, H, McGrath, RT, Zaky, AA, Pollock, CA & Saad, S 2016, 'Maternal Obesity Promotes Diabetic Nephropathy in Rodent Offspring', Scientific Reports, vol. 6, no. 1.
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AbstractMaternal obesity is known to increase the risk of obesity and diabetes in offspring. Though diabetes is a key risk factor for the development of chronic kidney disease (CKD), the relationship between maternal obesity and CKD has not been clearly defined. In this study, a mouse model of maternal obesity was employed to determine the impact of maternal obesity on development of diabetic nephropathy in offspring. 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 diet. At postnatal Week 8, offspring were randomly administered low dose streptozotocin (STZ, 55 mg/kg/day for five days) to induce diabetes. Assessment of renal damage took place at postnatal Week 32. We found that offspring of obese mothers had increased renal fibrosis, inflammation and oxidative stress. Importantly, offspring exposed to maternal obesity had increased susceptibility to renal damage when an additional insult, such as STZ-induced diabetes, was imposed. Specifically, renal inflammation and oxidative stress induced by diabetes was augmented by maternal obesity. Our findings suggest that developmental programming induced by maternal obesity has implications for renal health in offspring. Maternal obesity should be considered a risk factor for CKD.

Gleason, SM, Blackman, CJ, Chang, Y, Cook, AM, Laws, CA & Westoby, M 2016, 'Weak coordination among petiole, leaf, vein, and gas‐exchange traits across Australian angiosperm species and its possible implications', Ecology and Evolution, vol. 6, no. 1, pp. 267-278.
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AbstractClose coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life forms. However, it has also been suggested that this relationship may become weak or break down completely within the angiosperms. We examined coordination between hydraulic, leaf vein, and gas‐exchange traits across a diverse group of 35 evergreen Australian angiosperms, spanning a large range in leaf structure and habitat. Leaf‐specific conductance was calculated from petiole vessel anatomy and was also measured directly using the rehydration technique. Leaf vein density (thought to be a determinant of gas exchange rate), maximal stomatal conductance, and net CO2 assimilation rate were also measured for most species (n = 19–35). Vein density was not correlated with leaf‐specific conductance (either calculated or measured), stomatal conductance, nor maximal net CO2 assimilation, with r2 values ranging from 0.00 to 0.11, P values from 0.909 to 0.102, and n values from 19 to 35 in all cases. Leaf‐specific conductance calculated from petiole anatomy was weakly correlated with maximal stomatal conductance (r2 = 0.16; P = 0.022; n = 32), whereas the direct measurement of leaf‐specific conductance was weakly correlated with net maximal CO2 assimilation (r2 = 0.21; P = 0.005; n = 35). Calculated leaf‐specific conductance, xylem ultr...

Godecke, E, Armstrong, EA, Rai, T, Middleton, S, Ciccone, N, Whitworth, A, Rose, M, Holland, A, Ellery, F, Hankey, GJ, Cadilhac, DA & Bernhardt, J 2016, 'A randomized controlled trial of very early rehabilitation in speech after stroke', International Journal of Stroke, vol. 11, no. 5, pp. 586-592.
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Rationale The efficacy of rehabilitation therapy for aphasia caused by stroke is uncertain. Aims and hypothesis The Very Early Rehabilitation of Speech (VERSE) trial aims to determine if intensive prescribed aphasia therapy (VERSE) is more effective and cost saving than non-prescribed, intensive (usual care-plus) and non-intensive usual care (UC) therapy when started within 15 days of stroke onset and continued daily over four weeks. We hypothesize that aphasia therapy when started very early after stroke and delivered daily could enhance recovery of communication compared with UC. Sample size estimates A total of 246 participants (82 per arm) will provide 80% power to detect a 4.4% improvement on aphasia quotient between VERSE and UC plus at a significance level of α = 0.05. Setting Acute-care hospitals and accompanying rehabilitation services throughout Australia, 2014–2017. Design Three-arm, prospective, randomized, parallel group, open-label, blinded endpoint assessment (PROBE) trial. Participants Acute stroke in previous 14 days and aphasia diagnosed by aphasia quotient (AQ) of the Western Aphasia Battery (WAB). Randomization Computer-generated blocked randomization procedure stratified by aphasia severity according to Western Aphasia Battery, to one of three arms. Intervention All participants receive UC—usual ward-based aphasia therapy. Arm 1: UC—no additional therapy; Arm 2: UC-plus usual ward-based therapy; Arm 3: VERSE therapy—a prescribed and structured aphasia therap...

Gold, MJ, Hiebert, PR, Park, HY, Stefanowicz, D, Le, A, Starkey, MR, Deane, A, Brown, AC, Liu, G, Horvat, JC, Ibrahim, ZA, Sukkar, MB, Hansbro, PM, Carlsten, C, VanEeden, S, Sin, DD, McNagny, KM, Knight, DA & Hirota, JA 2016, 'Mucosal production of uric acid by airway epithelial cells contributes to particulate matter-induced allergic sensitization', MUCOSAL IMMUNOLOGY, vol. 9, no. 3, pp. 809-820.
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Exposure to particulate matter (PM), a major component of air pollution, contributes to increased morbidity and mortality worldwide. PM induces innate immune responses and contributes to allergic sensitization, although the mechanisms governing this process remain unclear. Lung mucosal uric acid has also been linked to allergic sensitization. The links among PM exposure, uric acid, and allergic sensitization remain unexplored. We therefore investigated the mechanisms behind PM-induced allergic sensitization in the context of lung mucosal uric acid. PM 10 and house dust mite exposure selectively induced lung mucosal uric acid production and secretion in vivo, which did not occur with other challenges (lipopolysaccharide, virus, bacteria, or inflammatory/fibrotic stimuli). PM 10 -induced uric acid mediates allergic sensitization and augments antigen-specific T-cell proliferation, which is inhibited by uricase. We then demonstrate that human airway epithelial cells secrete uric acid basally and after stimulation through a previously unidentified mucosal secretion system. Our work discovers a previously unknown mechanism of air pollution-induced, uric acid-mediated, allergic sensitization that may be important in the pathogenesis of asthma.

Gorlach, MA, Voytova, TA, Lapine, M, Kivshar, YS & Belov, PA 2016, 'Nonlocal homogenization for nonlinear metamaterials', PHYSICAL REVIEW B, vol. 93, no. 16.
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©2016 American Physical Society. We present a consistent theoretical approach for calculating effective nonlinear susceptibilities of metamaterials taking into account both frequency and spatial dispersion. Employing the discrete dipole model, we demonstrate that effects of spatial dispersion become especially pronounced in the vicinity of effective permittivity resonance where nonlinear susceptibilities reach their maxima. In that case spatial dispersion may enable simultaneous generation of two harmonic signals with the same frequency and polarization but different wave vectors. We also prove that the derived expressions for nonlinear susceptibilities transform into the known form when spatial dispersion effects are negligible. In addition to revealing new physical phenomena, our results provide useful theoretical tools for analyzing resonant nonlinear metamaterials.

Gorrie, C, Mao, Y, Nguyen, T & Sutherland, T 2016, 'Endogenous neural progenitor cells in the repair of the injured spinal cord', Neural Regeneration Research, vol. 11, no. 7, pp. 1075-1075.
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Greaves, IK, Eichten, SR, Groszmann, M, Wang, A, Ying, H, Peacock, WJ & Dennis, ES 2016, 'Twenty-four–nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids', Proceedings of the National Academy of Sciences, vol. 113, no. 44, pp. E6895-E6902.
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Significance We show that the changes in DNA methylation that occur in F1 hybrids of Arabidopsis are mostly dependent on the presence of 24-nt siRNAs at the locus. The methylation change at a locus results in the two alleles becoming similar to each other in methylation pattern. The methylation changes occur through the processes of trans-chromosomal methylation and trans-chromosomal demethylation. These altered methylation states can be inherited in the F2 generation and can be associated with changes in levels of gene activity, which may contribute to the phenotypic heterogeneity in the F2.

Green, DW, Ben-Nissan, B, Yoon, K-S, Milthorpe, B & Jung, H-S 2016, 'Bioinspired materials for regenerative medicine: going beyond the human archetypes', Journal of Materials Chemistry B, vol. 4, no. 14, pp. 2396-2406.
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Living organisms are skilful innovators and fabricators of materials, driven by the forces of evolution. We describe the translation process between natural material innovations and human tissue engineering.

Griebel, A, Bennett, LT, Metzen, D, Cleverly, J, Burba, G & Arndt, SK 2016, 'Effects of inhomogeneities within the flux footprint on the interpretation of seasonal, annual, and interannual ecosystem carbon exchange', AGRICULTURAL AND FOREST METEOROLOGY, vol. 221, pp. 50-60.
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Gu, H 2016, 'Improving problem reduction for 0–1 Multidimensional Knapsack Problems with valid inequalities', Computers & Operations Research, vol. 71, pp. 82-89.
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Guangwu, X, Chengjun, T, Zhiwen, W, Shanlin, F, Liang, L & Yun, K 2016, 'The expression difference of AChE, BChE, PON-1 and FOS mRNA in rats died of acute phorate poisoning', Chinese Journal of Forensic Medicine, vol. 31, no. 3, pp. 249-252.
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Objective To investigate mRNA expression of the related genes (AChE,BChE,PON-1 and FOS) in SD rats died of acute phorate poisoning, and screen the significant organs and genes in the detection of death. Methods 12 grown-up female SD rats were divided into the acute poisoning group and the control group. Organ samples( heart, liver, lung, brain, small intestine) were collected respectively, and total RNA were isolated to be reversely transcribed to cDNA with gene primers of AChE, BChE, PON-1, FOS and interior label β-actin. The Real Time PCR was used to detect the comparative expression differences of them and the data of all the groups were analyzed statistically. Results In liver, the expression of AChE, BChE and FOS mRNA increased (P<0.05), while the expression of AChE mRNA decreased in lung and brain (P<0.05). Conclusion Liver and AChE could be served as the target organ and the gene expression mark for death by acute phorate poisoning respectively, which could also be set as the reference of the diagnose and death detection from acute phorate poisoning.

Guest, JR, Low, J, Tun, K, Wilson, B, Ng, C, Raingeard, D, Ulstrup, KE, Tanzil, JTI, Todd, PA, Toh, TC, McDougald, D, Chou, LM & Steinberg, PD 2016, 'Coral community response to bleaching on a highly disturbed reef', Scientific Reports, vol. 6, no. 1.
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AbstractWhile many studies of coral bleaching report on broad, regional scale responses, fewer examine variation in susceptibility among coral taxa and changes in community structure, before, during and after bleaching on individual reefs. Here we report in detail on the response to bleaching by a coral community on a highly disturbed reef site south of mainland Singapore before, during and after a major thermal anomaly in 2010. To estimate the capacity for resistance to thermal stress, we report on: a) overall bleaching severity during and after the event, b) differences in bleaching susceptibility among taxa during the event and c) changes in coral community structure one year before and after bleaching. Approximately two thirds of colonies bleached, however, post-bleaching recovery was quite rapid and, importantly, coral taxa that are usually highly susceptible were relatively unaffected. Although total coral cover declined, there was no significant change in coral taxonomic community structure before and after bleaching. Several factors may have contributed to the overall high resistance of corals at this site including Symbiodinium affiliation, turbidity and heterotrophy. Our results suggest that, despite experiencing chronic anthropogenic disturbances, turbid shallow reef communities may be remarkably resilient to acute thermal stress.

Guo, X, Sun, B, Zhang, J, Liu, H & Wang, G 2016, 'Ruthenium decorated hierarchically ordered macro-mesoporous carbon for lithium oxygen batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 4, no. 25, pp. 9774-9780.
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Haines, AM & Linacre, A 2016, 'A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling', Forensic Science International, vol. 262, pp. 190-195.
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Haines, AM, Tobe, SS & Linacre, A 2016, 'Optimization of Diamond Nucleic Acid Dye for Quantitative PCR', BioTechniques, vol. 61, no. 4, pp. 183-189.
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Hajduk, IV, Rodrigues, CDA & Harry, EJ 2016, 'Connecting the dots of the bacterial cell cycle: Coordinating chromosome replication and segregation with cell division', Seminars in Cell & Developmental Biology, vol. 53, pp. 2-9.
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© 2015. Proper division site selection is crucial for the survival of all organisms. What still eludes us is how bacteria position their division site with high precision, and in tight coordination with chromosome replication and segregation. Until recently, the general belief, at least in the model organisms Bacillus subtilis and Escherichia coli, was that spatial regulation of division comes about by the combined negative regulatory mechanisms of the Min system and nucleoid occlusion. However, as we review here, these two systems cannot be solely responsible for division site selection and we highlight additional regulatory mechanisms that are at play. In this review, we put forward evidence of how chromosome replication and segregation may have direct links with cell division in these bacteria and the benefit of recent advances in chromosome conformation capture techniques in providing important information about how these three processes mechanistically work together to achieve accurate generation of progenitor cells.

Hamidian, M & Hall, RM 2016, 'The resistance gene complement of D4, a multiply antibiotic-resistant ST25Acinetobacter baumanniiisolate, resides in two genomic islands and a plasmid', Journal of Antimicrobial Chemotherapy, vol. 71, no. 6, pp. 1730-1732.
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Hamidian, M, Ambrose, SJ & Hall, RM 2016, 'A large conjugative Acinetobacter baumannii plasmid carrying the sul2 sulphonamide and strAB streptomycin resistance genes', Plasmid, vol. 87-88, pp. 43-50.
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Acinetobacter baumannii is an important nosocomial pathogen that often complicates treatment because of its high level of resistance to antibiotics. Though plasmids can potentially introduce various genes into bacterial strains, compared to other Gram-negative bacteria, information about the unique A. baumannii plasmid repertoire is limited. Here, whole genome sequence data was used to determine the plasmid content of strain A297 (RUH875), the reference strain for the globally disseminated multiply resistant A. baumannii clone, global clone 1(GC1). A297 contains three plasmids. Two known plasmids were present; one, pA297-1 (pRAY*), carries the aadB gentamicin, kanamycin and tobramycin resistance gene and another is an 8.7kb cryptic plasmid often found in GC1 isolates. The third plasmid, pA297-3, is 200kb and carries the sul2 sulphonamide resistance gene and strAB streptomycin resistance gene within Tn6172 and a mer mercuric ion resistance module elsewhere. pA297-3 transferred sulphonamide, streptomycin and mercuric ion resistance at high frequency to a susceptible A. baumannii recipient, and contains several genes potentially involved in conjugative transfer. However, a relaxase gene was not found. It also includes several genes encoding proteins involved in DNA metabolism such as partitioning. However, a gene encoding a replication initiation protein could not be found. pA297-3 includes two copies of a Miniature Inverted-Repeat Transposable Element (MITE), named MITE-297, bracketing a 77.5kb fragment, which contains several IS and the mer module. Several plasmids related to but smaller than pA297-3 were found in the GenBank nucleotide database. They were found in different A. baumannii clones and are wide spread. They all contain either Tn6172 or a variant in the same position in the backbone as Tn6172 in pA297-3. Some related plasmids have lost the segment between the MITE-297 copies and retain only one MITE-297. Others have segments of various length...

Hamilton, LA, Tremblay, LA, Northcott, GL, Boake, M & Lim, RP 2016, 'The impact of variations of influent loading on the efficacy of an advanced tertiary sewage treatment plant to remove endocrine disrupting chemicals', Science of The Total Environment, vol. 560-561, pp. 101-109.
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© 2016 Elsevier B.V. The impact of changes in influent load on the removal of endocrine disrupting chemicals (EDCs) by sewage treatment has not been fully characterised. This study assessed the efficacy of an advanced tertiary sewage treatment plant (STP) to remove EDCs during normal and peak flow events of sewage influent using trace chemical analysis of selected EDCs and four estrogenic in vitro bioassays. During the summer holiday season, influent volume increased by 68%, nutrient concentrations by at least 26% and hydraulic retention time was reduced by 40% compared with base flow conditions. Despite these pressures on the treatment system the concentrations and mass loading of estrone, 17β-estradiol, estriol, Bisphenol A, 4-t-octylphenol and technical nonylphenol were not significantly higher (p > 0.05) during the peak flow conditions compared with base flow conditions. Chemical analysis and in vitro bioassays showed that the efficacy of the STP in removing EDCs was not affected by the different loadings between baseline and peak flow regimes. This study demonstrates that large flow variations within the design capacity of advanced multi-stage STPs should not reduce the removal efficacy of EDCs.

Hammer, JF, Jenkins, C, Bogema, D & Emery, D 2016, 'Mechanical transfer of Theileria orientalis: possible roles of biting arthropods, colostrum and husbandry practices in disease transmission', PARASITES & VECTORS, vol. 9.
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Hare, DJ & Double, KL 2016, 'Iron and dopamine: a toxic couple', Brain, vol. 139, no. 4, pp. 1026-1035.
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© 2016 The Author (2016). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. Iron accumulation is a cardinal feature of degenerating regions in the Parkinson's disease brain. As a potent pro-oxidant, redox-active iron may be a key player in upstream mechanisms that precipitate cell death in this disorder. Although an elevation in brain iron levels is a normal feature of ageing, the increase is greater in Parkinson's disease; on the other hand, the effects of the disease are most marked in the nigrostriatal dopaminergic system. In this Update, we explain that neurodegeneration in the affected regions may result from the potent redox couple formed by iron and dopamine itself, and discuss the clinical implications of this molecular trait in this dynamic and rapidly moving area of Parkinson's disease research.

Hare, DJ & New, EJ 2016, 'On the outside looking in: redefining the role of analytical chemistry in the biosciences', Chemical Communications, vol. 52, no. 58, pp. 8918-8934.
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Analytical chemistry has much to offer to an improved understanding of biological systems.

Hare, DJ, Faux, NG, Roberts, BR, Volitakis, I, Martins, RN & Bush, AI 2016, 'Lead and manganese levels in serum and erythrocytes in Alzheimer's disease and mild cognitive impairment: results from the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing', Metallomics, vol. 8, no. 6, pp. 628-632.
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Hare, DJ, Fryer, F, Paul, B, Bishop, DP & Doble, PA 2016, 'Characterisation of matrix-based polyatomic interference formation in laser ablation-inductively coupled plasma-mass spectrometry using dried micro-droplet ablation and its relevance for bioimaging', Analytical Methods, vol. 8, no. 41, pp. 7552-7556.
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Dried micro-droplets were used to characterise the formation of polyatomic interferences by LA-ICP-MS.

Hare, DJ, Jones, MWM, Wimmer, VC, Jenkins, NL, de Jonge, MD, Bush, AI & McColl, G 2016, 'High-resolution complementary chemical imaging of bio-elements in Caenorhabditis elegans', Metallomics, vol. 8, no. 2, pp. 156-160.
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A unified approach to chemical imaging was used to spatially profile essential bio-elements in Caenorhabditis elegans.

Hare, DJ, Raven, EP, Roberts, BR, Bogeski, M, Portbury, SD, McLean, CA, Masters, CL, Connor, JR, Bush, AI, Crouch, PJ & Doble, PA 2016, 'Laser ablation-inductively coupled plasma-mass spectrometry imaging of white and gray matter iron distribution in Alzheimer's disease frontal cortex', NeuroImage, vol. 137, pp. 124-131.
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© 2016. Iron deposition in the brain is a feature of normal aging, though in several neurodegenerative disorders, including Alzheimer's disease, the rate of iron accumulation is more advanced than in age-matched controls. Using laser ablation-inductively coupled plasma-mass spectrometry imaging we present here a pilot study that quantitatively assessed the iron content of white and gray matter in paraffin-embedded sections from the frontal cortex of Alzheimer's and control subjects. Using the phosphorus image as a confirmed proxy for the white/gray matter boundary, we found that increased intrusion of iron into gray matter occurs in the Alzheimer's brain compared to controls, which may be indicative of either a loss of iron homeostasis in this vulnerable brain region, or provide evidence of increased inflammatory processes as a response to chronic neurodegeneration. We also observed a trend of increasing iron within the white matter of the frontal cortex, potentially indicative of disrupted iron metabolism preceding loss of myelin integrity. Considering the known potential toxicity of excessive iron in the brain, our results provide supporting evidence for the continuous development of novel magnetic resonance imaging approaches for assessing white and gray matter iron accumulation in Alzheimer's disease.

Hare, DJ, Roberts, BR & McColl, G 2016, 'Profiling changes to natively-bound metals during Caenorhabditis elegans development', RSC Advances, vol. 6, no. 114, pp. 113689-113693.
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This paper describes a proof-of-concept study using SEC-ICP-MS to profile changes in metalloproteins duringCaenorhabditis elegansdevelopment.

Harmer, CJ, Hamidian, M, Ambrose, SJ & Hall, RM 2016, 'Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands', Plasmid, vol. 87-88, pp. 51-57.
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Haw, TJ, Starkey, MR, Nair, PM, Pavlidis, S, Liu, G, Nguyen, DH, Hsu, AC, Hanish, I, Kim, RY, Collison, AM, Inman, MD, Wark, PA, Foster, PS, Knight, DA, Mattes, J, Yagita, H, Adcock, IM, Horvat, JC & Hansbro, PM 2016, 'A pathogenic role for tumor necrosis factor-related apoptosis-inducing ligand in chronic obstructive pulmonary disease', Mucosal Immunology, vol. 9, no. 4, pp. 859-872.
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Chronic obstructive pulmonary disease (COPD) is a life-threatening inflammatory respiratory disorder, often induced by cigarette smoke (CS) exposure. The development of effective therapies is impaired by a lack of understanding of the underlining mechanisms. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine with inflammatory and apoptotic properties. We interrogated a mouse model of CS-induced experimental COPD and human tissues to identify a novel role for TRAIL in COPD pathogenesis. CS exposure of wild-type mice increased TRAIL and its receptor messenger RNA (mRNA) expression and protein levels, as well as the number of TRAIL(+)CD11b(+) monocytes in the lung. TRAIL and its receptor mRNA were also increased in human COPD. CS-exposed TRAIL-deficient mice had decreased pulmonary inflammation, pro-inflammatory mediators, emphysema-like alveolar enlargement, and improved lung function. TRAIL-deficient mice also developed spontaneous small airway changes with increased epithelial cell thickness and collagen deposition, independent of CS exposure. Importantly, therapeutic neutralization of TRAIL, after the establishment of early-stage experimental COPD, reduced pulmonary inflammation, emphysema-like alveolar enlargement, and small airway changes. These data provide further evidence for TRAIL being a pivotal inflammatory factor in respiratory diseases, and the first preclinical evidence to suggest that therapeutic agents that target TRAIL may be effective in COPD therapy.

He, F, Li, C, Zhang, X, Chen, Y, Deng, X, Liu, B, Hou, Z, Huang, S, Jin, D & Lin, J 2016, 'Optimization of upconversion luminescence of Nd³⁺-sensitized BaGdF₅-based nanostructures and their application in dual-modality imaging and drug delivery', Dalton Transactions, vol. 45, no. 4, pp. 1708-1716.
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Nd³⁺-sensitized BaGdF₅:20%Yb³⁺/2%Er³⁺@BaGdF₅:10%Yb³⁺@BaNdF₅@BaGdF₅ nanoparticles for dual-model imaging and pH-triggered drug release.

Heidrich, ES, Curtis, TP, Woodcock, S & Dolfing, J 2016, 'Quantification of effective exoelectrogens by most probable number (MPN) in a microbial fuel cell', Bioresource Technology, vol. 218, pp. 27-30.
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© 2016 The Author(s). The objective of this work was to quantify the number of exoelectrogens in wastewater capable of producing current in a microbial fuel cell by adapting the classical most probable number (MPN) methodology using current production as end point. Inoculating a series of microbial fuel cells with various dilutions of domestic wastewater and with acetate as test substrate yielded an apparent number of exoelectrogens of 17 per ml. Using current as a proxy for activity the apparent exoelectrogen growth rate was 0.03 h-1. With starch or wastewater as more complex test substrates similar apparent growth rates were obtained, but the apparent MPN based numbers of exoelectrogens in wastewater were significantly lower, probably because in contrast to acetate, complex substrates require complex food chains to deliver the electrons to the electrodes. Consequently, the apparent MPN is a function of the combined probabilities of members of the food chain being present.

Henriques, ST, Deplazes, E, Lawrence, N, Cheneval, O, Chaousis, S, Inserra, M, Thongyoo, P, King, GF, Mark, AE, Vetter, I, Craik, DJ & Schroeder, CI 2016, 'Interaction of Tarantula Venom Peptide ProTx-II with Lipid Membranes Is a Prerequisite for Its Inhibition of Human Voltage-gated Sodium Channel NaV1.7', Journal of Biological Chemistry, vol. 291, no. 33, pp. 17049-17065.
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Herdean, A, Nziengui, H, Zsiros, O, Solymosi, K, Garab, G, Lundin, B & Spetea, C 2016, 'The Arabidopsis Thylakoid Chloride Channel AtCLCe Functions in Chloride Homeostasis and Regulation of Photosynthetic Electron Transport', Frontiers in Plant Science, vol. 7, no. FEB2016, p. 115.
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Chloride ions can be translocated across cell membranes through Cl(-) channels or Cl(-)/H(+) exchangers. The thylakoid-located member of the Cl(-) channel CLC family in Arabidopsis thaliana (AtCLCe) was hypothesized to play a role in photosynthetic regulation based on the initial photosynthetic characterization of clce mutant lines. The reduced nitrate content of Arabidopsis clce mutants suggested a role in regulation of plant nitrate homeostasis. In this study, we aimed to further investigate the role of AtCLCe in the regulation of ion homeostasis and photosynthetic processes in the thylakoid membrane. We report that the size and composition of proton motive force were mildly altered in two independent Arabidopsis clce mutant lines. Most pronounced effects in the clce mutants were observed on the photosynthetic electron transport of dark-adapted plants, based on the altered shape and associated parameters of the polyphasic OJIP kinetics of chlorophyll a fluorescence induction. Other alterations were found in the kinetics of state transition and in the macro-organization of photosystem II supercomplexes, as indicated by circular dichroism measurements. Pre-treatment with KCl but not with KNO3 restored the wild-type photosynthetic phenotype. Analyses by transmission electron microscopy revealed a bow-like arrangement of the thylakoid network and a large thylakoid-free stromal region in chloroplast sections from the dark-adapted clce plants. Based on these data, we propose that AtCLCe functions in Cl(-) homeostasis after transition from light to dark, which affects chloroplast ultrastructure and regulation of photosynthetic electron transport.

Herdean, A, Teardo, E, Nilsson, AK, Pfeil, BE, Johansson, ON, Ünnep, R, Nagy, G, Zsiros, O, Dana, S, Solymosi, K, Garab, G, Szabó, I, Spetea, C & Lundin, B 2016, 'A voltage-dependent chloride channel fine-tunes photosynthesis in plants', Nature Communications, vol. 7, no. 1, p. 11654.
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AbstractIn natural habitats, plants frequently experience rapid changes in the intensity of sunlight. To cope with these changes and maximize growth, plants adjust photosynthetic light utilization in electron transport and photoprotective mechanisms. This involves a proton motive force (PMF) across the thylakoid membrane, postulated to be affected by unknown anion (Cl−) channels. Here we report that a bestrophin-like protein from Arabidopsis thaliana functions as a voltage-dependent Cl− channel in electrophysiological experiments. AtVCCN1 localizes to the thylakoid membrane, and fine-tunes PMF by anion influx into the lumen during illumination, adjusting electron transport and the photoprotective mechanisms. The activity of AtVCCN1 accelerates the activation of photoprotective mechanisms on sudden shifts to high light. Our results reveal that AtVCCN1, a member of a conserved anion channel family, acts as an early component in the rapid adjustment of photosynthesis in variable light environments.

Hitchcock, JN, Mitrovic, SM, Hadwen, WL, Growns, IO & Rohlfs, A-M 2016, 'Zooplankton responses to freshwater inflows and organic-matter pulses in a wave-dominated estuary', Marine and Freshwater Research, vol. 67, no. 9, pp. 1374-1374.
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Freshwater inflow events play a major role in structuring estuarine zooplankton communities. Freshwater inflow events affect zooplankton directly through advective forcing and changes in salinity, and indirectly through changes to resources by the delivery of organic carbon and nutrients that can stimulate microbial and primary production. Here, we investigate changes to estuarine zooplankton assemblage structure, density and δ13C stable isotopes during a period of highly variable freshwater inflow in the Bega River estuary, Australia. High inflows resulted in a reduction of salinity and a shift in the zooplankton assemblage structure from purely estuarine taxa towards freshwater taxa. The density of select genera of rotifers, cladocera and, in the upper estuary, copepods, increased following inflows, concurrent with increases in the concentration of dissolved organic carbon and bacterial biomass. Redundancy analysis found that environmental variables including discharge, dissolved organic carbon, salinity and bacterial biomass explained 66–73% of zooplankton variation. Stable isotope results indicated that all copepod and cladocera species tested were predominantly supported by allochthonous carbon from terrestrial sources. The present results have provided important evidence that freshwater inflows play a critical role in structuring zooplankton assemblages and supporting increased production through the delivery of allochthonous organic carbon.

Hitchcock, JN, Mitrovic, SM, Hadwen, WL, Roelke, DL, Growns, IO & Rohlfs, A-M 2016, 'Terrestrial dissolved organic carbon subsidizes estuarine zooplankton: An in situ mesocosm study', Limnology and Oceanography, vol. 61, no. 1, pp. 254-267.
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© 2016 Association for the Sciences of Limnology and Oceanography. Freshwater inflows play an important role in delivering dissolved organic carbon (DOC) to estuaries. Episodic inputs of DOC may support increased bacterial production. However, the role of DOC in supporting zooplankton production is widely deb ated. To evaluate this role we performed an in situ mesocosm experiment in the Bega River estuary, Australia. We added a DOC leachate derived from terrestrial vegetation to 400 L mesocosm bags as treatments of +1.5, +3, and +16 mg C L -1 and monitored changes in carbon, nitrogen, phosphorus, bacteria, chlorophyll a (Chl a), and zooplankton over 22 d. Bacterial biomass peaked at day 2 and was highest in the +16 mg C L -1 treatment. Chl a was not significantly different between treatments. Mesozooplankton was dominated by copepodites of Gladioferens pectinatus and Sulcanus conflictus between days 5-9 and by adults between days 9-15. Significantly higher numbers of copepods were present in the +16 treatment followed by the +3 mg C L -1 treatment compared with the controls. Stable carbon isotope signatures of copepods in the +16 mg C L -1 treatment were significantly different from the control and showed leachate carbon supported between 29.3% and 55.8% of copepod biomass. These results suggest that the impact of allochthonous DOC loading events on estuarine zooplankton occurs over short periods, and that the magnitude of response is, in part, controlled by the quantity of bioavailable DOC loaded to the system. Our findings underscore the importance of microbial dynamics stimulated by DOC loading events from freshwater inflows as a trophic path in estuarine food webs.

Ho, JS, Low, JH, Sim, LN, Webster, RD, Rice, SA, Fane, AG & Coster, HGL 2016, 'In-situ monitoring of biofouling on reverse osmosis membranes: Detection and mechanistic study using electrical impedance spectroscopy', Journal of Membrane Science, vol. 518, pp. 229-242.
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Ho, YYW, Brims, M, McNevin, D, Spector, TD, Martin, NG & Medland, SE 2016, 'Variation and Heritability in Hair Diameter and Curvature in an Australian Twin Sample', Twin Research and Human Genetics, vol. 19, no. 4, pp. 351-358.
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Hair diameter and curvature are two characteristics of human scalp hair used in forensic contexts. While previous data show that subjective categorization of hair curvature is highly heritable, the heritability of objectively measured curvature and diameter, and variability of hair characteristics within each individual have not yet been studied. The present study measured hair diameter and curvature using an optical fiber diameter analyzer in a sample of 2,332 twins and siblings. Heritability was estimated using maximum likelihood structural equation modeling. Results show sex differences in the magnitude of genetic influence for mean diameter and curvature, with the vast majority of the variance accounted for by genetic effects in males (diameter = 86%, curvature = 53%) and females (diameter = 77%, curvature = 61%). The consistency of diameter (variance within an individual) was also highly heritable, but did not show sex limitation, with 68% of the variance accounted for by genetic factors. Moderate phenotypic correlations were seen between diameter and consistency (r = 0.3) but there was little correlation between diameter and curvature (r = -0.13). A bivariate Cholesky analysis was used to estimate the genetic and environmental correlations between hair diameter and consistency, yielding genetic correlations of rgF = 0.27 for females and rgM = 0.25 for males.

Hoiles, W, Gupta, R, Cornell, B, Cranfield, C & Krishnamurthy, V 2016, 'The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study', PLOS ONE, vol. 11, no. 10.
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Holt, K, Kenyon, JJ, Hamidian, M, Schultz, MB, Pickard, DJ, Dougan, G & Hall, R 2016, 'Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1', Microbial Genomics, vol. 2, no. 2, p. e000052.
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The majority of Acinetobacter baumannii isolates that are multiply, extensively and pan-antibiotic resistant belong to two globally disseminated clones, GC1 and GC2, that were first noticed in the 1970s. Here, we investigated microevolution and phylodynamics within GC1 via analysis of 45 whole-genome sequences, including 23 sequenced for this study. The most recent common ancestor of GC1 arose around 1960 and later diverged into two phylogenetically distinct lineages. In the 1970s, the main lineage acquired the AbaR resistance island, conferring resistance to older antibiotics, via a horizontal gene transfer event. We estimate a mutation rate of ∼5 SNPs genome- 1 year- 1 and detected extensive recombination within GC1 genomes, introducing nucleotide diversity into the population at >20 times the substitution rate (the ratio of SNPs introduced by recombination compared with mutation was 22). The recombination events were non-randomly distributed in the genome and created significant diversity within loci encoding outer surface molecules (including the capsular polysaccharide, the outer core lipooligosaccharide and the outer membrane protein CarO), and spread antimicrobial resistance-conferring mutations affecting the gyrA and parC genes and insertion sequence insertions activating the ampC gene. Both GC1 lineages accumulated resistance to newer antibiotics through various genetic mechanisms, including the acquisition of plasmids and transposons or mutations in chromosomal genes. Our data show that GC1 has diversified into multiple successful extensively antibiotic-resistant subclones that differ in their surface structures. This has important implications for all avenues of control, including epidemiological tracking, antimicrobial therapy and vaccination.

Homaira, N, Sheils, J, Stelzer‐Braid, S, Lui, K, Oie, J, Snelling, T, Jaffe, A & Rawlinson, W 2016, 'Respiratory syncytial virus is present in the neonatal intensive care unit', Journal of Medical Virology, vol. 88, no. 2, pp. 196-201.
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Nosocomial transmission of respiratory syncytial virus (RSV) occurs in children within the neonatal intensive care unit (NICU). During peak community RSV transmission, three swabs were collected from the nose, hand and personal clothing of visitors and health care workers (HCW) in NICU once every week for eight weeks. Nasal swabs were collected from every third neonate and from any neonate clinically suspected of having a respiratory infection. Environmental sampling of high touch areas was done once during the study period. All swabs were tested for RSV using real time RT‐PCR. There were 173 (519 total) and 109 (327 total) swabs, each of nose, hand and dress from 84 HCWs and 80 visitors respectively and 81 nasal swabs from 55 neonates collected. Thirty five environmental swabs from surfaces of the beds, side tables, counter tops, chairs, tables and computers were collected. Overall 1% of nasal swabs from each of HCWs, visitors and neonates, 4% of dress specimens from visitors and 9% of environmental swabs were positive for RSV‐RNA. The results suggest that though the risk for RSV in the NICU remains low, personnel clothing are contaminated with RSV‐RNA and may have a role in transmission. J. Med. Virol. 88:196–201, 2016. © 2015 Wiley Periodicals, Inc.

Hong, J, Aramesh, M, Shimoni, O, Seo, DH, Yick, S, Greig, A, Charles, C, Prawer, S & Murphy, AB 2016, 'Plasma Catalytic Synthesis of Ammonia Using Functionalized-Carbon Coatings in an Atmospheric-Pressure Non-equilibrium Discharge', Plasma Chemistry and Plasma Processing, vol. 36, no. 4, pp. 917-940.
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© 2016, Springer Science+Business Media New York. We investigate the synthesis of ammonia in a non-equilibrium atmospheric-pressure plasma using functionalized-nanodiamond and diamond-like-carbon coatings on α-Al2O3 spheres as catalysts. Oxygenated nanodiamonds were found to increase the production yield of ammonia, while hydrogenated nanodiamonds decreased the yield. Neither type of nanodiamond affected the plasma properties significantly. Using diffuse-reflectance FT-IR and XPS, the role of different functional groups on the catalyst surface was investigated. Evidence is presented that the carbonyl group is associated with an efficient surface adsorption and desorption of hydrogen in ammonia synthesis on the surface of the nanodiamonds, and an increased production of ammonia. Conformal diamond-like-carbon coatings, deposited by plasma-enhanced chemical vapour deposition, led to a plasma with a higher electron density, and increased the production of ammonia.

Hoonhorst, SJM, Lo Tam Loi, AT, Pouwels, SD, Faiz, A, Telenga, ED, van den Berge, M, Koenderman, L, Lammers, J-WJ, Boezen, HM, van Oosterhout, AJM, Lodewijk, ME, Timens, W, Postma, DS & ten Hacken, NHT 2016, 'Advanced glycation endproducts and their receptor in different body compartments in COPD', Respiratory Research, vol. 17, no. 1.
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© 2016 Hoonhorst et al. Background: Chronic obstructive pulmonary disease (COPD) is a chronic lung disease characterized by chronic airway inflammation and emphysema, and is caused by exposure to noxious particles or gases, e.g. cigarette smoke. Smoking and oxidative stress lead to accelerated formation and accumulation of advanced glycation end products (AGEs), causing local tissue damage either directly or by binding the receptor for AGEs (RAGE). This study assessed the association of AGEs or RAGE in plasma, sputum, bronchial biopsies and skin with COPD and lung function, and their variance between these body compartments. Methods: Healthy smoking and never-smoking controls (n = 191) and COPD patients (n = 97, GOLD stage I-IV) were included. Autofluorescence (SAF) was measured in the skin, AGEs (pentosidine, CML and CEL) and sRAGE in blood and sputum by ELISA, and in bronchial biopsies by immunohistochemistry. eQTL analysis was performed in bronchial biopsies. Results: COPD patients showed higher SAF values and lower plasma sRAGE levels compared to controls and these values associated with decreased lung function (p <0.001; adjusting for relevant covariates). Lower plasma sRAGE levels significantly and independently predicted higher SAF values (p < 0.001). One SNP (rs2071278) was identified within a region of 50 kB flanking the AGER gene, which was associated with the gene and protein expression levels of AGER and another SNP (rs2071278) which was associated with the accumulation of AGEs in the skin. Conclusion: In COPD, AGEs accumulate differentially in body compartments, i.e. they accumulate in the skin, but not in plasma, sputum and bronchial biopsies. The association between lower sRAGE and higher SAF levels supports the hypothesis that the protective mechanism of sRAGE as a decoy-receptor is impaired in COPD.

Hopkins, FE, Bell, TG, Yang, M, Suggett, DJ & Steinke, M 2016, 'Air exposure of coral is a significant source of dimethylsulfide (DMS) to the atmosphere', Scientific Reports, vol. 6, no. 1.
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AbstractCorals are prolific producers of dimethylsulfoniopropionate (DMSP). High atmospheric concentrations of the DMSP breakdown product dimethylsulfide (DMS) have been linked to coral reefs during low tides. DMS is a potentially key sulfur source to the tropical atmosphere, but DMS emission from corals during tidal exposure is not well quantified. Here we show that gas phase DMS concentrations (DMSgas) increased by an order of magnitude when three Indo-Pacific corals were exposed to air in laboratory experiments. Upon re-submersion, an additional rapid rise in DMSgas was observed, reflecting increased production by the coral and/or dissolution of DMS-rich mucus formed by the coral during air exposure. Depletion in DMS following re-submersion was likely due to biologically-driven conversion of DMS to dimethylsulfoxide (DMSO). Fast Repetition Rate fluorometry showed downregulated photosynthesis during air exposure but rapid recovery upon re-submersion, suggesting that DMS enhances coral tolerance to oxidative stress during a process that can induce photoinhibition. We estimate that DMS emission from exposed coral reefs may be comparable in magnitude to emissions from other marine DMS hotspots. Coral DMS emission likely comprises a regular and significant source of sulfur to the tropical marine atmosphere, which is currently unrecognised in global DMS emission estimates and Earth System Models.

Hoque, MM, Naser, IB, Bari, SMN, Zhu, J, Mekalanos, JJ & Faruque, SM 2016, 'Quorum Regulated Resistance of Vibrio cholerae against Environmental Bacteriophages', Scientific Reports, vol. 6, no. 1, p. 37956.
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AbstractPredation by bacteriophages can significantly influence the population structure of bacterial communities. Vibrio cholerae the causative agent of cholera epidemics interacts with numerous phages in the aquatic ecosystem, and in the intestine of cholera patients. Seasonal epidemics of cholera reportedly collapse due to predation of the pathogen by phages. However, it is not clear how sufficient number of the bacteria survive to seed the environment in the subsequent epidemic season. We found that bacterial cell density-dependent gene expression termed “quorum sensing” which is regulated by signal molecules called autoinducers (AIs) can protect V. cholerae against predatory phages. V. cholerae mutant strains carrying inactivated AI synthase genes were significantly more susceptible to multiple phages compared to the parent bacteria. Likewise when mixed cultures of phage and bacteria were supplemented with exogenous autoinducers CAI-1 or AI-2 produced by recombinant strains carrying cloned AI synthase genes, increased survival of V. cholerae and a decrease in phage titer was observed. Mutational analyses suggested that the observed effects of autoinducers are mediated in part through the quorum sensing-dependent production of haemaglutinin protease, and partly through downregulation of phage receptors. These results have implication in developing strategies for phage mediated control of cholera.

Hortle, E, Nijagal, B, Bauer, DC, Jensen, LM, Ahn, SB, Cockburn, IA, Lampkin, S, Tull, D, McConville, MJ, McMorran, BJ, Foote, SJ & Burgio, G 2016, 'Adenosine monophosphate deaminase 3 activation shortens erythrocyte half-life and provides malaria resistance in mice', Blood, vol. 128, no. 9, pp. 1290-1301.
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Key PointsAMPD3 activation reduces red blood cell half-life, which is associated with increased oxidative stress and phosphatidylserine exposure. AMPD3 activation causes malaria resistance through increased RBC turnover and increased RBC production.

Hossain, K, Al Khamici, H, Holt, S & Valenzuela, S 2016, 'Cholesterol Promotes Interaction of the Protein CLIC1 with Phospholipid Monolayers at the Air–Water Interface', Membranes, vol. 6, no. 1, pp. 15-15.
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CLIC1 is a Chloride Intracellular Ion Channel protein that exists either in a soluble state in the cytoplasm or as a membrane bound protein. Members of the CLIC family are largely soluble proteins that possess the intriguing property of spontaneous insertion into phospholipid bilayers to form integral membrane ion channels. The regulatory role of cholesterol in the ion-channel activity of CLIC1 in tethered lipid bilayers was previously assessed using impedance spectroscopy. Here we extend this investigation by evaluating the influence of cholesterol on the spontaneous membrane insertion of CLIC1 into Langmuir film monolayers prepared using 1-palmitoyl-2-oleoylphosphatidylcholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-ethanolamine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine alone or in combination with cholesterol. The spontaneous membrane insertion of CLIC1 was shown to be dependent on the presence of cholesterol in the membrane. Furthermore, pre-incubation of CLIC1 with cholesterol prior to its addition to the Langmuir film, showed no membrane insertion even in monolayers containing cholesterol, suggesting the formation of a CLIC1-cholesterol pre-complex. Our results therefore suggest that CLIC1 membrane interaction involves CLIC1 binding to cholesterol located in the membrane for its initial docking followed by insertion. Subsequent structural rearrangements of the protein would likely also be required along with oligomerisation to form functional ion channels.

Hosseinpour-Mashkani, SM, Maddahfar, M & Sobhani-Nasab, A 2016, 'Precipitation Synthesis, Characterization, Morphological Control, and Photocatalyst Application of ZnWO4 Nanoparticles', Journal of Electronic Materials, vol. 45, no. 7, pp. 3612-3620.
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Hosseinzadeh Adli, A, Karami, C, Zhand, S, Talei, R & Moradi, A 2016, 'Mutations in the Basal Core Promoter and Precore/Core Regions of Hepatitis B Virus in Patients Co-Infected With Human Immunodeficiency Virus', Medical Laboratory Journal, vol. 10, no. 4, pp. 32-39.
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Hou, Z, Deng, K, Li, C, Deng, X, Lian, H, Cheng, Z, Jin, D & Lin, J 2016, '808 nm Light-triggered and hyaluronic acid-targeted dual-photosensitizers nanoplatform by fully utilizing Nd3+-sensitized upconversion emission with enhanced anti-tumor efficacy', Biomaterials, vol. 101, pp. 32-46.
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© 2016 Elsevier Ltd.The current near-infrared (NIR) light-induced photodynamic therapy (PDT) can enhance the tissue penetration depth to trigger photosensitizers (PSs) far from the surface. NIR-mediated PDT is still challenged by overheating effect on normal tissues, limited tumor selectivity and low reactive oxygen species (ROS) yields. Here we construct a dual-agent photosensitizing nanoplatform by combining UV-blue upconversion emitting NaYF4:Yb/Tm@NaYF4:Yb@NaNdF4:Yb@NaYF4 (labeled as UCNPs) multi-shell nanocrystals with titanium dioxide (TiO2, UV-light-excited PS) and hypocrellin A (HA, blue-light-excited PS), which can induce cancer cell apoptosis by 808 nm light-triggered and hyaluronic acid (Hyal)-targeted PDT. In this construction strategy, the crystallized TiO2 shells on the surface of UCNPs can play dual roles as UV-light excited PS and conjugation site for Hyal, and then Hyal is served as targeting-ligand as well as the carrier of HA simultaneously. The step-by-step reactive mode of loading PSs and modifying targeting-ligands is a controllable and ordered design based on the use of one intermediate product as the reaction site for the next component. The Nd3+-sensitized UCNPs with quenching reduction layer can efficiently convert 808 nm NIR light to UV-blue emission for simultaneous activation of two PSs with enhanced intracellular ROS generation. Through the in vitro and in vivo experiment results, the dual-photosensitizers nanoplatform presents enhanced anti-tumor efficacy by effective targeting cellular uptake and taking full advantage of upconversion emission, which may make a major step toward next generation of NIR-mediated PDT.

Howe, ENW, Busschaert, N, Wu, X, Berry, SN, Ho, J, Light, ME, Czech, DD, Klein, HA, Kitchen, JA & Gale, PA 2016, 'pH-Regulated Nonelectrogenic Anion Transport by Phenylthiosemicarbazones', Journal of the American Chemical Society, vol. 138, no. 26, pp. 8301-8308.
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Hsu, AC-Y, Parsons, K, Moheimani, F, Knight, DA, Hansbro, PM, Fujita, T & Wark, PA 2016, 'Impaired Antiviral Stress Granule and IFN-β Enhanceosome Formation Enhances Susceptibility to Influenza Infection in Chronic Obstructive Pulmonary Disease Epithelium', American Journal of Respiratory Cell and Molecular Biology, vol. 55, no. 1, pp. 117-127.
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Chronic obstructive pulmonary disease (COPD) is a serious lung disease that progressively worsens lung function. Those affected are highly susceptible to influenza virus infections that result in exacerbations with exaggerated symptoms with increased mortality. The mechanisms underpinning this increased susceptibility to infection in COPD are unclear. In this study, we show that primary bronchial epithelial cells (pBECs) from subjects with COPD have impaired induction of type I IFN (IFN-β) and lead to heightened viral replication after influenza viral infection. COPD pBECs have reduced protein levels of protein kinase (PK) R and decreased formation of PKR-mediated antiviral stress granules, which are critical in initiating type I IFN inductions. In addition, reduced protein expression of p300 resulted in decreased activation of IFN regulatory factor 3 and subsequent formation of IFN-β enhanceosome in COPD pBECs. The decreased p300 induction was the result of enhanced levels of microRNA (miR)-132. Ectopic expression of PKR or miR-132 antagomiR alone failed to restore IFN-β induction, whereas cotreatment increased antiviral stress granule formation, induction of p300, and IFN-β in COPD pBECs. This study reveals that decreased induction of both PKR and p300 proteins contribute to impaired induction of IFN-β in COPD pBECs upon influenza infection.

Huete, A 2016, 'Vegetation's responses to climate variability', Nature, vol. 531, no. 7593, pp. 181-182.
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Huete, AR 2016, 'Peer review report 1 On “Parameterizing ecosystem light use efficiency and water use efficiency to estimate maize gross primary production and evapotranspiration using MODIS EVI”', Agricultural and Forest Meteorology, vol. 217, pp. 167-167.
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Huete, AR 2016, 'Peer review report 1 On “Parameterizing ecosystem light use efficiency and water use efficiency to estimate maize gross primary production and evapotranspiration using MODIS EVI”', Agricultural and Forest Meteorology, vol. 217, pp. 172-172.
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Huo, L, Zhou, J, Wu, R, Ren, J, Zhang, S, Zhang, J & Xu, S 2016, 'Dual-functional β-NaYF_4: Yb^3+, Er^3+ nanoparticles for bioimaging and temperature sensing', Optical Materials Express, vol. 6, no. 4, pp. 1056-1056.
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Hexagonal-phase NaYF4: Yb3+, Er3+ nanoparticles (NPs) have been widely used as the most efficient NIR-to-visible upconversion (UC) luminescent and probe in bioscience. Here, we exploited not only the function of dual-mode emission of β-NaYF4: Yb3+, Er3+ NPs in the near infrared (NIR) and visible regions with single wavelength excitation at 980 nm, but also the function of physiological temperature sensing with the luminescence of Er3+ in the visible region. The structural and optical characteristics of β-NaYF4: Yb3+, Er3+ NPs were obtained using X-ray diffraction (XRD), scanning electron microscopy (SEM),and fluorescence spectral measurements, respectively; the mechanism for the energy transfer has been suggested with emphasis on the optimized Er/Yb concentration for most efficient UC. Due to the UC and down-shifting NIR properties, we achieved the dual-functional nanoparticles with potential application in physiological range temperature sensing and bioimaging simultaneously.

Huque, MH, Anderson, C, Walton, R & Ryan, L 2016, 'Individual level covariate adjusted conditional autoregressive (indiCAR) model for disease mapping', International Journal of Health Geographics, vol. 15, no. 1, pp. 1-13.
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© 2016 The Author(s). Background: Mapping disease rates over a region provides a visual illustration of underlying geographical variation of the disease and can be useful to generate new hypotheses on the disease aetiology. However, methods to fit the popular and widely used conditional autoregressive (CAR) models for disease mapping are not feasible in many applications due to memory constraints, particularly when the sample size is large. We propose a new algorithm to fit a CAR model that can accommodate both individual and group level covariates while adjusting for spatial correlation in the disease rates, termed indiCAR. Our method scales well and works in very large datasets where other methods fail. Results: We evaluate the performance of the indiCAR method through simulation studies. Our simulation results indicate that the indiCAR provides reliable estimates of all the regression and random effect parameters. We also apply indiCAR to the analysis of data on neutropenia admissions in New South Wales (NSW), Australia. Our analyses reveal that lower rates of neutropenia admissions are significantly associated with individual level predictors including higher age, male gender, residence in an outer regional area and a group level predictor of social disadvantage, the socio-economic index for areas. A large value for the spatial dependence parameter is estimated after adjusting for individual and area level covariates. This suggests the presence of important variation in the management of cancer patients across NSW. Conclusions: Incorporating individual covariate data in disease mapping studies improves the estimation of fixed and random effect parameters by utilizing information from multiple sources. Health registries routinely collect individual and area level information and thus could benefit by using indiCAR for mapping disease rates. Moreover, the natural applicability of indiCAR in a distributed computing framework enhances its application in...

Huque, MH, Bondell, HD, Carroll, RJ & Ryan, LM 2016, 'Spatial Regression with Covariate Measurement Error: A Semiparametric Approach', Biometrics, vol. 72, no. 3, pp. 678-686.
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Summary Spatial data have become increasingly common in epidemiology and public health research thanks to advances in GIS (Geographic Information Systems) technology. In health research, for example, it is common for epidemiologists to incorporate geographically indexed data into their studies. In practice, however, the spatially defined covariates are often measured with error. Naive estimators of regression coefficients are attenuated if measurement error is ignored. Moreover, the classical measurement error theory is inapplicable in the context of spatial modeling because of the presence of spatial correlation among the observations. We propose a semiparametric regression approach to obtain bias-corrected estimates of regression parameters and derive their large sample properties. We evaluate the performance of the proposed method through simulation studies and illustrate using data on Ischemic Heart Disease (IHD). Both simulation and practical application demonstrate that the proposed method can be effective in practice.

Huque, MH, Carroll, RJ, Diao, N, Christiani, DC & Ryan, LM 2016, 'Exposure Enriched Case‐Control (EECC) Design for the Assessment of Gene–Environment Interaction', Genetic Epidemiology, vol. 40, no. 7, pp. 570-578.
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ABSTRACTGenetic susceptibility and environmental exposure both play an important role in the aetiology of many diseases. Case‐control studies are often the first choice to explore the joint influence of genetic and environmental factors on the risk of developing a rare disease. In practice, however, such studies may have limited power, especially when susceptibility genes are rare and exposure distributions are highly skewed. We propose a variant of the classical case‐control study, the exposure enriched case‐control (EECC) design, where not only cases, but also high (or low) exposed individuals are oversampled, depending on the skewness of the exposure distribution. Of course, a traditional logistic regression model is no longer valid and results in biased parameter estimation. We show that addition of a simple covariate to the regression model removes this bias and yields reliable estimates of main and interaction effects of interest. We also discuss optimal design, showing that judicious oversampling of high/low exposed individuals can boost study power considerably. We illustrate our results using data from a study involving arsenic exposure and detoxification genes in Bangladesh.

Iezzi, VL, Büttner, TFS, Tehranchi, A, Loranger, S, Kabakova, IV, Eggleton, BJ & Kashyap, R 2016, 'Temporal characterization of a multi-wavelength Brillouin–erbium fiber laser', New Journal of Physics, vol. 18, no. 5, pp. 055003-055003.
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This paper provides the first detailed temporal characterization of a multi-wavelength-Brillouin-erbium fiber laser (MWBEFL) by measuring the optical intensity of the individual frequency channels with high temporal resolution. It is found that the power in each channel is highly unstable due to the excitation of several cavity modes for typical conditions of operation. Also provided is the real-time measurements of the MWBEFL output power for two configurations that were previously reported to emit phase-locked picosecond pulse trains, concluded from their autocorrelation measurements. Real-time measurements reveal a high degree of instability without the formation of a stable pulse train. Finally, we model the MWBEFL using coupled wave equations describing the evolution of the Brillouin pump, Stokes and acoustic waves in the presence of stimulated Brillouin scattering, and the optical Kerr effect. A good qualitative consistency between the simulation and experimental results is evident, in which the interference signal at the output shows strong instability as well as the chaotic behavior due to the dynamics of participating pump and Stokes waves.

Ing, M, Oliver, RA, Oliver, BGG, Walsh, WR & Williamson, JP 2016, 'Evaluation of Transbronchial Lung Cryobiopsy Size and Freezing Time: A Prognostic Animal Study', Respiration, vol. 92, no. 1, pp. 34-39.
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<b><i>Background:</i></b> Transbronchial lung biopsy using a cryoprobe is a novel way of sampling lung parenchyma. Correlation of freezing time with biopsy size and complications has not been evaluated in vivo. <b><i>Objectives:</i></b> The primary aim of the study is to evaluate the correlation between transbronchial cryobiopsy freezing time and size. The secondary aims are to evaluate histological quality of the biopsy and evaluate procedure-associated complications. <b><i>Methods:</i></b> Transbronchial lung cryobiopsies were obtained from two anaesthetised sheep using a 1.9-mm cryoprobe inserted into a flexible bronchoscope under fluoroscopic guidance. Freezing times ranged from 1 to 6 s (n = 49). The cryobiopsies were evaluated histologically with respect to their size and quality. Complications of bleeding and pneumothorax were recorded. <b><i>Results:</i></b> The mean cross-sectional area of the cryobiopsy ranged from 4.7 ± 2.1 to 15.7 ± 15.3 mm². There was a significant positive correlation between increasing freezing time and cryobiopsy cross-sectional area (p = 0.028). All biopsies contained lung tissue with preserved parenchyma. Crush and freeze artefacts were not observed and tissue architecture was intact in all specimens. Small blood vessels and terminal bronchioles were observed in 88% of specimens. All cryobiopsies caused nil or mild haemorrhage with the exception of only 1 episode of severe haemorrhage at 6 s freezing time. Pneumothoraces occurred at 2, 5 and 6 s freezing time and required chest tube insertion. The most significant haemorrhage and pneumothoraces occurred at 5 and 6 s. Our results suggest an initial freezing time of 3 s can provide the maximal biopsy size while minimising major complications. <b><i>Conclusion:</i></b> The optimal transbronchial cryobiopsy freezing time is ...

Irga, PJ & Torpy, FR 2016, 'A survey of the aeromycota of Sydney and its correspondence with environmental conditions: grass as a component of urban forestry could be a major determinant', Aerobiologia, vol. 32, no. 2, pp. 171-185.
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© 2015, Springer Science+Business Media Dordrecht. A comprehensive survey of airborne fungi has been lacking for the Sydney region. This study determined the diversity and abundance of outdoor airborne fungal concentrations in urban Sydney. Monthly air samples were taken from 11 sites in central Sydney, and culturable fungi identified and quantified. The genus Cladosporium was the most frequently isolated fungal genus, with a frequency of 78 % and a mean density of 335 CFU m−3. The next most frequently encountered genus was Alternaria, occurring in 53 % of samples with a mean of 124 CFU m−3. Other frequently identified fungi, in decreasing occurrence, were as follows: Penicillium, Fusarium, Epicoccum, Phoma, Acremonium and Aureobasidium. Additionally, seasonal and spatial trends of airborne fungi were assessed, with increases in total culturable fungal concentrations experienced in the summer months. The correspondence between a range of key environmental variables and the phenology of airborne fungal propagules was also examined, with temperature, wind speed and proximal greenspace having the largest influence on fungal propagule density. If the greenspace was comprised of grass, stronger associations with fungal behaviour were observed.

Irga, PJ & Torpy, FR 2016, 'Indoor air pollutants in occupational buildings in a sub-tropical climate: Comparison among ventilation types', BUILDING AND ENVIRONMENT, vol. 98, pp. 190-199.
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© 2016 Elsevier Ltd. Few studies have concurrently assessed both abiotic and biotic air pollutants in the built environment in sub-tropical areas. The investigation comprised a field study of air pollutants in eleven indoor environments in Sydney throughout one year, to elucidate Indoor/Outdoor ratios of carbon dioxide, carbon monoxide, total volatile organic compounds, nitric oxide, nitrogen dioxide, sulfur dioxide, total suspended particulate matter, suspended particles <10 μm in diameter (PM10) and particulate matter <2.5 μm (PM2.5). Further, a concurrent assessment of airborne fungi was conducted along with the other air pollutants to determine their diversity and abundance for urban Sydney and to establish baseline Indoor/Outdoor ratios of airborne fungi. Building ventilation types were identified as natural, mechanical and mixed-type ventilation, to assess whether building ventilation type has an impact on prevalence and concentrations of indoor air pollutants. We found that generally the indoor air quality of a typical Australian office building is relatively good. The ventilation type of the buildings did affect indoor air quality; however not to the extent that occupant health was at risk in any case. Low concentrations of airborne fungi were encountered in samples, across all buildings and months, with naturally ventilated buildings having higher concentrations. Buildings with high airborne fungal concentrations also supported higher diversity of fungal species. Few organisms of concern to public health were identified. Significant differences were observed when comparing the structure of airborne fungal communities across building types, with buildings with centralised mechanical (air conditioning) systems harbouring different communities to the other ventilation types.

James, SA, Hare, DJ, Jenkins, NL, de Jonge, MD, Bush, AI & McColl, G 2016, 'φXANES: In vivo imaging of metal-protein coordination environments', Scientific Reports, vol. 6, no. 1.
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AbstractWe have developed an X-ray absorption near edge structure spectroscopy method using fluorescence detection for visualizing in vivo coordination environments of metals in biological specimens. This approach, which we term fluorescence imaging XANES (φXANES), allows us to spatially depict metal-protein associations in a native, hydrated state whilst avoiding intrinsic chemical damage from radiation. This method was validated using iron-challenged Caenorhabditis elegans to observe marked alterations in redox environment.

Jamie, JF, Vemulpad, SR, Kichu, M, Kuzhiumparambil, U & Velmurugan, R 2016, 'Traditional medicine partnerships – fostering two way exchange of knowledge, skills and capacity strengthening', Acta Horticulturae, no. 1126, pp. 21-30.
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Jarnicki, AG, Schilter, H, Liu, G, Wheeldon, K, Essilfie, A, Foot, JS, Yow, TT, Jarolimek, W & Hansbro, PM 2016, 'The inhibitor of semicarbazide‐sensitive amine oxidase, PXS‐4728A, ameliorates key features of chronic obstructive pulmonary disease in a mouse model', British Journal of Pharmacology, vol. 173, no. 22, pp. 3161-3175.
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Background and PurposeChronic obstructive pulmonary disease (COPD) is a major cause of illness and death, often induced by cigarette smoking (CS). It is characterized by pulmonary inflammation and fibrosis that impairs lung function. Existing treatments aim to control symptoms but have low efficacy, and there are no broadly effective treatments. A new potential target is the ectoenzyme, semicarbazide‐sensitive mono‐amine oxidase (SSAO; also known as vascular adhesion protein‐1). SSAO is elevated in smokers' serum and is a pro‐inflammatory enzyme facilitating adhesion and transmigration of leukocytes from the vasculature to sites of inflammation.Experimental ApproachPXS‐4728A was developed as a low MW inhibitor of SSAO. A model of COPD induced by CS in mice reproduces key aspects of human COPD, including chronic airway inflammation, fibrosis and impaired lung function. This model was used to assess suppression of SSAO activity and amelioration of inflammation and other characteristic features of COPD.Key ResultsTreatment with PXS‐4728A completely inhibited lung and systemic SSAO activity induced by acute and chronic CS‐exposure. Daily oral treatment inhibited airway inflammation (immune cell influx and inflammatory factors) induced by acute CS‐exposure. Therapeutic treatment during chronic CS‐exposure, when the key features of experimental COPD develop and progress, substantially suppressed inflammatory cell influx and fibrosis in the airways and improved lung function.Conclusions and ImplicationsTreatment with a low MW inhibitor of SSAO, PXS‐4728A, suppressed airway inflammation and fibrosis and improved lung function in experimental COPD, demonstrating the therapeutic potential of PXS‐4728A for this debilitating disease.

Jeffries, TC, Curlevski, NJ, Brown, MV, Harrison, DP, Doblin, MA, Petrou, K, Ralph, PJ & Seymour, JR 2016, 'Partitioning of fungal assemblages across different marine habitats', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 8, no. 2, pp. 235-238.
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© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd. Fungi are a highly diverse group of microbes that fundamentally influence the biogeochemistry of the biosphere, but we currently know little about the diversity and distribution of fungi in aquatic habitats. Here we describe shifts in marine fungal community composition across different marine habitats, using targeted pyrosequencing of the fungal Internal Transcribed Spacer (ITS) region. Our results demonstrate strong partitioning of fungal community composition between estuarine, coastal and oceanic samples, with each habitat hosting discrete communities that are controlled by patterns in salinity, temperature, oxygen and nutrients. Whereas estuarine habitats comprised a significant proportion of fungal groups often found in terrestrial habitats, the open ocean sites were dominated by previously unidentified groups. The patterns observed here indicate that fungi are potentially a significant, although largely overlooked, feature of the ocean's microbiota, but greater efforts to characterize marine species are required before the full ecological and biogeochemical importance of marine fungi can be ascertained.

Jeffries, TC, Fontes, MLS, Harrison, DP, Van-Dongen-Vogels, V, Eyre, BD, Ralph, PJ & Seymour, JR 2016, 'Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary', FRONTIERS IN MICROBIOLOGY, vol. 6, no. JAN, pp. 1-17.
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© 2016 Jeffries, Schmitz Fontes, Harrison, Van-Dongen-Vogels, Eyre, Ralph and Seymour. The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide i...

Jenkins, C & Bogema, DR 2016, 'Factors associated with seroconversion to the major piroplasm surface protein of the bovine haemoparasite Theileria orientalis', PARASITES & VECTORS, vol. 9.
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Jensen, TO, Stelzer‐Braid, S, Willenborg, C, Cheung, C, Andresen, D, Rawlinson, W & Clezy, K 2016, 'Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward', Journal of Medical Virology, vol. 88, no. 10, pp. 1827-1831.
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We describe an outbreak of respiratory syncytial virus (RSV) infection on a hematology ward without allogeneic stem cell transplant patients. Twelve patients and one staff member infected with RSV were identified from the laboratory database. Five patients had lower respiratory tract infection, seven had upper respiratory tract infection, one was asymptomatic, and there were two (15.4%) deaths. Most patients had overlapping periods of potential infectiousness on the ward. Sequencing was possible on eight specimens and five of these had identical sequences. Results were consistent with transmission occurring both on the ward and by introduction of RSV from the community. J. Med. Virol. 88:1827–1831, 2016. © 2016 Wiley Periodicals, Inc.

Jeong, S, Cho, K, Bae, H, Keshvardoust, P, Rice, SA, Vigneswaran, S, Lee, S & Leiknes, T 2016, 'Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment', Chemical Engineering Journal, vol. 294, pp. 30-39.
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Jerger, M, Reshitnyk, Y, Oppliger, M, Potočnik, A, Mondal, M, Wallraff, A, Goodenough, K, Wehner, S, Juliusson, K, Langford, NK & Fedorov, A 2016, 'Contextuality without nonlocality in a superconducting quantum system', Nature Communications, vol. 7, no. 1, p. 12930.
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AbstractClassical realism demands that system properties exist independently of whether they are measured, while noncontextuality demands that the results of measurements do not depend on what other measurements are performed in conjunction with them. The Bell–Kochen–Specker theorem states that noncontextual realism cannot reproduce the measurement statistics of a single three-level quantum system (qutrit). Noncontextual realistic models may thus be tested using a single qutrit without relying on the notion of quantum entanglement in contrast to Bell inequality tests. It is challenging to refute such models experimentally, since imperfections may introduce loopholes that enable a realist interpretation. Here we use a superconducting qutrit with deterministic, binary-outcome readouts to violate a noncontextuality inequality while addressing the detection, individual-existence and compatibility loopholes. This evidence of state-dependent contextuality also demonstrates the fitness of superconducting quantum circuits for fault-tolerant quantum computation in surface-code architectures, currently the most promising route to scalable quantum computing.

Jha, SR, Hannu, MK, Gore, K, Chang, S, Newton, P, Wilhelm, K, Hayward, CS, Jabbour, A, Kotlyar, E, Keogh, A, Dhital, K, Granger, E, Jansz, P, Spratt, PM, Montgomery, E, Harkess, M, Tunicliff, P, Davidson, PM & Macdonald, PS 2016, 'Cognitive impairment improves the predictive validity of physical frailty for mortality in patients with advanced heart failure referred for heart transplantation', JOURNAL OF HEART AND LUNG TRANSPLANTATION, vol. 35, no. 9, pp. 1092-1100.
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© 2016 International Society for Heart and Lung Transplantation Background The aim of this study was to identify whether the addition of cognitive impairment, depression, or both, to the assessment of physical frailty provides better outcome prediction in patients with advanced heart failure referred for heart transplantation (HT). Methods Beginning in March 2013, all patients with advanced heart failure referred to our Transplant Unit have undergone a physical frailty assessment using the Fried frailty phenotype. Cognition was assessed with the Montreal Cognitive Assessment and depression with the Depression in Medical Illness questionnaire. We assessed the value of 4 composite frailty measures: physical frailty (PF ≥ 3 of 5 = frailty), “cognitive frailty” (CogF ≥ 3 of 6 = frail), “depressive frailty” (DepF ≥ 3 of 6 = frail), and “cognitive-depressive frailty” (ComF ≥ 3 of 7 = frail) in predicting outcomes. Results Frailty was assessed in 156 patients (109 men, 47 women), aged 53 ± 13 years, and with a left ventricular ejection fraction of 27% ± 14%. Inclusion of cognitive impairment or depression in the definition of frailty increased the proportion classified as frail from 33% using PF to 42% using ComF. During follow-up, 28 patients died before ventricular assist device implantation or HT. Frailty was associated with significantly lower ventricular assist device- and HT-free survival, with CogF best capturing early mortality: 12-month survival for non-frail and frail cohorts was 81% ± 5% vs 58% ± 10% (p < 0.02) using PF and 85% ± 5% vs 56% ± 9% (p < 0.002) using CogF. Combining the Depression in Medical Illness score with PF or CogF did not strengthen the relationship between frailty and mortality. Conclusions The addition of cognitive impairment to the assessment of PF strengthened its capacity to identify advanced heart failure patients referred for HT who are at high risk of early death.

Jha, SR, Hannu, MK, Ther, MO, Chang, S, Montgomery, E, Harkess, M, Wilhelm, K, Hayward, CS, Jabbour, A, Spratt, PM, Newton, P, Davidson, PM & Macdonald, PS 2016, 'The Prevalence and Prognostic Significance of Frailty in Patients With Advanced Heart Failure Referred for Heart Transplantation', TRANSPLANTATION, vol. 100, no. 2, pp. 429-436.
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Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved. Background Frailty is a clinically recognized syndrome of decreased physiological reserve. The heightened state of vulnerability in these patients confers a greater risk of adverse outcomes after even minor stressors. Our aim was to assess the prevalence and prognostic significance of the frailty phenotype in patients referred for heart transplantation. Methods Consecutive patients referred or on the waiting list for heart transplantation from March 2013 underwent frailty assessment. Frailty was defined as a positive response to 3 or more of the following 5 components: weak grip strength, slowed walking speed, poor appetite, physical inactivity, and exhaustion. In addition, markers of disease severity were obtained, and all patients underwent cognitive (Montreal Cognitive Assessment) and depression (Depression in Medical Illness-10) screening. Results One hundred twenty patients (83 men:37 women; age, 53 ± 12 years, range, 16-73 years; left ventricular ejection fraction, 27 ± 14%) underwent frailty assessment. Thirty-nine of 120 patients (33%) were assessed as frail. Frailty was associated with New York Heart Association class IV heart failure, lower body mass index, elevated intracardiac filling pressures, lower cardiac index, anemia, hypoalbuminemia, hyperbilirubinemia, cognitive impairment, and depression (all ρ < 0.05). Frailty was independent of age, sex, heart failure duration, left ventricular ejection fraction, or renal function. Frailty was an independent predictor of increased all-cause mortality: 1 year actuarial survival was 79 ± 5% in the nonfrail group compared with only 54 ± 9% for the frail group (P < 0.005). Conclusions Frailty is prevalent among patients with advanced symptomatic heart failure referred for heart transplantation and is associated with increased mortality.

Jia-Jia, ZHOU & Jian-Rong, QIU 2016, 'Upconversion Spectroscopic Investigation of Single Nanoparticles', Journal of Inorganic Materials, vol. 31, no. 10, pp. 1023-1023.
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Jin, D 2016, 'Bright future for upconversion', Nature Photonics, vol. 10, no. 9, pp. 567-569.
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Jin, YK, Lundgren, P, Lutz, A, Raina, J-B, Howells, EJ, Paley, AS, Willis, BL & van Oppen, MJH 2016, 'Genetic markers for antioxidant capacity in a reef-building coral', Science Advances, vol. 2, no. 5.
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We identify the first quantitative trait loci for antioxidant capacity in corals, providing possible new avenues for management and restoration approaches.

Jones, K, Benson, S & Roux, C 2016, 'The forensic analysis of office paper using oxygen Isotope Ratio Mass Spectrometry, part 2: Characterising the source materials and the effect of production and usage on the δ 18 O values of cellulose and paper', Forensic Science International, vol. 268, pp. 151-158.
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© 2016 For casework applications, understanding the source processes used to create a material and the effects of those sources on the results obtained by Isotope Ratio Mass Spectrometry (IRMS) of a bulk material is important. Likewise, understanding the effect of environment, home/office printing processes and some forensic testing in at least a basic context, ensures that in casework, enough information on the effects of these variables is available during comparison and interpretation. In this study, which focuses on oxygen isotopic abundance measurements, both fractionation and mixing effects were observed within the pulping and production process. Also observed in the carbon isotopic experiments, sampling that included toner changed the measured isotopic abundance values of the paper and should be avoided in casework. Inkjet printing processes were not shown to have an effect on the paper oxygen abundance values. Samples that were treated for fingerprints using 1,2-Indandione-Zn prior to sampling showed the greatest risk for misinterpretation of whether two samples had originated from the same source. While this study provides a good basis and understanding of the effects of a range of factors on document paper oxygen isotope values, further testing for a range of specific casework scenarios is required and should be undertaken on a case by case basis as the need arises.

Jones, K, Benson, S & Roux, C 2016, 'The forensic analysis of office paper using oxygen isotope ratio mass spectrometry. Part 1: Understanding the background population and homogeneity of paper for the comparison and discrimination of samples', Forensic Science International, vol. 262, pp. 97-107.
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© 2016. Isotope ratio mass spectrometry (IRMS) using carbon isotopes has previously been shown to be a robust and discriminating technique for the comparison of document papers. This study aims to examine the inter and intra sample variability for oxygen isotopes measured in standard 80gsm white document papers, to inform the comparison of document papers in forensic casework.123 paper samples collected from Australia and New Zealand over a 24-month period were measured for their bulk oxygen isotopic abundance and were found to sit within a range of 15 ‰. A homogeneity study was undertaken which included examining the variability of samples at the sheet, ream and brand source levels. The results of this study were used to construct guidelines for sample comparison and as such, 95% confidence intervals were observed to be inappropriate for use given the high intra sample variability. Instead, a 1.4 ‰ discrimination range (0.7 ‰ either side of the measured value) was defined for use as a benchmark for discrimination when samples were measured in the same sequence. Utilising this value, 82% of the samples could be discriminated using a paired comparison, demonstrating a strong potential for use within forensic casework.

Jones, PM & George, AM 2016, 'Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding', Scientific Reports, vol. 6, no. 1, pp. 1-10.
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AbstractMCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors’ dynamics that may be of utility in drug design.

Joss, TV, Burke, CM, Hudson, BJ, Darling, AE, Forer, M, Alber, DG, Charles, IG & Stow, NW 2016, 'Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients', Frontiers in Microbiology, vol. 6, no. JAN, pp. 1-11.
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© 2016 Joss, Burke, Hudson, Darling, Forer, Alber, Charles and Stow. Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus.

Joyce, P, Wardle, J & Zaslawski, C 2016, 'Medical student attitudes towards complementary and alternative medicine (CAM) in medical education: a critical review', Journal of Complementary and Integrative Medicine, vol. 13, no. 4, pp. 333-345.
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Abstract Background This paper aims to remedy a gap in the knowledge by presenting the first critical review of the literature on major themes relating to medical students perceptions and attitudes towards the exponentially growing field of complementary and alternative medicine (CAM). Methods After a comprehensive database search of the literature, 21 papers were chosen as suitable for the review. The results from these papers were tabled and discussed. Results The results indicated that medical students lacked knowledge of CAM and are generally positive towards CAM education (especially in the preclinical years, if it provided evidence of efficacy and post-placement). Medical students thought that CAM should generally be incorporated into the medical curriculum mainly so they can confidently undertake referral to CAM practitioners. Being able to communicate with future patients about their CAM use was a major motivation for medical students to learn about CAM and a factor for medical student support of further incorporation of CAM content in the medical curricula. Educational exposure to CAM in many forms and in many papers was shown to significantly affect medical student attitudes to CAM. This may be reflective of the fact that, outside direct CAM training, there may be limited accessible opportunities for medical students and if integration is to occur, educational exposure is most important. ...

Jun, MY, Karki, R, Paudel, KR, Sharma, BR, Adhikari, D & Kim, D-W 2016, 'Alkaloid rich fraction from Nelumbo nucifera targets VSMC proliferation and migration to suppress restenosis in balloon-injured rat carotid artery', Atherosclerosis, vol. 248, pp. 179-189.
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© 2016 Elsevier Ireland Ltd. Aims: Restenosis- an adverse consequence following angioplasty, and atherosclerosis are characterized by abnormal vascular smooth muscle cell (VSMC) proliferation and migration leading to neo-intima formation. In the present study, we investigated the inhibitory effects of alkaloid rich fraction (ARF) from Nelumbo nucifera and isolated compound neferine on platelet-derived growth factor (PDGF-BB) induced VSMC proliferation and migration in vitro and neo-intima formation in a rat carotid artery injury model. Methods: PDGF-BB induced VSMC proliferation and migration was assessed using colorimetric assay and modified Boyden chamber method respectively. Gene expression of cell cycle associated molecules was determined by reverse transcription-polymerase chain reaction (RT-PCR). The signaling molecules such as PDGF-Rβ, extracellular regulated kinase (ERK)1/2, c-Jun N-terminal kinase (JNK), P38, metalloproteinase (MMP)-9 and nuclear factor-kappa B (NF-κB) were determined by western blot analysis. Stress fiber formation was evaluated using immunofluorescence microscopy. The rat carotid artery balloon injury model was performed to assess the effect of ARF on neo-intima formation. Results: ARF possessed the strongest anti-oxidant activities. The anti-proliferative activity of both ARF and neferine was due to suppression of cyclin D1, cyclin E and cyclin-dependent kinase (Cdk) gene expression. Moreover, ARF and neferine inhibited PDGF-Rβ, ERK1/2, JNK and P38 activations and NF-κB translocation. Also, ARF and neferine inhibited VSMC migration by inhibiting MMP-9 activity without affecting cytoskeleton remodeling. In a rat carotid artery injury model, ARF inhibited neo-intima formation. Conclusion: Our results indicate that ARF targets VSMC proliferation and migration to attenuate neo-intima formation by inhibition of PDGF-Rβ mediated signaling.

Jung, J, Park, B, Lee, JA, You, S, Alraek, T, Zhao-Xiang, B, Birch, S, Kim, T-H, Hao, X, Zaslawski, C, Kang, B-K & Lee, MS 2016, 'Standardization and future directions in pattern identification research: International brainstorming session', CHINESE JOURNAL OF INTEGRATIVE MEDICINE, vol. 22, no. 9, pp. 714-720.
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Kabakova, IV, de Hoogh, A, van der Wel, REC, Wulf, M, le Feber, B & Kuipers, L 2016, 'Imaging of electric and magnetic fields near plasmonic nanowires', Scientific Reports, vol. 6, no. 1, p. 22665.
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AbstractNear-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire’s evanescent field and the probe’s response function. As a result, we find that the probe’s sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments.

Kapetanovic, R, Bokil, NJ, Achard, MES, Ong, CY, Peters, KM, Stocks, CJ, Phan, M, Monteleone, M, Schroder, K, Irvine, KM, Saunders, BM, Walker, MJ, Stacey, KJ, McEwan, AG, Schembri, MA & Sweet, MJ 2016, 'Salmonella employs multiple mechanisms to subvert the TLR‐inducible zinc‐mediated antimicrobial response of human macrophages', The FASEB Journal, vol. 30, no. 5, pp. 1901-1912.
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© FASEB. We aimed to characterize antimicrobial zinc trafficking within macrophages and to determine whether the professional intramacrophage pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) subverts this pathway. Using both Escherichia coli and S. Typhimurium, we show that TLR signaling promotes the accumulation of vesicular zinc within primary human macrophages. Vesicular zinc is delivered to E. coli to promote microbial clearance, whereas S. Typhimurium evades this response via Salmonella pathogenicity island (SPI)-1. Even in the absence of SPI-1 and the zinc exporter ZntA, S. Typhimurium resists the innate immune zinc stress response, implying the existence of additional host subversion mechanisms. We also demonstrate the combinatorial antimicrobial effects of zinc and copper, a pathway that S. Typhimurium again evades. Our use of complementary tools and approaches, including confocal microscopy, direct assessment of intramacrophage bacterial zinc stress responses, specific E. coli and S. Typhimurium mutants, and inductively coupled plasma mass spectroscopy, has enabled carefully controlled characterization of this novel innate immune antimicrobial pathway. In summary, our study provides new insights at the cellular level into the well-documented effects of zinc in promoting host defense against infectious disease, as well as the complex host subversion strategies employed by S. Typhimurium to combat this pathway.

Karami, C, H Adli, A, Zhand, S, Tabarraei, A, Talei, R, Saeidi, M & Moradi, A 2016, 'Study of Genotype, Subtype and Mutation in the S Gene in Hepatitis B Patients Co-infected with HIV in Iran', Jundishapur Journal of Microbiology, vol. 9, no. 12, pp. 1-5.
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Background: Co-infection with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) is common due to shared routes of transmission, as reported approximately 10% of 33 million HIV-infected patients worldwide are chronically infected with HBV. Mutations of HBsAg especially within the “a” determinant could alter the antigenicity of the protein, causing failure of HBsAg neutralization and escaping from the host’s immune system. This results in active viral replication and liver disease. Objectives: The aim of the survey was to identify HBV genotype and subtype, and different mutations in HBV S gene in hepatitis B patients co-infected with HIV in Iran. Methods: PCR performance and HBV-DNA extraction from plasma of 124 samples obtained from treatment naive HIV/HBV coinfected participants were according to the protocol. Direct sequencing and alignment of surface gene were carried out using reference sequences from the Gene Bank database. Results: From 124 HIV/HBV ELISA positive samples, 40 were HBV DNA-positive. Themean age of patients was 33.88 years. 20% of them were female and 80% were male. All isolates belonged to the sub genotype D1/ayw2 and genotype D. There were 50 point mutations including 23 (46%) missense and 27 (54%) silent mutations in amino acid level. Twenty three amino acid mutations occurred in different immune epitopes such as 11 (47.82%) in B cell, 6 (26.08%) in T helper and 2 (%8.6) in CTL. The prevalence of mutations in both “a” determinant region and Major Hydrophilic Region (MHR) was 5 (21.73%). Conclusions: Our findings showed that P127T and A70P (Outside of MHR) were the most frequently occurring substitution mutations. P127T, P132T, G130R, and S136Y substitutions placed in the first loop of the “a” determinant and the other substitutions of P142T and D144N occurred in the second loop of “a” determinant. The results of our study showed that most of the mutations occurred in B cell epitopes. The mutation in a surface gene of H...

Karan, M, Liddell, M, Prober, SM, Arndt, S, Beringer, J, Boer, M, Cleverly, J, Eamus, D, Grace, P, Van Gorsel, E, Hero, J-M, Hutley, L, Macfarlane, C, Metcalfe, D, Meyer, W, Pendall, E, Sebastian, A & Wardlaw, T 2016, 'The Australian SuperSite Network: A continental, long-term terrestrial ecosystem observatory', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 568, pp. 1263-1274.
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© 2016 Elsevier B.V. Ecosystem monitoring networks aim to collect data on physical, chemical and biological systems and their interactions that shape the biosphere. Here we introduce the Australian SuperSite Network that, along with complementary facilities of Australia's Terrestrial Ecosystem Research Network (TERN), delivers field infrastructure and diverse, ecosystem-related datasets for use by researchers, educators and policy makers. The SuperSite Network uses infrastructure replicated across research sites in different biomes, to allow comparisons across ecosystems and improve scalability of findings to regional, continental and global scales. This conforms with the approaches of other ecosystem monitoring networks such as Critical Zone Observatories, the U.S. National Ecological Observatory Network; Analysis and Experimentation on Ecosystems, Europe; Chinese Ecosystem Research Network; International Long Term Ecological Research network and the United States Long Term Ecological Research Network. The Australian SuperSite Network currently involves 10 SuperSites across a diverse range of biomes, including tropical rainforest, grassland and savanna; wet and dry sclerophyll forest and woodland; and semi-arid grassland, woodland and savanna. The focus of the SuperSite Network is on using vegetation, faunal and biophysical monitoring to develop a process-based understanding of ecosystem function and change in Australian biomes; and to link this with data streams provided by the series of flux towers across the network. The Australian SuperSite Network is also intended to support a range of auxiliary researchers who contribute to the growing body of knowledge within and across the SuperSite Network, public outreach and education to promote environmental awareness and the role of ecosystem monitoring in the management of Australian environments.

Kaul, H, Suman, M, Khan, Z, Ullah, MI, Ashfaq, UA & Idrees, S 2016, 'Missense mutation in SLC4A11 in two Pakistani families affected with congenital hereditary endothelial dystrophy (CHED2)', Clinical and Experimental Optometry, vol. 99, no. 1, pp. 73-77.
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Kawamura, K, Kawanabe, T, Shimizu, M, Nagano, AJ, Saeki, N, Okazaki, K, Kaji, M, Dennis, ES, Osabe, K & Fujimoto, R 2016, 'Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis', Plant Gene, vol. 5, pp. 1-7.
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© 2015 The Authors. Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia. Most Japanese commercial cultivars of Chinese cabbage use an F 1 hybrid seed production system because of the high yielding cultivars produced. An efficient method for predicting hybrid performance in the parental generations is desired, and genetic distance between parental lines might be a good indicator of the level of hybrid vigor in a cross. Information concerning the genetic relationships among parental candidate inbred lines is useful for variety protection. The number of DNA markers available that can be used to assess the purity of inbred lines is limited in B. rapa. The aim of this study is to use DNA markers to assess the genetic distance between inbred lines to examine early developmental and yield heterosis so as to develop methods for selecting the best parental lines for the production of hybrids. We screened highly polymorphic SSR and CAPS markers to assess the genetic uniformity of inbred lines and characterize their genetic relationship. We examined the early size and yield heterosis in 32 F 1 hybrids of Chinese cabbage. There was a moderate correlation in mid-parent heterosis between leaf size at 21 days after sowing and harvested biomass but not in best-parent heterosis. In contrast there was no correlation between genetic distance and mid-parent or best-parent heterosis, indicating that genetic distance does not predict the heterosis phenotype.

Kawamura, K, Kawanabe, T, Shimizu, M, Okazaki, K, Kaji, M, Dennis, ES, Osabe, K & Fujimoto, R 2016, 'Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars', Data in Brief, vol. 6, pp. 229-237.
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Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia, and most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system. Self-incompatibility is successfully used for the production of F1 hybrid seeds in B. rapa vegetables to avoid contamination by non-hybrid seeds, and the strength of self-incompatibility is important for harvesting a highly pure F1 seeds. Prediction of agronomically important traits such as disease resistance based on DNA markers is useful. In this dataset, we identified the S haplotypes by DNA markers and evaluated the strength of self-incompatibility in Chinese cabbage inbred lines. The data described the predicted disease resistance to Fusarium yellows or clubroot in 22 Chinese cabbage inbred lines using gene associated or gene linked DNA markers.

Kawanabe, T, Ishikura, S, Miyaji, N, Sasaki, T, Wu, LM, Itabashi, E, Takada, S, Shimizu, M, Takasaki-Yasuda, T, Osabe, K, Peacock, WJ, Dennis, ES & Fujimoto, R 2016, 'Role of DNA methylation in hybrid vigor in Arabidopsis thaliana', Proceedings of the National Academy of Sciences, vol. 113, no. 43, pp. E6704-E6711.
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Significance Hybrid vigor is an important phenomenon in basic genetics and in agricultural practice, but the bases of the superior performance of the hybrid relative to its parents in biomass and seed production remain elusive. In recent years, it has been suggested that epigenetic controls on levels of gene action are involved. Using mutants of genes involved in DNA methylation, we show that RNA polymerase IV or methyltransferase I do not contribute to the generation of the heterotic phenotype but that decrease in DNA methylation 1, a nucleosome remodeller with an effect on DNA methylation level, is required to produce a full level of hybrid vigor.

Kawanabe, T, Osabe, K, Itabashi, E, Okazaki, K, Dennis, ES & Fujimoto, R 2016, 'Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in Brassica rapa L.', GENES & GENETIC SYSTEMS, vol. 91, no. 1, pp. 1-10.
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Keast, VJ, Myles, TA, Shahcheraghi, N & Cortie, MB 2016, 'Corrosion processes of triangular silver nanoparticles compared to bulk silver', Journal of Nanoparticle Research, vol. 18, no. 2, pp. 1-11.
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Excessive corrosion of silver nanoparticles is a significant impediment to their use in a variety of potential applications in the biosensing, plasmonic and antimicrobial fields. Here we examine the environmental degradation of triangular silver nanoparticles (AgNP) in laboratory air. In the early stages of corrosion, transmission electron microscopy shows that dissolution of the single-crystal, triangular, AgNP (side lengths 50–120 nm) is observed with the accompanying formation of smaller, polycrystalline Ag particles nearby. The new particles are then observed to corrode to Ag2S and after 21 days nearly full corrosion has occurred, but some with minor Ag inclusions remaining. In contrast, a bulk Ag sheet, studied in cross section, showed an adherent corrosion layer of only around 20–50 nm in thickness after over a decade of being exposed to ambient air. The results have implications for antibacterial properties and ecotoxicology of AgNP during corrosion as the dissolution and reformation of Ag particles during corrosion will likely be accompanied by the release of Ag+ ions.

Keast, VJ, Walhout, CJ, Pedersen, T, Shahcheraghi, N, Cortie, MB & Mitchell, DRG 2016, 'Higher Order Plasmonic Modes Excited in Ag Triangular Nanoplates by an Electron Beam', Plasmonics, vol. 11, no. 4, pp. 1081-1086.
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© 2015, Springer Science+Business Media New York. Ag triangular nanoplates are known to generate strong plasmonic resonances when excited by both light and electron beams. Experimental electron energy-loss spectra (EELS) and maps were acquired using an aberration-corrected JEOL-ARM microscope. The corner, edge and centre modes that are often observed in such structures were also observed in these measurements. In addition, novel higher order internal modes were observed and were found to be well reproduced by theoretical calculations using boundary element method (BEM). These modes are “dark modes” so are not observed in the optical extinction spectra. They are confined surface propagating modes and are analogous to laser cavity modes.

Kelleway, JJ, Saintilan, N, Macreadie, PI & Ralph, PJ 2016, 'Sedimentary Factors are Key Predictors of Carbon Storage in SE Australian Saltmarshes', ECOSYSTEMS, vol. 19, no. 5, pp. 865-880.
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Kelleway, JJ, Saintilan, N, Macreadie, PI, Skilbeck, CG, Zawadzki, A & Ralph, PJ 2016, 'Seventy years of continuous encroachment substantially increases 'blue carbon' capacity as mangroves replace intertidal salt marshes', GLOBAL CHANGE BIOLOGY, vol. 22, no. 3, pp. 1097-1109.
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Kendig, MD, Cheung, AMK, Raymond, JS & Corbit, LH 2016, 'Contexts Paired with Junk Food Impair Goal-Directed Behavior in Rats: Implications for Decision Making in Obesogenic Environments', Frontiers in Behavioral Neuroscience, vol. 10, no. Nov, p. 216.
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The high prevalence of obesity and related metabolic diseases calls for greater understanding of the factors that drive excess energy intake. Calorie-dense palatable foods are readily available and often are paired with highly salient environmental cues. These cues can trigger food-seeking and consumption in the absence of hunger. Here we examined the effects of palatable food-paired environmental cues on control of instrumental food-seeking behavior. In Experiment 1, adult male rats received exposures to one context containing three 'junk' foods (JFs context) and another containing chow (Chow context). Next, rats were food-deprived and trained to perform instrumental responses (lever-press) for two novel food rewards in a third, distinct context. Contextual influences on flexible control of food-seeking behavior were then assessed by outcome devaluation tests held in the JF, chow and training contexts. Devaluation was achieved using specific satiety and test order was counterbalanced. Rats exhibited goal-directed control over behavior when tested in the training and chow-paired contexts. Notably, performance was habitual (insensitive to devaluation) when tested in the JF context. In Experiment 2 we tested whether the impairment found in the JF context could be ameliorated by the presentation of a discrete auditory cue paired with the chow context, relative to a second cue paired with the JF context. Consistent with the results of Experiment 1, the devaluation effect was not significant when rats were tested in the JF context with the JF cue. However, presenting the chow cue increased the impact of the devaluation treatment leading to a robust devaluation effect. Further tests confirmed that performance in the chow context was goal-directed and that sensory-specific satiety in the JF context was intact. These results show that environments paired with palatable foods can impair goal-directed control over food-seeking behavior, but that this deficit was ...

Keogh, RH, Carroll, RJ, Tooze, JA, Kirkpatrick, SI & Freedman, LS 2016, 'Statistical issues related to dietary intake as the response variable in intervention trials', Statistics in Medicine, vol. 35, no. 25, pp. 4493-4508.
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The focus of this paper is dietary intervention trials. We explore the statistical issues involved when the response variable, intake of a food or nutrient, is based on self‐report data that are subject to inherent measurement error. There has been little work on handling error in this context. A particular feature of self‐reported dietary intake data is that the error may be differential by intervention group. Measurement error methods require information on the nature of the errors in the self‐report data. We assume that there is a calibration sub‐study in which unbiased biomarker data are available. We outline methods for handling measurement error in this setting and use theory and simulations to investigate how self‐report and biomarker data may be combined to estimate the intervention effect. Methods are illustrated using data from the Trial of Nonpharmacologic Intervention in the Elderly, in which the intervention was a sodium‐lowering diet and the response was sodium intake. Simulations are used to investigate the methods under differential error, differing reliability of self‐reports relative to biomarkers and different proportions of individuals in the calibration sub‐study. When the reliability of self‐report measurements is comparable with that of the biomarker, it is advantageous to use the self‐report data in addition to the biomarker to estimate the intervention effect. If, however, the reliability of the self‐report data is low compared with that in the biomarker, then, there is little to be gained by using the self‐report data. Our findings have important implications for the design of dietary intervention trials. © 2016 The Authors.Statistics in Medicinepublished by John Wiley & Sons Ltd.

Khachadorian, S, Gillen, R, Ton-That, C, Zhu, L, Maultzsch, J, Phillips, MR & Hoffmann, A 2016, 'Revealing the origin of high-energy Raman local mode in nitrogen doped ZnO nanowires', PHYSICA STATUS SOLIDI-RAPID RESEARCH LETTERS, vol. 10, no. 4, pp. 334-338.
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© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Raman scattering experiments complemented by density functional theory (DFT) calculations of phonon frequencies have been performed to understand the origin of observed high-energy local Raman modes at 2269 cm-1 and 2282 cm-1 on N-plasma treated ZnO nanowires (NWs). We show that these modes increase in intensity with prolonged N-plasma treatment. Our results reveal that the origin of the high-energy Raman local mode is a loosely bound N2 molecule in the vicinity of a zinc vacancy, which according to our latest work acts as a shallow acceptor and leads to the donor-acceptor-pair transition at 3.232 eV [Phys. Rev. B 92, 024103 (2015)]. Moreover the results provide a more thorough description of nitrogen related complexes in ZnO NWs. Scanning electron microscopy (SEM) image of ZnONWs.

Khuu, A, Chadwick, S, Spindler, X, Lam, R, Moret, S & Roux, C 2016, 'Evaluation of one-step luminescent cyanoacrylate fuming', FORENSIC SCIENCE INTERNATIONAL, vol. 263, pp. 126-131.
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© 2016 Elsevier Ireland Ltd. One-step luminescent cyanoacrylates have recently been introduced as an alternative to the conventional cyanoacrylate fuming methods. These new techniques do not require the application of a luminescent post-treatment in order to enhance cyanoacrylate-developed fingermarks. In this study, three one-step polymer cyanoacrylates: CN Yellow Crystals (Aneval Inc.), PolyCyano UV (Foster + Freeman Ltd.) and PECA Multiband (BVDA), and one monomer cyanoacrylate: Lumikit™ (Crime Scene Technology), were evaluated against a conventional two-step cyanoacrylate fuming method (Cyanobloom (Foster + Freeman Ltd.) with rhodamine 6G stain). The manufacturers' recommended conditions or conditions compatible with the MVC™ 1000/D (Foster + Freeman Ltd.) were assessed with fingermarks aged for up to 8 weeks on non-porous and semi-porous substrates. Under white light, Cyanobloom generally gave better development than the one-step treatments across the substrates. Similarly when viewed under the respective luminescent conditions, Cyanobloom with rhodamine 6G stain resulted in improved contrast against the one-step treatments except on polystyrene, where PolyCyano UV and PECA Multiband gave better visualisation. Rhodamine 6G post-treatment of one-step samples did not significantly enhance the contrast of any of the one-step treatments against Cyanobloom/rhodamine 6G-treated samples.

Kianinia, M, Shimoni, O, Bendavid, A, Schell, AW, Randolph, SJ, Toth, M, Aharonovich, I & Lobo, CJ 2016, 'Robust, directed assembly of fluorescent nanodiamonds', NANOSCALE, vol. 8, no. 42, pp. 18032-18037.
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© 2016 The Royal Society of Chemistry. Arrays of fluorescent nanoparticles are highly sought after for applications in sensing, nanophotonics and quantum communications. Here we present a simple and robust method of assembling fluorescent nanodiamonds into macroscopic arrays. Remarkably, the yield of this directed assembly process is greater than 90% and the assembled patterns withstand ultra-sonication for more than three hours. The assembly process is based on covalent bonding of carboxyl to amine functional carbon seeds and is applicable to any material, and to non-planar surfaces. Our results pave the way to directed assembly of sensors and nanophotonics devices.

Kianinia, M, Tawfik, SA, Regan, B, Tran, TT, Ford, MJ, Aharonovich, I & Toth, M 2016, 'Robust Solid State Quantum System Operating at 800 K', ACS Photonics, vol. 4, no. 4, pp. 768-773.
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Realization of Quantum information and communications technologies requiresrobust, stable solid state single photon sources. However, most existingsources cease to function above cryogenic or room temperature due to thermalionization or strong phonon coupling which impede their emissive and quantumproperties. Here we present an efficient single photon source based on a defectin a van der Waals crystal that is optically stable and operates at elevatedtemperatures of up to 800 K. The quantum nature of the source and the photonpurity are maintained upon heating to 800 K and cooling back to roomtemperature. Our report of a robust high temperature solid state single photonsource constitutes a significant step to-wards practical, integrated quantumtechnologies for real-world environments.

Kim, I, Kweon, JH, Park, J, Kim, KW, Ahn, IS, Cho, KK, Ahn, JH, Wang, G, Ryu, HS & Ahn, HJ 2016, 'Effect of sodium salt in poly(ethylene oxide) electrolyte on initial discharge capacity of Na/poly(ethylene oxide)/S battery', Journal of Ceramic Processing Research, vol. 17, no. 8, pp. 799-802.
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To investigate the effects of sodium salt in a poly(ethylene oxide) (PEO) electrolyte on the initial discharge properties of a Na/S cell, various concentrations of NaCF3SO3 from 0.1 to 2.0 m were added to the electrolyte. Scanning electron microscopy and differential scanning calorimetry results showed a continuous decrease in the crystallinity of the PEO electrolyte with increasing amounts of sodium salt. The ionic conductivity of the PEO electrolyte at 70 °C increased with increasing sodium salt concentration up to 0.33 m, at which point the highest ionic conductivity of 1.732 × 10−4 S cm−1 was obtained. However, the ionic conductivity decreased at 2.0 m sodium salt. The same trend was seen in the initial discharge capacity, in that the highest value of 435 mAh g−1 was achieved at a sodium salt concentration of 0.33 m. These results demonstrate that 0.33 m of sodium salt is the optimum composition for Na/S batteries.

Kim, M-S 2016, 'Optimal management for alcoholic liver disease: Conventional medications, natural therapy or combination?', World Journal of Gastroenterology, vol. 22, no. 1, pp. 8-8.
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© The Author(s) 2016. Alcohol consumption is the principal factor in the pathogenesis of chronic liver diseases. Alcoholic liver disease (ALD) is defined by histological lesions on the liver that can range from simple hepatic steatosis to more advanced stages such as alcoholic steatohepatitis, cirrhosis, hepatocellular carcinoma and liver failure. As one of the oldest forms of liver injury known to humans, ALD is still a leading cause of liver-related morbidity and mortality and the burden is exerting on medical systems with hospitalization and management costs rising constantly worldwide. Although the biological mechanisms, including increasing of acetaldehyde, oxidative stress with induction of cytochrome p450 2E1, inflammatory cytokine release, abnormal lipid metabolism and induction of hepatocyte apoptosis, by which chronic alcohol consumption triggers serious complex progression of ALD is well established, there is no universally accepted therapy to prevent or reverse. In this article, we have briefly reviewed the pathogenesis of ALD and the molecular targets for development of novel therapies. This review is focused on current therapeutic strategies for ALD, including lifestyle modification with nutrition supplements, available pharmacological drugs and new agents that are under development, liver transplantation, application of complementary medicines, and their combination. The relevant molecular mechanisms of each conventional medication and natural agent have been reviewed according to current available knowledge in the literature. We also summarized efficacy vs safety on conventional and herbal medicines which are specifically used for the prevention and treatment of ALD. Through a system review, this article highlighted that the combination of pharmaceutical drugs with naturally occurring agents may offer an optimal management for ALD and its complications. It is worthwhile to conduct large-scale, multiple centre clinical trials to further p...

Kim, RY, Rae, B, Neal, R, Donovan, C, Pinkerton, J, Balachandran, L, Starkey, MR, Knight, DA, Horvat, JC & Hansbro, PM 2016, 'Elucidating novel disease mechanisms in severe asthma', Clinical & Translational Immunology, vol. 5, no. 7, pp. e91-e91.
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Corticosteroids are broadly active and potent anti‐inflammatory agents that, despite the introduction of biologics, remain as the mainstay therapy for many chronic inflammatory diseases, including inflammatory bowel diseases, nephrotic syndrome, rheumatoid arthritis, chronic obstructive pulmonary disease and asthma. Significantly, there are cohorts of these patients with poor sensitivity to steroid treatment even with high doses, which can lead to many iatrogenic side effects. The dose‐limiting toxicity of corticosteroids, and the lack of effective therapeutic alternatives, leads to substantial excess morbidity and healthcare expenditure. We have developed novel murine models of respiratory infection‐induced, severe, steroid‐resistant asthma that recapitulate the hallmark features of the human disease. These models can be used to elucidate novel disease mechanisms and identify new therapeutic targets in severe asthma. Hypothesis‐driven studies can elucidate the roles of specific factors and pathways. Alternatively, 'Omics approaches can be used to rapidly generate new targets. Similar approaches can be used in other diseases.

King, DJM, Middleburgh, SC, McGregor, AG & Cortie, MB 2016, 'Predicting the formation and stability of single phase high-entropy alloys', Acta Materialia, vol. 104, pp. 172-179.
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Crown Copyright © 2015 Published by Elsevier Ltd on behalf of Acta Materialia Inc. A method for rapidly predicting the formation and stability of undiscovered single phase high-entropy alloys (SPHEAs) is provided. Our software implementation of the algorithm uses data for 73 metallic elements and rapidly combines them - 4, 5 or 6 elements at a time - using the Miedema semi-empirical methodology to yield estimates of formation enthalpy. Approximately 186,000,000 compositions of 4, 5 and 6 element alloys were screened, and ∼1900 new equimolar SPHEAs predicted. Of the 185 experimentally reported HEA systems currently known, the model correctly predicted the stability of the SPHEA structure in 177. The other sixteen are suggested to actually form a partially ordered solid solution - a finding supported by other recent experimental and theoretical work. The stability of each alloy at a specific temperature can also be predicted, allowing precipitation temperatures (and the likely precipitate) to be forecast. This combinatorial algorithm is described in detail, and its software implementation is freely accessible through a web-service allowing rapid advances in the design, development and discovery of new technologically important alloys.

King, SR, Shimmon, S, Gentle, AR, Westerhausen, MT, Dowd, A & McDonagh, AM 2016, 'Remarkable thermal stability of gold nanoparticles functionalised with ruthenium phthalocyanine complexes', Nanotechnology, vol. 27, no. 21, pp. 215702-215702.
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© 2016 IOP Publishing Ltd. A gold nanoparticle (AuNP) ruthenium phthalocyanine (RuPc) nanocomposite has been synthesised that exhibits high thermal stability. Electrical resistance measurements revealed that the nanocomposite is stable up to ∼320 °C. Examination of the nanocomposite and the RuPc stabiliser complex using thermogravimetric analysis and differential scanning calorimetry show that the remarkable thermal stability is due to the RuPc molecules, which provide an effective barrier to sintering of the AuNPs.

Kipnis, V, Freedman, LS, Carroll, RJ & Midthune, D 2016, 'A Bivariate Measurement Error Model for Semicontinuous and Continuous Variables: Application to Nutritional Epidemiology', Biometrics, vol. 72, no. 1, pp. 106-115.
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SummarySemicontinuous data in the form of a mixture of a large portion of zero values and continuously distributed positive values frequently arise in many areas of biostatistics. This article is motivated by the analysis of relationships between disease outcomes and intakes of episodically consumed dietary components. An important aspect of studies in nutritional epidemiology is that true diet is unobservable and commonly evaluated by food frequency questionnaires with substantial measurement error. Following the regression calibration approach for measurement error correction, unknown individual intakes in the risk model are replaced by their conditional expectations given mismeasured intakes and other model covariates. Those regression calibration predictors are estimated using short-term unbiased reference measurements in a calibration substudy. Since dietary intakes are often “energy-adjusted,” e.g., by using ratios of the intake of interest to total energy intake, the correct estimation of the regression calibration predictor for each energy-adjusted episodically consumed dietary component requires modeling short-term reference measurements of the component (a semicontinuous variable), and energy (a continuous variable) simultaneously in a bivariate model. In this article, we develop such a bivariate model, together with its application to regression calibration. We illustrate the new methodology using data from the NIH-AARP Diet and Health Study (Schatzkin et al., 2001, American Journal of Epidemiology  154, 1119–1125), and also evaluate its performance in a simulation study.

Koedsin, W, Intararuang, W, Ritchie, R & Huete, A 2016, 'An Integrated Field and Remote Sensing Method for Mapping Seagrass Species, Cover, and Biomass in Southern Thailand', Remote Sensing, vol. 8, no. 4, pp. 292-292.
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Accurate and up-to-date maps of seagrass biodiversity are important for marine resource management but it is very challenging to test the accuracy of remote sensing techniques for mapping seagrass in coastal waters with variable water turbidity. In this study, Worldview-2 (WV-2) imagery was combined with field sampling to demonstrate the capability of mapping species type, percentage cover, and above-ground biomass of seagrasses in monsoonal southern Thailand. A high accuracy positioning technique, involving the Real Time Kinematic (RTK) Global Navigation Satellite System (GNSS), was used to record field sample data positions and reduce uncertainties in matching locations between satellite and field data sets. Our results showed high accuracy (90.67%) in mapping seagrass distribution and moderate accuracies for mapping percentage cover and species type (73.74% and 75.00%, respectively). Seagrass species type mapping was successfully achieved despite discrimination confusion among Halophila ovalis, Thalassia hemprichii, and Enhalus acoroides species with greater than 50% cover. The green, yellow, and near infrared spectral channels of WV-2 were used to estimate the above-ground biomass using a multiple linear regression model (RMSE of ±10.38 g·DW/m2, R = 0.68). The average total above-ground biomass was 23.95 ± 10.38 g·DW/m2. The seagrass maps produced in this study are an important step towards measuring the attributes of seagrass biodiversity and can be used as inputs to seagrass dynamic models and conservation efforts.

Kohli, GS, John, U, Van Dolah, FM & Murray, SA 2016, 'Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes', ISME JOURNAL, vol. 10, no. 8, pp. 1877-1890.
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© 2016 International Society for Microbial Ecology All rights reserved. Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success.

Kok, LF, Marsh-Wakefield, F, Marshall, JE, Gillis, C, Halliday, GM & Byrne, SN 2016, 'B cells are required for sunlight protection of mice from a CNS-targeted autoimmune attack', Journal of Autoimmunity, vol. 73, pp. 10-23.
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Kolíbal, M, Novák, L, Shanley, T, Toth, M & Šikola, T 2016, 'Silicon oxide nanowire growth mechanisms revealed by real-time electron microscopy', Nanoscale, vol. 8, no. 1, pp. 266-275.
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© 2016 The Royal Society of Chemistry. Growth of one-dimensional materials is possible through numerous mechanisms that affect the nanowire structure and morphology. Here, we explain why a wide range of morphologies is observed when silicon oxide nanowires are grown on silicon substrates using liquid gallium catalyst droplets. We show that a gallium oxide overlayer is needed for nanowire nucleation at typical growth temperatures, and that it can decompose during growth and, hence, dramatically alter the nanowire morphology. Gallium oxide decomposition is attributed to etching caused by hydrogen that can be supplied by thermal dissociation of H2O (a common impurity). We show that H2O dissociation is catalyzed by silicon substrates at temperatures as low as 320 °C, identify the material supply pathways and processes that rate-limit nanowire growth under dry and wet atmospheres, and present a detailed growth model that explains contradictory results reported in prior studies. We also show that under wet atmospheres the Ga droplets can be mobile and promote nanowire growth as they traverse the silicon substrate.

Kondaveeti, S, Cornejo, DR & Petri, DFS 2016, 'Alginate/magnetite hybrid beads for magnetically stimulated release of dopamine', Colloids and Surfaces B: Biointerfaces, vol. 138, pp. 94-101.
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Koyyalamudi, SR, Kuzhiumparambil, U, Nath, CE, Byrne, JA, Fraser, CJ, O'Brien, TA, Earl, JW & Shaw, PJ 2016, 'Development and Validation of a High Pressure Liquid Chromatography-UV Method for the Determination of Treosulfan and Its Epoxy Metabolites in Human Plasma and Its Application in Pharmacokinetic Studies', JOURNAL OF CHROMATOGRAPHIC SCIENCE, vol. 54, no. 3, pp. 326-333.
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Kretschmer, K, Sun, B & Wang, G 2016, 'Highly Efficient Rechargeable Sodium-Oxygen Battery Using Carbon Paper As Binder and Catalyst Free Air Cathode', ECS Meeting Abstracts, vol. MA2016-03, no. 2, pp. 1166-1166.
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Metal-air batteries, which utilize conversion chemistry rather than intercalation mechanisms, have attracted large research interest due to their high theoretical energy density. Much work has been devoted to investigate and optimize Li-O2 cell, which suffer from large overpotential and poor energy efficiency due to complex cell chemistry and undesired side reactions. Recently, Janek et al. have reported the approach of substituting lithium with sodium in an air battery system and surprised the research community with outstanding performance. Their Na-O2 was reversibly charged/discharged at very low overpotentials using a pure carbon cathode without the addition of a catalyst [1]. They further more claimed that low surface area can provide a more efficient cycling performance as well as high absolute capacity [2]. To further understand the impact of the carbon material used as air cathode inside the Na-O2 system, we investigated a range of carbonized fiber based materials. We found that commercially available and heat-treated filter paper provides outstanding oxygen reduction reaction and oxygen evolution reaction activities without any additional catalyst. An initial absolute capacity of 1.26 mAh cm-2 and low overpotential <400 mV could be achieved when cycled between 1.8 and 3.0 V at 100 µA cm-2 without any capacity restriction. References: [1] P. Hartmann, C.L. Bender, J. Janek et al., N at. mater. 2013, 12, 228-232. [2] C.L. Bender, P. Hartmann, J. Janek et al. Adv. Energy Mater. 2014, 4

Kretschmer, K, Sun, B, Xie, X, Chen, S & Wang, G 2016, 'A free-standing LiFePO4-carbon paper hybrid cathode for flexible lithium-ion batteries', GREEN CHEMISTRY, vol. 18, no. 9, pp. 2691-2698.
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© 2016 The Royal Society of Chemistry. Lithium-ion batteries (LIBs) are widely implemented to power portable electronic devices and are increasingly in demand for large-scale applications. One of the major obstacles for this technology is still the low cost-efficiency of its electrochemical active materials and production processes. In this work, we present a novel impregnation-carbothermal reduction method to generate a LiFePO4-carbon paper hybrid electrode, which doesn't require a metallic current collector, polymeric binder or conducting additives to function as a cathode material in a LIB system. A shell of LiFePO4 crystals was grown in situ on carbon fibres during the carbonization of microcrystalline cellulose. The LiFePO4-carbon paper electrode achieved an initial reversible areal capacity of 197 μA h cm-2 increasing to 222 μA h cm-2 after 500 cycles at a current density of 0.1 mA cm-2. The hybrid electrode also demonstrated a superior cycling performance for up to 1000 cycles. The free-standing electrode could be potentially applied for flexible lithium-ion batteries.

Kumar, M, Kuzhiumparambil, U, Pernice, M, Jiang, Z & Ralph, PJ 2016, 'Metabolomics: an emerging frontier of systems biology in marine macrophytes', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 16, pp. 76-92.
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© 2016. Metabolomics is a rapidly emerging discipline within functional genomics which is increasingly being applied to understand biochemical phenotypes across a range of biological systems. Metabolomics measures all (or a subset) metabolites in a cell at a specific time point, reflecting a snapshot of all the regulatory events responding to the external environmental conditions. Although metabolomics and systems biology approaches have been applied to the study of terrestrial plants, few marine macrophytes have been examined using these novel technologies. Marine macrophytes (including seaweeds and seagrasses) are marine ecosystem engineers delivering a range of ecologically and economically valuable biological services; however they are under threat from a wide range of anthropogenic stressors, climate variation, invasive species and pathogens. Investigating metabolomic regulation in these organisms is crucial to understand their acclimation, adaptation and defence responses to environmental challenges. This review describes the current analytical tools available to study metabolomics in marine macrophytes, along with their limitations for both targeted and non-targeted workflows. To illustrate recent advances in systems biology studies in marine macrophytes, we describe how metabolites are used in chemical defence to deter a broad range of invasive species and pathogens, as well as metabolomic reprogramming leading to acclimation or adaptive strategies to environmental and anthropogenic stresses. Where possible, the mechanistic processes associated with primary and secondary plant metabolism governing cellular homeostasis under extreme environments are discussed. Further, we provide a comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowledge from a system biology approach to marine macrophytes. Finally, functional integration of metabolomics with the allied 'omics' disciplines of transcriptomics a...

Kundukad, B, Seviour, T, Liang, Y, Rice, SA, Kjelleberg, S & Doyle, PS 2016, 'Mechanical properties of the superficial biofilm layer determine the architecture of biofilms', Soft Matter, vol. 12, no. 26, pp. 5718-5726.
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Kwok, C & Lim, D 2016, 'Evaluation of a Culturally Tailored Education to Promote Breast and Cervical Cancer Screening Among Chinese-Australian Women', Journal of Cancer Education, vol. 31, no. 3, pp. 595-601.
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© 2015, American Association for Cancer Education. This paper aims to evaluate the impact of the culturally sensitive and linguistically appropriate education program on the following: (i) awareness of screening practices (breast awareness, mammogram, and Pap smear test); (ii) screening intention within the next six months; and (iii) knowledge about breast and cervical cancer among Chinese-Australian women. Titled “Happy and Healthy Life in Sydney,” this was a quasi-experimental study with both pre- and post-test design. A convenience sample of 288 Chinese women was recruited through Chinese organizations such as churches and community centers. Participants completed the questionnaires before and after the educational program. The results show that the program was effective in promoting awareness of breast and cervical cancer screening and resulted in increased participative intentions in both mammogram and Pap smear testing within the next 6 months. Results also indicate that knowledge and belief scores were significantly increased. Conclusion: Our study supports that educational programs which use culturally sensitive and linguistically appropriate strategies are effective in improving both knowledge of breast and cervical cancer and awareness of their early detection practices among Chinese-Australian women.

Kwon, D, Choi, S, Wang, G & Park, S 2016, 'Germanium-based multiphase material as a high-capacity and cycle-stable anode for lithium-ion batteries', RSC Advances, vol. 6, no. 92, pp. 89176-89180.
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Cu-incorporated porous Ge-based anodes with high electrical conductivity are prepared by a simple carbothermic reduction process of CuGeO₃. The Cu–Ge-based anodes exhibit outstanding capacity retention at 25 °C and 60 °C.

Labbate, M, Seymour, JR, Lauro, F & Brown, MV 2016, 'Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments', Frontiers in Microbiology, vol. 7, no. JUL.
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Laiolo, L, McInnes, AS, Matear, R & Doblin, MA 2016, 'Key Drivers of Seasonal Plankton Dynamics in Cyclonic and Anticyclonic Eddies off East Australia', Frontiers in Marine Science, vol. 3, no. AUG, pp. 1-14.
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© 2016 Laiolo, McInnes, Matear and Doblin. Mesoscale eddies in the south west Pacific region are prominent ocean features that represent distinctive environments for phytoplankton. Here, we examine the seasonal plankton dynamics associated with averaged cyclonic and anticyclonic eddies (CE and ACE, respectively) off eastern Australia. We do this through building seasonal climatologies of mixed layer depth (MLD) and surface chlorophyll-a for both CE and ACE by combining remotely sensed sea surface height (TOPEX/Poseidon, Envisat, Jason-1, and OSTM/Jason-2), remotely sensed ocean color (GlobColour) and in situ profiles of temperature, salinity and pressure from Argo floats. Using the CE and ACE seasonal climatologies, we assimilate the surface chlorophyll-a data into both a single (WOMBAT), and multi-phytoplankton class (EMS) biogeochemical model to investigate the level of complexity required to simulate the phytoplankton chlorophyll-a. For the two eddy types, the data assimilation showed both biogeochemical models only needed one set of parameters to represent phytoplankton but needed different parameters for zooplankton. To assess the simulated phytoplankton behavior we compared EMS model simulations with a ship-based experiment that involved incubating a winter phytoplankton community sampled from below the mixed layer under ambient and two higher light intensities with and without nutrient enrichment. By the end of the 5-day field experiment, large diatom abundance was four times greater in all treatments compared to the initial community, with a corresponding decline in pico-cyanobacteria. The experimental results were consistent with the simulated behavior in CE and ACE, where the seasonal deepening of the mixed layer during winter produced a rapid increase in large phytoplankton. Our model simulations suggest that CE off East Australia are not only characterized by a higher chlorophyll-a concentration compared to ACE, but also by a higher concentr...

Lam, M, Royce, SG, Donovan, C, Jelinic, M, Parry, LJ, Samuel, CS & Bourke, JE 2016, 'Serelaxin Elicits Bronchodilation and Enhances β-Adrenoceptor-Mediated Airway Relaxation', Frontiers in Pharmacology, vol. 7, no. OCT.
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© 2016 Lam, Royce, Donovan, Jelinic, Parry, Samuel and Bourke. Treatment with β-adrenoceptor agonists does not fully overcome the symptoms associated with severe asthma. Serelaxin elicits potent uterine and vascular relaxation via its cognate receptor, RXFP1, and nitric oxide (NO) signaling, and is being clinically evaluated for the treatment of acute heart failure. However, its direct bronchodilator efficacy has yet to be explored. Tracheal rings were prepared from male Sprague-Dawley rats (250-350 g) and tricolor guinea pigs, and precision cut lung slices (PCLSs) containing intrapulmonary airways were prepared from rats only. Recombinant human serelaxin (rhRLX) alone and in combination with rosiglitazone (PPARγ agonist; recently described as a novel dilator) or β-adrenoceptor agonists (isoprenaline, salbutamol) were added either to pre-contracted airways, or before contraction with methacholine or endothelin-1. Regulation of rhRLX responses by epithelial removal, indomethacin (cyclooxygenase inhibitor), L-NAME (nitric oxide synthase inhibitor), SQ22536 (adenylate cyclase inhibitor) and ODQ (guanylate cyclase inhibitor) were also evaluated. Immunohistochemistry was used to localize RXFP1 to airway epithelium and smooth muscle. rhRLX elicited relaxation in rat trachea and PCLS, more slowly than rosiglitazone or isoprenaline, but potentiated relaxation to both these dilators. It markedly increased β-adrenoceptor agonist potency in guinea pig trachea. rhRLX, rosiglitazone, and isoprenaline pretreatment also inhibited the development of rat tracheal contraction. Bronchoprotection by rhRLX increased with longer pre-incubation time, and was partially reduced by epithelial removal, indomethacin and/or L-NAME. SQ22536 and ODQ also partially inhibited rhRLX-mediated relaxation in both intact and epithelial-denuded trachea. RXFP1 expression in the airways was at higher levels in epithelium than smooth muscle. In summary, rhRLX elicits large and small airway relaxation via...

Lam, R, Hofstetter, O, Lennard, C, Roux, C & Spindler, X 2016, 'Evaluation of multi-target immunogenic reagents for the detection of latent and body fluid-contaminated fingermarks', FORENSIC SCIENCE INTERNATIONAL, vol. 264, pp. 168-175.
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© 2016 Elsevier Ireland Ltd Fingermark enhancement reagents capable of molecular recognition offer a highly selective and sensitive method of detection. Antibodies and aptamers provide a high degree of adaptability for visualisation, allowing for the selection of the most appropriate visualisation wavelength for a particular substrate without the need for specialist equipment or image processing. However, the major hurdle to overcome is the balance between sensitivity and selectivity. Single-target molecular recognition is highly specific, purported to have better detection limits than chemical reactions or stains, and can provide information about the donor or activity, but often results in incomplete ridge pattern development. Consequently, the development and evaluation of multi-target biomolecular reagents for fingermark enhancement was investigated, with the focus on endogenous eccrine secretions. To assess the suitability of the immunogenic reagents for potential operational use, a variety of parameters (i.e., processing time, fixing and working solution conditions) were optimised on a wide range of non-porous and semi-porous substrates. The relative performance of immunogenic reagents was compared to that of routine techniques applied to latent marks and marks in blood, semen and saliva. The incorporation of these novel reagents into routine technique sequences was also investigated. The experimental results indicated that the multi-target immunogenic reagents were not a suitable alternative to routine detection methods or sequences, but may have promise as a “last resort” method for difficult substrates or cases.

Lao, W, Jin, X, Tan, Y, Xiao, L, Padula, M, Bishop, D, Reedy, B, Ong, M, Kamal, M & Qu, X 2016, 'Characterisation of Bone Beneficial Components from Australian Wallaby Bone', Medicines, vol. 3, no. 3, pp. 23-23.
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Background: Osteoporosis is a condition in which the bones become brittle, increasing the risk of fractures. Complementary medicines have traditionally used animal bones for managing bone disorders, such as osteoporosis. This study aimed to discover new natural products for these types of conditions by determining mineral and protein content of bone extracts derived from the Australian wallaby. Methods: Inductively coupled plasma-mass spectrometry and Fourier transform infrared spectroscopic analysis were used for mineral tests, proteome analysis was using LC/MS/MS and the effects of wallaby bone extracts (WBE)s on calcium deposition and alkaline phosphatase activity were evaluated in osteogenic cells derived from adipose tissue-derived stem cells (ADSCs). Results: Concentrations of calcium and phosphorus were 26.21% and 14.72% in WBE respectively. Additionally, minerals found were wide in variety and high in concentration, while heavy metal concentrations of aluminium, iron, zinc and other elements were at safe levels for human consumption. Proteome analysis showed that extracts contained high amounts of bone remodelling proteins, such as osteomodulin, osteopontin and osteoglycin. Furthermore, in vitro evaluation of WBEs showed increased deposition of calcium in osteoblasts with enhanced alkaline phosphatase activity in differentiated adipose-derived stem cells. Conclusion: Our results demonstrate that wallaby bone extracts possess proteins and minerals beneficial for bone metabolism. WBEs may therefore be used for developing natural products for conditions such as osteoporosis and further investigation to understand biomolecular mechanism by which WBEs prevent osteoporosis is warranted.

Lapine, M, McPhedran, RC & Poulton, CG 2016, 'Slow convergence to effective medium in finite discrete metamaterials', Physical Review B, vol. 93, no. 23.
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© 2016 American Physical Society. It is known that metamaterial properties may differ significantly from the predictions of effective-medium theory. In many cases this is due to the finite size and discrete structure, which cannot be neglected in practical samples with a relatively small amount of elements. We analyze the response of finite discrete metamaterial objects of a spherical shape and demonstrate the role of boundary effects in these structures, pointing out an interplay between the size of the structure and the dissipation. We conclude that the discrepancy between the actual resonance frequency of a sphere and the effective-medium prediction is inversely proportional to the size of the sphere.

Lawrence, A, Eglezos, S & Huston, W 2016, 'Environmental Legionella spp. collected in urban test sites of South East Queensland, Australia, are virulent to human macrophages in vitro', Research in Microbiology, vol. 167, no. 2, pp. 149-153.
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Lawrence, A, Fraser, T, Gillett, A, Tyndall, JDA, Timms, P, Polkinghorne, A & Huston, WM 2016, 'Chlamydia Serine Protease Inhibitor, targeting HtrA, as a New Treatment for Koala Chlamydia infection', Scientific Reports, vol. 6, no. 1, pp. 1-12.
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AbstractThe koala, an iconic marsupial native to Australia, is a threatened species in many parts of the country. One major factor in the decline is disease caused by infection with Chlamydia. Current therapeutic strategies to treat chlamydiosis in the koala are limited. This study examines the effectiveness of an inhibitor, JO146, which targets the HtrA serine protease for treatment of C. pecorum and C. pneumoniae in vitro and ex vivo with the aim of developing a novel therapeutic for koala Chlamydia infections. Clinical isolates from koalas were examined for their susceptibility to JO146. In vitro studies demonstrated that treatment with JO146 during the mid-replicative phase of C. pecorum or C. pneumoniae infections resulted in a significant loss of infectious progeny. Ex vivo primary koala tissue cultures were used to demonstrate the efficacy of JO146 and the non-toxic nature of this compound on peripheral blood mononuclear cells and primary cell lines established from koala tissues collected at necropsy. Our results suggest that inhibition of the serine protease HtrA could be a novel treatment strategy for chlamydiosis in koalas.

Le Brun, AP, Clifton, LA, Holt, SA, Holden, PJ & Lakey, JH 2016, 'Deuterium Labeling Strategies for Creating Contrast in Structure–Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry', vol. 566, pp. 231-252.
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Lee, BB, Toh, S-L, Ryan, S, Simpson, JM, Clezy, K, Bossa, L, Rice, SA, Marial, O, Weber, G, Kaur, J, Boswell-Ruys, C, Goodall, S, Middleton, J, Tudehope, M & Kotsiou, G 2016, 'Probiotics [LGG-BB12 or RC14-GR1] versus placebo as prophylaxis for urinary tract infection in persons with spinal cord injury [ProSCIUTTU]: a study protocol for a randomised controlled trial', BMC UROLOGY, vol. 16, no. 1.
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© 2016 Lee et al. Background: Urinary tract infections [UTIs] are very common in people with Spinal Cord Injury [SCI]. UTIs are increasingly difficult and expensive to treat as the organisms that cause them become more antibiotic resistant. Among the SCI population, there is a high rate of multi-resistant organism [MRO] colonisation. Non-antibiotic prevention strategies are needed to prevent UTI without increasing resistance. Probiotics have been reported to be beneficial in preventing UTIs in post-menopausal women in several in vivo and in vitro studies. The main aim of this study is to determine whether probiotic therapy with combinations of Lactobacillus reuteri RC-14 + Lactobacillus rhamnosus GR-1 [RC14-GR1] and/or Lactobacillus rhamnosus GG + Bifidobacterium BB-12 [LGG-BB12] are effective in preventing UTI in people with SCI compared to placebo. Method: This is a multi-site randomised double-blind double-dummy placebo-controlled factorial design study conducted in New South Wales, Australia. All participants have a neurogenic bladder as a result of spinal injury. Recruitment started in April 2011. Participants are randomised to one of four arms, designed for factorial analysis of LGG-BB12 and/or RC14-GR1 v Placebo. This involves 24 weeks of daily oral treatment with RC14-GR1 + LGG-BB12, RC14-GR1 + placebo, LGG-BB12 + placebo or two placebo capsules. Randomisation is stratified by bladder management type and inpatient status. Participants are assessed at baseline, three months and six months for Short Form Health Survey [SF-36], microbiological swabs of rectum, nose and groin; urine culture and urinary catheters for subjects with indwelling catheters. A bowel questionnaire is administered at baseline and three months to assess effect of probiotics on bowel function. The primary outcome is time from randomisation to occurrence of symptomatic UTI. The secondary outcomes are change of MRO status and bowel function, quality of life and cost-effectivenes...

Lee, CYY & Wand, MP 2016, 'Variational methods for fitting complex Bayesian mixed effects models to health data', Statistics in Medicine, vol. 35, no. 2, pp. 165-188.
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We consider approximate inference methods for Bayesian inference to longitudinal and multilevel data within the context of health science studies. The complexity of these grouped data often necessitates the use of sophisticated statistical models. However, the large size of these data can pose significant challenges for model fitting in terms of computational speed and memory storage. Our methodology is motivated by a study that examines trends in cesarean section rates in the largest state of Australia, New South Wales, between 1994 and 2010. We propose a group‐specific curve model that encapsulates the complex nonlinear features of the overall and hospital‐specific trends in cesarean section rates while taking into account hospital variability over time. We use penalized spline‐based smooth functions that represent trends and implement a fully mean field variational Bayes approach to model fitting. Our mean field variational Bayes algorithms allow a fast (up to the order of thousands) and streamlined analytical approximate inference for complex mixed effects models, with minor degradation in accuracy compared with the standard Markov chain Monte Carlo methods. Copyright © 2015 John Wiley & Sons, Ltd.

Lee, H, Golicz, AA, Bayer, PE, Jiao, Y, Tang, H, Paterson, AH, Sablok, G, Krishnaraj, RR, Chan, C-KK, Batley, J, Kendrick, GA, Larkum, AWD, Ralph, PJ & Edwards, D 2016, 'The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)', Plant Physiology, vol. 172, no. 1, pp. 272-283.
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Seagrasses are marine angiosperms that evolved from land plants but returned to the sea around 140 million years ago during the early evolution of monocotyledonous plants. They successfully adapted to abiotic stresses associated with growth in the marine environment, and today, seagrasses are distributed in coastal waters worldwide. Seagrass meadows are an important oceanic carbon sink and provide food and breeding grounds for diverse marine species. Here, we report the assembly and characterization of the Zostera muelleri genome, a southern hemisphere temperate species. Multiple genes were lost or modified in Z. muelleri compared with terrestrial or floating aquatic plants that are associated with their adaptation to life in the ocean. These include genes for hormone biosynthesis and signaling and cell wall catabolism. There is evidence of whole-genome duplication in Z. muelleri; however, an ancient pan-commelinid duplication event is absent, highlighting the early divergence of this species from the main monocot lineages.

Lee, H-H, Paudel, KR, Jeong, J, Wi, A-J, Park, W-S, Kim, D-W & Oak, M-H 2016, 'Antiatherogenic Effect of Camellia japonica Fruit Extract in High Fat Diet‐Fed Rats', Evidence-Based Complementary and Alternative Medicine, vol. 2016, no. 1, pp. 1-8.
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Hypercholesterolemia is a well‐known etiological factor for cardiovascular disease and a common symptom of most types of metabolic disorders. Camellia japonica is a traditional garden plant, and its flower and seed have been used as a base oil of traditional cosmetics in East Asia. The present study was carried out to evaluate the effect of C. japonica fruit extracts (CJF) in a high fat diet‐ (HFD‐) induced hypercholesterolemic rat model. CJF was administered orally at three different doses: 100, 400, and 800 mg·kg−1·day−1 (CJF 100, 400, and 800, resp.). Our results showed that CJF possessed strong cholesterol‐lowering potency as indicated by the decrease in serum total cholesterol (TC), triglyceride (TG), and low‐density lipoprotein (LDL), accompanied by an increase in serum high‐density lipoprotein (HDL). Furthermore, CJF reduced serum lipid peroxidation by suppressing the formation of thiobarbituric acid reactive substance. In addition, oil red O (ORO) staining of rat arteries showed decreased lipid‐positive staining in the CJF‐treated groups compared to the control HFD group. Taken together, these results suggest that CJF could be a potent herbal therapeutic option and source of a functional food for the prevention and treatment of atherosclerosis and other diseases associated with hypercholesterolemia.

Lee, KWK, Yam, JKH, Mukherjee, M, Periasamy, S, Steinberg, PD, Kjelleberg, S & Rice, SA 2016, 'Interspecific diversity reduces and functionally substitutes for intraspecific variation in biofilm communities', The ISME Journal, vol. 10, no. 4, pp. 846-857.
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Abstract Diversity has a key role in the dynamics and resilience of communities and both interspecific (species) and intraspecific (genotypic) diversity can have important effects on community structure and function. However, a critical and unresolved question for understanding the ecology of a community is to what extent these two levels of diversity are functionally substitutable? Here we show, for a mixed-species biofilm community composed of Pseudomonas aeruginosa, P. protegens and Klebsiella pneumoniae, that increased interspecific diversity reduces and functionally substitutes for intraspecific diversity in mediating tolerance to stress. Biofilm populations generated high percentages of genotypic variants, which were largely absent in biofilm communities. Biofilms with either high intra- or interspecific diversity were more tolerant to SDS stress than biofilms with no or low diversity. Unexpectedly, genotypic variants decreased the tolerance of biofilm communities when experimentally introduced into the communities. For example, substituting P. protegens wild type with its genotypic variant within biofilm communities decreased SDS tolerance by twofold, apparently due to perturbation of interspecific interactions. A decrease in variant frequency was also observed when biofilm populations were exposed to cell-free effluents from another species, suggesting that extracellular factors have a role in selection against the appearance of intraspecific variants. This work demonstrates the functional substitution of inter- and intraspecific diversity for an emergent property of biofilms. It also provides a potential explanation for a long-standing paradox in microbiology, in which morphotypic variants are common in laboratory grown biofilm populations, but are rare in diverse, environmental biofilm communities.

Lee, MS, Lee, JA, Alraek, T, Zhao-xiang, B, Birch, S, Goto, H, Jung, J, Shung-te, K, Moon, S-K, Park, B, Park, K-M, You, S, Yun, K-J & Zaslawski, C 2016, 'Current research and future directions in pattern identification: Results of an international symposium', CHINESE JOURNAL OF INTEGRATIVE MEDICINE, vol. 22, no. 12, pp. 947-955.
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A symposium on pattern identification (PI) was held at the Korea Institute of Oriental Medicine (KIOM) on October 2, 2013, in Daejeon, South Korea. This symposium was convened to provide information on the current research in PI as well as suggest future research directions. The participants discussed the nature of PI, possible research questions, strategies and future international collaborations in pattern research. With eight presentations and an extensive panel discussion, the symposium allowed participants to discuss research methods in traditional medicine for PI. One speaker presented the topic, ‘Clinical pattern differentiation and contemporary research in PI.’ Two speakers presented current trends in research on blood stasis while the remaining five other delegates discussed the research methods and future directions of PI research. The participants engaged in in-depth discussions regarding the nature of PI, potential research questions, strategies and future international collaborations in pattern research.

Lee, S-H, Blake, IM, Larsen, AG, McDonald, JA, Ohkubo, K, Fukuzumi, S, Reimers, JR & Crossley, MJ 2016, 'Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria', Chemical Science, vol. 7, no. 10, pp. 6534-6550.
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Synthetically flexible, rigid, tetrad molecules are shown to closely mimic structural and photochemical properties of the bacterial photosynthetic reaction centre.

Lélé, MI & Leslie, LM 2016, 'Intraseasonal variability of low-level moisture transport over West Africa', Climate Dynamics, vol. 47, no. 11, pp. 3575-3591.
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© 2016, The Author(s). The vertically integrated surface-850 hPa atmospheric water vapor flux is investigated, to account for the total low-level moisture flux contribution to rainfall over West Africa (WA), based on NCEP–NCAR reanalysis data. The focus is the contributions to total moisture transport and convergence by the mean circulation, the synoptic (<10 days), and climate (>10 day) scale anomalies. For WA, the time-mean flow and climate anomalies are comparable. Similarly, for meridional and zonal components, transports by the time-mean and climate anomalies are the largest contributors to mean meridional and zonal moisture transport. While the climate anomalies are responsible for driving moisture poleward from the Atlantic Ocean to the Guinea coast, and westward from the western Atlantic Ocean into the Sahel, the synoptic anomalies contribute to transporting moisture zonally out of the Sahel. Moreover, the spatial distribution of moisture flux convergence reveals a close similarity to the observed 2005 relatively wet and 2006 relatively dry accumulative rainfall. Convergence in WA is mainly the result of moisture transport by the mean flow. An enhanced (weak) flux convergence by the mean flow is characteristic of wet (dry) Sahel rainfall seasons. During wet April-June rainy seasons in the Guinea coast, enhanced convergence due to synoptic anomalies is observed in the region, whereas it is suppressed during dry April-June seasons. In the Sahel, however, during the dry rainy seasons, the convergence region due to synoptic anomalies is displaced southward.

Leuenberger, C, Schuoler, C, Bye, H, Mignan, C, Rechsteiner, T, Hillinger, S, Opitz, I, Marsland, B, Faiz, A, Hiemstra, PS, Timens, W, Camici, GG, Kohler, M, Huber, LC & Brock, M 2016, 'MicroRNA-223 controls the expression of histone deacetylase 2: a novel axis in COPD', Journal of Molecular Medicine, vol. 94, no. 6, pp. 725-734.
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UNLABELLED: Reduced activity of histone deacetylase 2 (HDAC2) has been described in patients with chronic obstructive pulmonary disease (COPD), but the mechanisms resulting in decreased expression of this important epigenetic modifier remain unknown. Here, we employed several in vitro experiments to address the role of microRNAs (miRNAs) on the regulation of HDAC2 in endothelial cells. Manipulation of miRNA levels in human pulmonary artery endothelial cells (HPAEC) was achieved by using electroporation with anti-miRNAs and miRNA mimics. Target prediction software identified miR-223 as a potential repressor of HDAC2. In subsequent stimulation experiments using inflammatory cytokines known to be increased in patients with COPD, miR-223 was found to be significantly induced. Functional analysis demonstrated that overexpression of miR-223 decreased HDAC2 expression and activity in HPAEC. Conversely, HDAC2 expression and activity was preserved in anti-miR-223-treated cells. Direct miRNA-target interaction was confirmed by reporter gene assay. In a next step, reduced expression of HDAC2 was found to increase the levels of the chemokine fractalkine (CX3CL1). In vivo studies confirmed elevated expression levels of miR-223 in mice exposed to cigarette smoke and in emphysematous lung tissue from LPS-treated mice. Moreover, a significant inverse correlation of miR-223 and HDAC2 expression was found in two independent cohorts of COPD patients. These data emphasize that miR-223, the most prevalent miRNA in COPD, controls expression and activity of HDAC2 in pulmonary cells, which, in turn, might alter the expression profile of chemokines. This pathway provides a novel pathogenic link between dysregulated miRNA expression and epigenetic activity in COPD. KEY MESSAGES: Histone deacetylase 2 is directly targeted by miR-223. Levels of miR-223 are induced by interleukin-1β and tumor necrosis factor-α. miR-223 controls the expression of fractalkine by targeting histone dea...

Levin, RA, Beltran, VH, Hill, R, Kjelleberg, S, McDougald, D, Steinberg, PD & van Oppen, MJH 2016, 'Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances', Molecular Biology and Evolution, vol. 33, no. 11, pp. 3032-3032.
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Levin, RA, Beltran, VH, Hill, R, Kjelleberg, S, McDougald, D, Steinberg, PD & van Oppen, MJH 2016, 'Sex, Scavengers, and Chaperones: Transcriptome Secrets of DivergentSymbiodiniumThermal Tolerances', Molecular Biology and Evolution, vol. 33, no. 9, pp. 2201-2215.
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Lewis, J, Molnar, A, Allsop, D, Copeland, J & Fu, S 2016, 'Rapid elimination of Carboxy-THC in a cohort of chronic cannabis users', INTERNATIONAL JOURNAL OF LEGAL MEDICINE, vol. 130, no. 1, pp. 147-152.
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© 2015, Springer-Verlag Berlin Heidelberg. Urinary 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid (Carboxy-THC) concentrations, normalised to creatinine output, have been demonstrated to be a useful tool in the interpretation of the results of a series of urine tests for cannabis. These tests, often termed historical data, can be used to identify potential chronic cannabis users who may present occupational health and safety risks within the workplace. Conversely, the data can also be used to support employee claims of previous regular, rather than recent, cannabis use. This study aimed at examining the mean elimination of Carboxy-THC in 37 chronic users undergoing voluntary abstinence over a 2-week period. Urine specimens were collected prior to the study and after 1 and 2 weeks of abstinence. Carboxy-THC levels in urine were measured by gas chromatography–mass spectrometry (GC–MS) following alkaline hydrolysis, organic solvent extraction and derivatisation to form its pentafluoropropionic derivative. The creatinine-normalised Carboxy-THC concentrations declined rapidly over the 2 weeks of abstinence period and the majority of chronic cannabis users (73 %) reduced their urinary Carboxy-THC levels to below the 15-μg/L confirmatory cutoff within that time. The study further highlights the value of historical urinary Carboxy-THC data as a means of identifying potential occupational health and safety risks among chronic cannabis users.

Li, D, Zhang, Y, Wen, S, Song, Y, Tang, Y, Zhu, X, Shen, M, Mignani, S, Majoral, J-P, Zhao, Q & Shi, X 2016, 'Construction of polydopamine-coated gold nanostars for CT imaging and enhanced photothermal therapy of tumors: an innovative theranostic strategy', Journal of Materials Chemistry B, vol. 4, no. 23, pp. 4216-4226.
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A theranostic nanoplatform for in vivo CT imaging and enhanced PTT of tumors is reported.

Li, H, Keadle, SK, Kipnis, V & Carroll, RJ 2016, 'Longitudinal functional additive model with continuous proportional outcomes for physical activity data', Stat, vol. 5, no. 1, pp. 242-250.
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Motivated by physical activity data obtained from the BodyMedia FIT device (http://www.bodymedia.com), we take a functional data approach for longitudinal studies with continuous proportional outcomes. The functional structure depends on three factors. In our three‐factor model, the regression structures are specified as curves measured at various factor points with random effects that have a correlation structure. The random curve for the continuous factor is summarized using a few important principal components. The difficulties in handling the continuous proportion variables are solved by using a quasilikelihood‐type approximation. We develop an efficient algorithm to fit the model, which involves the selection of the number of principal components. The method is evaluated empirically by a simulation study. This approach is applied to the BodyMedia data with 935 males and 84 consecutive days of observation, for a total of 78,540 observations. We show that sleep efficiency increases with increasing physical activity, while its variance decreases at the same time. Copyright © 2016 John Wiley & Sons, Ltd.

Li, K, Zhou, Y, Rasmita, A, Aharonovich, I & Gao, WB 2016, 'Nonblinking Emitters with Nearly Lifetime-Limited Linewidths in CVD Nanodiamonds', Physical Review Applied, vol. 6, no. 2.
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Li, Y, Gu, Y, Yuan, W, Cao, T, Li, K, Yang, S, Zhou, Z & Li, F 2016, 'Core–Shell–Shell NaYbF₄:Tm@CaF₂@NaDyF₄ Nanocomposites for Upconversion/T₂-Weighted MRI/Computed Tomography Lymphatic Imaging', ACS Applied Materials & Interfaces, vol. 8, no. 30, pp. 19208-19216.
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Liana, AE, Chia, EW, Marquis, CP, Gunawan, C, Gooding, JJ & Amal, R 2016, 'Adsorption of T4 bacteriophages on planar indium tin oxide surface via controlled surface tailoring', Journal of Colloid and Interface Science, vol. 468, pp. 192-199.
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© 2016 Elsevier Inc. The work investigates the influence of surface physicochemical properties of planar indium tin oxide (ITO) as a model substrate on T4 bacteriophage adsorption. A comparative T4 bacteriophage adsorption study shows a significant difference in bacteriophage adsorption observed on chemically modified planar ITO when compared to similarly modified particulate ITO, which infers that trends observed in virus-particle interaction studies are not necessarily transferrable to predict virus-planar surface adsorption behaviour. We also found that ITO surfaces modified with methyl groups, (resulting in increased surface roughness and hydrophobicity) remained capable of adsorbing T4 bacteriophage. The adsorption of T4 onto bare, amine and carboxylic functionalised planar ITO suggests the presence of a unique binding behaviour involving specific functional groups on planar ITO surface beyond the non-specific electrostatic interactions that dominate phage to particle interactions. The paper demonstrates the significance of physicochemical properties of surfaces on bacteriophage-surface interactions.

Liang, L, Care, A, Zhang, R, Lu, Y, Packer, NH, Sunna, A, Qian, Y & Zvyagin, AV 2016, 'Facile Assembly of Functional Upconversion Nanoparticles for Targeted Cancer Imaging and Photodynamic Therapy', ACS Applied Materials & Interfaces, vol. 8, no. 19, pp. 11945-11953.
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The treatment depth of existing photodynamic therapy (PDT) is limited because of the absorption of visible excitation light in biological tissue. It can be augmented by means of upconversion nanoparticles (UCNPs) transforming deep-penetrating near-infrared (NIR) light to visible light, exciting PDT drugs. We report here a facile strategy to assemble such PDT nanocomposites functionalized for cancer targeting, based on coating of the UCNPs with a silica layer encapsulating the Rose Bengal photosensitizer and bioconjugation to antibodies through a bifunctional fusion protein consisting of a solid-binding peptide linker genetically fused to Streptococcus Protein G'. The fusion protein (Linker-Protein G) mediates the functionalization of silica-coated UCNPs with cancer cell antibodies, allowing for specific target recognition and delivery. The resulting nanocomposites were shown to target cancer cells specifically, generate intracellular reactive oxygen species under 980 nm excitation, and induce NIR-triggered phototoxicity to suppress cancer cell growth in vitro.

Liao, J, Yang, Z, Shao, B, Li, J, Qiu, J, Song, Z & Yang, Y 2016, 'Preparation and Photoluminescence Modification of NaGdF<SUB>4</SUB> :Eu<SUP>3</SUP><SUP>+</SUP> Nanorods in a Crystalline Colloidal Array', Science of Advanced Materials, vol. 8, no. 4, pp. 697-702.
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© 2016 by American Scientific Publishers. A crystalline colloidal array was prepared by an ion exchange method, and its structure was characterized. Eu3+ doped NaGdF4 nanorods were added into the crystalline colloidal array, leading to an ordered crystalline colloidal array including the nanorods. The photoluminescence properties of NaGdF4:Eu3+ nanorods in the array were investigated. A significant suppression of photoluminescence of NaGdF4:Eu3+ nanorods in the range of the photonic band gap was observed.

Liao, Y, Williams, TJ, Walsh, JC, Ji, M, Poljak, A, Curmi, PMG, Duggin, IG & Cavicchioli, R 2016, 'Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function', SCIENTIFIC REPORTS, vol. 6, pp. 1-15.
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No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.

Liao, Y, Williams, TJ, Ye, J, Charlesworth, J, Burns, BP, Poljak, A, Raftery, MJ & Cavicchioli, R 2016, 'Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi', Scientific Reports, vol. 6, no. 1, pp. 1-17.
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AbstractBiofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.

Lichtenberg, M, Larkum, AWD & Kuehl, M 2016, 'Photosynthetic Acclimation of Symbiodinium in hospite Depends on Vertical Position in the Tissue of the Scleractinian Coral Montastrea curta', FRONTIERS IN MICROBIOLOGY, vol. 7.
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Lienhard, B, Schröder, T, Mouradian, S, Dolde, F, Tran, TT, Aharonovich, I & Englund, D 2016, 'Bright and photostable single-photon emitter in silicon carbide', Optica, vol. 3, no. 7, pp. 768-768.
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Lim, CED, Ng, RWC, Cheng, NCL, Cigolini, M, Kwok, C & Brennan, F 2016, 'Advance care planning for haemodialysis patients', Cochrane Database of Systematic Reviews, vol. 2016, no. 7.
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© 2016 The Cochrane Collaboration. Background: End-stage kidney disease (ESKD) is a chronic, debilitative and progressive illness that may need interventions such as dialysis, transplantation, dietary and fluid restrictions. Most patients with ESKD will require renal replacement therapy, such as kidney transplantation or maintenance dialysis. Advance care planning traditionally encompass instructions via living wills, and concern patient preferences about interventions such as cardiopulmonary resuscitation and feeding tubes, or circumstances around assigning surrogate decision makers. Most people undergoing haemodialysis are not aware of advance care planning and few patients formalise their wishes as advance directives and of those who do, many do not discuss their decisions with a physician. Advance care planning involves planning for future healthcare decisions and preferences of the patient in advance while comprehension is intact. It is an essential part of good palliative care that likely improves the lives and deaths of haemodialysis patients. Objectives: The objective of this review was to determine whether advance care planning in haemodialysis patients, compared with no or less structured forms of advance care planning, can result in fewer hospital admissions or less use of treatments with life-prolonging or curative intent, and if patient's wishes were followed at end-of-life. Search methods: We searched the Cochrane Kidney and Transplant Specialised Register to 27 June 2016 through contact with the Information Specialist using search terms relevant to this review. We also searched the Cumulative Index of Nursing and Allied Health Literature (CINAHL), and Social Work Abstracts (OvidSP). Selection criteria: All randomised controlled trials (RCTs) and quasi-RCTs (RCTs in which allocation to treatment was obtained by alternation, use of alternate medical records, date of birth or other predictable methods) looking at advance care planning versus no form o...

Lim, CED, Ng, RWC, Xu, K, Cheng, NCL, Xue, CCL, Liu, JP & Chen, N 2016, 'Acupuncture for polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, no. 5.
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Lin, C-Y, Chen, H & Pakpour, AH 2016, 'Correlation between adherence to antiepileptic drugs and quality of life in patients with epilepsy: A longitudinal study', Epilepsy & Behavior, vol. 63, pp. 103-108.
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Lin, G, Karnaushenko, DD, Bermúdez, GSC, Schmidt, OG & Makarov, D 2016, 'Droplet Microfluidics: Magnetic Suspension Array Technology: Controlled Synthesis and Screening in Microfluidic Networks (Small 33/2016)', Small, vol. 12, no. 33, pp. 4580-4580.
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Lin, G, Karnaushenko, DD, Bermúdez, GSC, Schmidt, OG & Makarov, D 2016, 'Magnetic Suspension Array Technology: Controlled Synthesis and Screening in Microfluidic Networks', Small, vol. 12, no. 33, pp. 4553-4562.
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Information tagging and processing are vital in information‐intensive applications, e.g., telecommunication and high‐throughput drug screening. Magnetic suspension array technology may offer intrinsic advantages to screening applications by enabling high distinguishability, the ease of code generation, and the feasibility of fast code readout, though the practical applicability of magnetic suspension array technology remains hampered by the lack of quality administration of encoded microcarriers. Here, a logic‐controlled microfluidic system enabling controlled synthesis of magnetic suspension arrays in multiphase flow networks is realized. The smart and compact system offers a practical solution for the quality administration and screening of encoded magnetic microcarriers and addresses the universal need of process control for synthesis in microfluidic networks, i.e., on‐demand creation of droplet templates for high information capacity. The demonstration of magnetic suspension array technology enabled by magnetic in‐flow cytometry opens the avenue toward point‐of‐care multiplexed bead‐based assays, clinical diagnostics, and drug discovery.

Ling, Y, Yan, D-X, Wang, P-F, Wang, M, Wen, Q, Liu, F & Wang, Y-G 2016, 'Highly Efficient Power Conversion from Salinity Gradients with Ion-Selective Polymeric Nanopores', Chinese Physics Letters, vol. 33, no. 9, pp. 096103-096103.
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Liu, B, Li, C, Xie, Z, Hou, Z, Cheng, Z, Jin, D & Lin, J 2016, '808 nm photocontrolled UCL imaging guided chemo/photothermal synergistic therapy with single UCNPs-CuS@PAA nanocomposite', Dalton Transactions, vol. 45, no. 33, pp. 13061-13069.
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Recently, incorporating multiple components into one nanostructured matrix to construct a multifunctional nanomedical platform has attracted more and more attention for simultaneous anticancer diagnosis and therapy.

Liu, B, Zhang, X, Li, C, He, F, Chen, Y, Huang, S, Jin, D, Yang, P, Cheng, Z & Lin, J 2016, 'Magnetically targeted delivery of DOX loaded Cu₉S₅@mSiO₂@Fe₃O₄-PEG nanocomposites for combined MR imaging and chemo/photothermal synergistic therapy', Nanoscale, vol. 8, no. 25, pp. 12560-12569.
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The combination of multi-theranostic modes in a controlled fashion has received tremendous attention for the construction of cooperative therapeutic systems in nanomedicine. Herein, we have synthesized a smart magnetically targeted nanocarrier system, Cu9S5@mSiO2@Fe3O4-PEG (labelled as CMF), which integrates NIR triggered photothermal therapy, pH/NIR-responsive chemotherapy and MR imaging into one nanoplatform to enhance the therapeutic efficacy. This new multifunctional paradigm has a uniform and monodisperse sesame ball-like structure by decorating tiny Fe3O4 nanoparticles on the surface of Cu9S5@mSiO2 before a further PEG modification to improve its hydrophilicity and biocompatibility. With doxorubicin (DOX) payload, the as-obtained CMF-DOX composites can simultaneously provide an intense heating effect and enhanced DOX release upon 980 nm NIR light exposure, achieving a combined chemo/photothermal therapy. Under the influence of an external magnetic field, the magnetically targeted synergistic therapeutic effect of CMF-DOX can lead to highly superior inhibition of animal H22 tumor in vivo when compared to any of the single approaches alone. The results revealed that this Cu9S5 based magnetically targeted chemo/photothermal synergistic nanocarrier system has great promise in future MR imaging assisted tumor targeted therapy of cancer.

Liu, D, Xu, X, Du, Y, Qin, X, Zhang, Y, Ma, C, Wen, S, Ren, W, Goldys, EM, Piper, JA, Dou, S, Liu, X & Jin, D 2016, 'Three-dimensional controlled growth of monodisperse sub-50 nm heterogeneous nanocrystals', Nature Communications, vol. 7, no. 1, pp. 1-8.
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AbstractThe ultimate frontier in nanomaterials engineering is to realize their composition control with atomic scale precision to enable fabrication of nanoparticles with desirable size, shape and surface properties. Such control becomes even more useful when growing hybrid nanocrystals designed to integrate multiple functionalities. Here we report achieving such degree of control in a family of rare-earth-doped nanomaterials. We experimentally verify the co-existence and different roles of oleate anions (OA−) and molecules (OAH) in the crystal formation. We identify that the control over the ratio of OA− to OAH can be used to directionally inhibit, promote or etch the crystallographic facets of the nanoparticles. This control enables selective grafting of shells with complex morphologies grown over nanocrystal cores, thus allowing the fabrication of a diverse library of monodisperse sub-50 nm nanoparticles. With such programmable additive and subtractive engineering a variety of three-dimensional shapes can be implemented using a bottom–up scalable approach.

Liu, D, Xu, X, Wang, F, Zhou, J, Mi, C, Zhang, L, Lu, Y, Ma, C, Goldys, E, Lin, J & Jin, D 2016, 'Emission stability and reversibility of upconversion nanocrystals', Journal of Materials Chemistry C, vol. 4, no. 39, pp. 9227-9234.
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We report the emission stability and reversibility of NaYF₄:Yb³⁺,Er³⁺ core and core–shell nanocrystals at different temperatures and pH values.

Liu, G, Cooley, MA, Jarnicki, AG, Hsu, AC-Y, Nair, PM, Haw, TJ, Fricker, M, Gellatly, SL, Kim, RY, Inman, MD, Tjin, G, Wark, PAB, Walker, MM, Horvat, JC, Oliver, BG, Argraves, WS, Knight, DA, Burgess, JK & Hansbro, PM 2016, 'Fibulin-1 regulates the pathogenesis of tissue remodeling in respiratory diseases', JCI Insight, vol. 1, no. 9.
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Liu, J, Han, L, Ma, H, Tian, H, Yang, J, Zhang, Q, Seligmann, BJ, Wang, S & Liu, J 2016, 'Template-free synthesis of carbon doped TiO2 mesoporous microplates for enhanced visible light photodegradation', Science Bulletin, vol. 61, no. 19, pp. 1543-1550.
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Liu, L, Lv, H, Wang, C, Ao, Z & Wang, G 2016, 'Fabrication of the protonated graphitic carbon nitride nanosheets as enhanced electrochemical sensing platforms for hydrogen peroxide and paracetamol detection', Electrochimica Acta, vol. 206, pp. 259-269.
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Liu, L, Wang, J, Wang, C & Wang, G 2016, 'Facile synthesis of graphitic carbon nitride/nanostructured α-Fe2O3 composites and their excellent electrochemical performance for supercapacitor and enzyme-free glucose detection applications', Applied Surface Science, vol. 390, pp. 303-310.
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© 2016 Elsevier B.V.The graphitic carbon nitride (g-C3N4)/iron oxide (α-Fe2O3) composites have been prepared by a one-step pyrolysis of Prussian blue (PB) and melamine. The Fe2O3 nanoparticles derived from PB effectively protect the thin layers of g-C3N4 from restacking and expanding. The as-prepared g-C3N4/α-Fe2O3 composites exhibit a large specific surface area, and demonstrate their excellent electrochemical performance in the supercapacitor and non-enzymatic detection of glucose. The g-C3N4/α-Fe2O3 composites facilitate the faster faradic reaction in 1.0 M KOH electrolyte, and deliver the highest specific capacitance (580 F g−1) at the current density of 1.0 A g−1. The resultant composites also show an excellent long cycle life (up to 1000 cycles) at the current density of 2 A g−1. In addition, the modified electrode based on the g-C3N4/α-Fe2O3 hybrids are also used for the non-enzymatic detection of glucose. The as-fabricated modified electrode exhibits good electrochemical performance towards the oxidation of glucose with a response time <3 s and a linear range of 2.0 × 10−6 − 2.4 × 10−3 mol L−1. The electrode modified by the g-C3N4/α-Fe2O3 composites exhibits good anti-interference performance and stability. The g-C3N4/α-Fe2O3 hybrids have great potential in the application of electrochemical storage devices and sensors.

Liu, N, Huang, X, Huang, X, Liu, S, Chen, H, Li, X & Peng, W 2016, 'Application of H-1 magnetic resonance spectroscopy in the diagnosis and treatment of mild cognitive impairment', INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL MEDICINE, vol. 9, no. 2, pp. 2430-2436.

Liu, S, Gunawan, C, Barraud, N, Rice, SA, Harry, EJ & Amal, R 2016, 'Understanding, Monitoring, and Controlling Biofilm Growth in Drinking Water Distribution Systems', Environmental Science & Technology, vol. 50, no. 17, pp. 8954-8976.
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© 2016 American Chemical Society. In drinking water distribution systems (DWDS), biofilms are the predominant mode of microbial growth, with the presence of extracellular polymeric substance (EPS) protecting the biomass from environmental and shear stresses. Biofilm formation poses a significant problem to the drinking water industry as a potential source of bacterial contamination, including pathogens, and, in many cases, also affecting the taste and odor of drinking water and promoting the corrosion of pipes. This article critically reviews important research findings on biofilm growth in DWDS, examining the factors affecting their formation and characteristics as well as the various technologies to characterize and monitor and, ultimately, to control their growth. Research indicates that temperature fluctuations potentially affect not only the initial bacteria-to-surface attachment but also the growth rates of biofilms. For the latter, the effect is unique for each type of biofilm-forming bacteria; ammonia-oxidizing bacteria, for example, grow more-developed biofilms at a typical summer temperature of 22 °C compared to 12 °C in fall, and the opposite occurs for the pathogenic Vibrio cholerae. Recent investigations have found the formation of thinner yet denser biofilms under high and turbulent flow regimes of drinking water, in comparison to the more porous and loosely attached biofilms at low flow rates. Furthermore, in addition to the rather well-known tendency of significant biofilm growth on corrosion-prone metal pipes, research efforts also found leaching of growth-promoting organic compounds from the increasingly popular use of polymer-based pipes. Knowledge of the unique microbial members of drinking water biofilms and, importantly, the influence of water characteristics and operational conditions on their growth can be applied to optimize various operational parameters to minimize biofilm accumulation. More-detailed characterizations of the b...

Liu, T, Solntsev, AS, Boes, A, Nguyen, T, Will, C, Mitchell, A, Neshev, DN & Sukhorukov, AA 2016, 'Experimental demonstration of bidirectional light transfer in adiabatic waveguide structures', Optics Letters, vol. 41, no. 22, pp. 5278-5278.
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We propose and demonstrate a novel type of optical integrated structure consisting of three adiabatically coupled waveguides arranged in an N-shaped geometry. Unlike conventional adiabatic three-waveguide couplers mimicking the stimulated Raman adiabatic passage process which utilize solely the counter-intuitive coupling and, thus, operate only in one direction, our structure achieves complete bidirectional light transfer between two waveguides through the counter-intuitive and intuitive coupling in either direction over a wide wavelength range. Moreover, the light transfer through the intuitive coupling is more efficient and robust than through the counter-intuitive coupling.

Liu, T, Tian, H, Liu, J, Liu, L & Liu, S 2016, 'Inorganic-Salts Assisted Self-Assembly of Pluronic F127-Organosilica into Ordered Mesostructures', Journal of Nanoscience and Nanotechnology, vol. 16, no. 9, pp. 9173-9179.
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Liu, X, Shi, C, Zhai, C, Cheng, M, Liu, Q & Wang, G 2016, 'Cobalt-Based Layered Metal–Organic Framework as an Ultrahigh Capacity Supercapacitor Electrode Material', ACS Applied Materials & Interfaces, vol. 8, no. 7, pp. 4585-4591.
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© 2016 American Chemical Society. Metal-organic frameworks (MOFs) have recently received increasing interest due to their potential application in the energy storage and conversion field. Herein, cobalt-based layered MOF ({[Co(Hmt)(tfbdc)(H2O)2]·(H2O)2}n, Co-LMOF; Hmt = hexamethylenetetramine; H2tfbdc = 2,3,5,6-tetrafluoroterephthalic acid) has been evaluated as an electrode material for supercapacitors. The Co-LMOF electrode exhibits a high specific capacitance and excellent cycling stability. Its maximum specific capacitance is 2474 F g-1 at a current density of 1 A g-1, and the specific capacitance retention is about 94.3% after 2000 cycles. The excellent electrochemical property may be ascribed to the intrinsic nature of Co-LMOF, enough space available for the storage and diffusion of the electrolyte, and the particles of nanoscale size.

Liu, Y-S, Gadau, M, Zhang, G-X, Liu, H, Wang, F-C, Zaslawski, C, Li, T, Tan, Y-S, Berle, C, Li, W-H, Bangrazi, S, Liguori, S & Zhang, S-P 2016, 'Acupuncture Treatment of Lateral Elbow Pain: A Nonrandomized Pilot Study', EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 2016.
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© 2016 Yan-Song Liu et al. In planning for a large-scale multicenter trial to evaluate the effect of acupuncture for the treatment of lateral elbow pain, a pilot study was conducted. This was a prospective, investigator- and patient-blinded, nonrandomized, placebo controlled trial. Subjects were evaluated at baseline, before fourth, seventh, and ninth treatment, and at a two-week posttreatment follow-up. The treatment group received unilateral acupuncture at LI 10 and LI 11 at the affected side with manual needle manipulation; the control group received sham-laser acupuncture at the same acupoints. Measures included (i) disabilities of the arm, shoulder, and hand (DASH) questionnaire, (ii) pain-free grip strength (PFGS), and (iii) a visual analogue scale (VAS) for pain. Significant differences in DASH score, PFGS, and VAS between treatment and control group were found at the ninth treatment (n = 20 for each group, P < 0.05). Only DASH showed significant differences compared to the control for all the measurement time points after treatment commenced and appears to be a sensitive and appropriate primary outcome measure for the future multisite trial. Results from this pilot study provided relevant information about treatment efficacy, credibility of control treatment, and sensitivity of different outcome measures for the planning of the future trial.

Loo, C-Y, Rohanizadeh, R, Young, PM, Traini, D, Cavaliere, R, Whitchurch, CB & Lee, W-H 2016, 'Combination of Silver Nanoparticles and Curcumin Nanoparticles for Enhanced Anti-biofilm Activities', Journal of Agricultural and Food Chemistry, vol. 64, no. 12, pp. 2513-2522.
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© 2015 American Chemical Society. Biofilm tolerance has become a serious clinical concern in the treatment of nosocomial pneumonia owing to the resistance to various antibiotics. There is an urgent need to develop alternative antimicrobial agents or combination drug therapies that are effective via different mechanisms. Silver nanoparticles (AgNPs) have been developed as an anti-biofilm agent for the treatment of infections associated with the use of mechanical ventilations, such as endotracheal intubation. Meanwhile curcumin, a phenolic plant extract, has displayed natural anti-biofilm properties through the inhibition of bacterial quorum sensing systems. The aim of this study was to investigate the possible synergistic/additive interactions of AgNPs and curcumin nanoparticles (Cur-NPs) against both Gram-negative (Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) microorganisms. The combination of AgNPs and Cur-NPs (termed Cur-SNPs) at 100 μg/mL disrupted 50% of established bacterial biofilms (formed on microtiter plates). However, further increase in the concentration of Cur-SNPs failed to effectively eliminate the biofilms. To achieve the same effect, at least 500 μg/mL Cur-NP alone was needed. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) revealed that combination therapy (Cur-SNPs) was the most potent to eradicate preformed biofilm compared to monodrug therapy. These agents are also nontoxic to healthy human bronchial epithelial cells (BEAS2B).

Lund, ME, Greer, J, Dixit, A, Alvarado, R, McCauley-Winter, P, To, J, Tanaka, A, Hutchinson, AT, Robinson, MW, Simpson, AM, O’Brien, BA, Dalton, JP & Donnelly, S 2016, 'A parasite-derived 68-mer peptide ameliorates autoimmune disease in murine models of Type 1 diabetes and multiple sclerosis', Scientific Reports, vol. 6, no. 1, pp. 1-11.
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AbstractHelminth parasites secrete molecules that potently modulate the immune responses of their hosts and, therefore, have potential for the treatment of immune-mediated human diseases. FhHDM-1, a 68-mer peptide secreted by the helminth parasite Fasciola hepatica, ameliorated disease in two different murine models of autoimmunity, type 1 diabetes and relapsing-remitting immune-mediated demyelination. Unexpectedly, FhHDM-1 treatment did not affect the proliferation of auto-antigen specific T cells or their production of cytokines. However, in both conditions, the reduction in clinical symptoms was associated with the absence of immune cell infiltrates in the target organ (islets and the brain tissue). Furthermore, after parenteral administration, the FhHDM-1 peptide interacted with macrophages and reduced their capacity to secrete pro-inflammatory cytokines, such as TNF and IL-6. We propose this inhibition of innate pro-inflammatory immune responses, which are central to the initiation of autoimmunity in both diseases, prevented the trafficking of autoreactive lymphocytes from the periphery to the site of autoimmunity (as opposed to directly modulating their function per se), and thus prevented tissue destruction. The ability of FhHDM-1 to modulate macrophage function, combined with its efficacy in disease prevention in multiple models, suggests that FhHDM-1 has considerable potential as a treatment for autoimmune diseases.

Lund, ME, To, J, O'Brien, BA & Donnelly, S 2016, 'The choice of phorbol 12-myristate 13-acetate differentiation protocol influences the response of THP-1 macrophages to a pro-inflammatory stimulus', JOURNAL OF IMMUNOLOGICAL METHODS, vol. 430, pp. 64-70.
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© 2016. The human monocytic cell line, THP-1, is the most widely used model for primary human monocytes/macrophages. This is because, following differentiation using phorbol 12-myristate 13-acetate (PMA), THP-1 cells acquire a macrophage-like phenotype, which mimics, in many respects, primary human macrophages. Despite the widespread use of THP-1 cells in studies elucidating macrophage responses to inflammatory stimuli, as well as the development and screening of potential therapeutics, there is currently no standardised protocol for the reliable differentiation of THP-1 monocytes to a macrophage phenotype using PMA. Consequently, reports using THP-1 cells have demonstrated significant phenotypic and functional differences between resultant THP-1 macrophage populations, which are largely attributable to the varying PMA differentiation methods used. Thus, to guarantee consistency and reproducibility between studies, and to ensure the relevance of THP-1 cells as an appropriate model for primary human macrophages, it is crucial to develop a standardised protocol for the differentiation of THP-1 macrophages. Accordingly, we compared the function and phenotype of THP-1 macrophages generated using the range of published PMA differentiation protocols, specifically in response to the pro-inflammatory stimulus, lipopolysaccharide (LPS). Our results demonstrated that the function of the resultant THP-1 macrophage populations, as determined by tumour necrosis factor (TNF) secretion in response to LPS stimulation, varied significantly, and was dependent upon the concentration of PMA used to stimulate the differentiation of monocytes, and the period of rest following PMA exposure. These data indicate that exposure of monocytic THP-1 cells to 25 nM PMA over 48 h, followed by a recovery period of 24 h in culture in the absence of PMA, was the optimal protocol for the differentiation of THP-1 cells.

Lv, Y, Xin, B, Li, J, Chen, K, Jin, D, Lou, W & Xu, X 2016, 'Pancreatic intraglandular metastasis of the ductal adenocarcinoma: cases of 2 and literature review', INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL MEDICINE, vol. 9, no. 10, pp. 20324-20330.

Ma, C, Xu, X, Wang, F, Zhou, Z, Wen, S, Liu, D, Fang, J, Lang, CI & Jin, D 2016, 'Probing the Interior Crystal Quality in the Development of More Efficient and Smaller Upconversion Nanoparticles', The Journal of Physical Chemistry Letters, vol. 7, no. 16, pp. 3252-3258.
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© 2016 American Chemical Society. Optical biomedical imaging using luminescent nanoparticles as contrast agents prefers small size, as they can be used at high dosages and efficiently cleared from body. Reducing nanoparticle size is critical for the stability and specificity for the fluorescence nanoparticles probes for in vitro diagnostics and subcellular imaging. The development of smaller and brighter upconversion nanoparticles (UCNPs) is accordingly a goal for complex imaging in bioenvironments. At present, however, small UCNPs are reported to exhibit less emission intensity due to increased surface deactivation and decreased number of dopants. Here we show that smaller and more efficient UCNPs can be made by improving the interior crystal quality via controlling heating rate during synthesis. We further developed a unique quantitative method for optical characterizations on the single UCNPs with varied sizes and the corresponding shell passivated UCNPs, confirming that the internal crystal quality dominates the relative emission efficiency of the UCNPs.

Ma, X, Huete, A, Cleverly, J, Eamus, D, Chevallier, F, Joiner, J, Poulter, B, Zhang, Y, Guanter, L, Meyer, W, Xie, Z & Ponce-Campos, G 2016, 'Drought rapidly diminishes the large net CO2 uptake in 2011 over semi-arid Australia', SCIENTIFIC REPORTS, vol. 6.
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Each year, terrestrial ecosystems absorb more than a quarter of the anthropogenic carbon emissions, termed as land carbon sink. An exceptionally large land carbon sink anomaly was recorded in 2011, of which more than half was attributed to Australia. However, the persistence and spatially attribution of this carbon sink remain largely unknown. Here we conducted an observation-based study to characterize the Australian land carbon sink through the novel coupling of satellite retrievals of atmospheric CO2 and photosynthesis and in-situ flux tower measures. We show the 2010–11 carbon sink was primarily ascribed to savannas and grasslands. When all biomes were normalized by rainfall, shrublands however, were most efficient in absorbing carbon. We found the 2010–11 net CO2 uptake was highly transient with rapid dissipation through drought. The size of the 2010–11 carbon sink over Australia (0.97 Pg) was reduced to 0.48 Pg in 2011–12, and was nearly eliminated in 2012–13 (0.08 Pg). We further report evidence of an earlier 2000–01 large net CO2 uptake, demonstrating a repetitive nature of this land carbon sink. Given a significant increasing trend in extreme wet year precipitation over Australia, we suggest that carbon sink episodes will exert greater future impacts on global carbon cycle.

Ma, X, Huete, A, Poulter, B, Eamus, D & Cleverly, J 2016, 'Australia's 'great green boom' of 2010–11 has been undone by drought', The Conversation.

Ma, Y & Carroll, RJ 2016, 'Semiparametric Estimation in the Secondary Analysis of Case–Control Studies', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 78, no. 1, pp. 127-151.
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Summary We study the regression relationship between covariates in case–control data: an area known as the secondary analysis of case–control studies. The context is such that only the form of the regression mean is specified, so that we allow an arbitrary regression error distribution, which can depend on the covariates and thus can be heteroscedastic. Under mild regularity conditions we establish the theoretical identifiability of such models. Previous work in this context has either specified a fully parametric distribution for the regression errors, specified a homoscedastic distribution for the regression errors, has specified the rate of disease in the population (we refer to this as the true population) or has made a rare disease approximation. We construct a class of semiparametric estimation procedures that rely on none of these. The estimators differ from the usual semiparametric estimators in that they draw conclusions about the true population, while technically operating in a hypothetical superpopulation. We also construct estimators with a unique feature, in that they are robust against the misspecification of the regression error distribution in terms of variance structure, whereas all other non-parametric effects are estimated despite the biased samples. We establish the asymptotic properties of the estimators and illustrate their finite sample performance through simulation studies, as well as through an empirical example on the relationship between red meat consumption and hetero-cyclic amines. Our analysis verified the positive relationship between red meat consumption and two forms of hetro-cyclic amines, indicating that increased red meat consumption leads to increased levels of MeIQx and PhIP, both being risk factors for colorectal cancer. Computer software as well as data to illustrate the methodology are available from http://www.stat.tamu.edu/~carroll/matlab__programs/software.php .

Macha, IJ, Ben-Nissan, B, Santos, J, Cazalbou, S & Milthorpe, B 2016, 'Hydroxyapatite/PLA Biocomposite Thin Films for Slow Drug Delivery of Antibiotics for the Treatment of Bone and Implant-Related Infections', Key Engineering Materials, vol. 696, pp. 271-276.
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Drug delivery systems were developed from coralline hydroxyapatite (HAp) and biodegradable polylactic acid (PLA). Gentamicin (GM) was loaded in either directly to PLA (PLAGM) or in HAp microspheres. Drug loaded HAp was used to make thin film composites (PLAHApGM). Dissolution studies were carried out in phosphate buffered saline (PBS. The release profiles suggested that HAp particles improved drug stabilization and availability as well control the release rate. The release also displays a steady state release. In vitro studies in human Adipose Derived Stem Cells (hADSCs) showed substantial quantities of cells adhering to hydroxyapatite containing composites. The results suggested that the systems could be tailored to release different clinical active substances for a wide range of biomedical applications.

Macha, IJ, Charvillat, C, Cazalbou, S, Grossin, D, Boonyang, U & Ben-Nissan, B 2016, 'Comparative study of coral conversion, Part 3: Intermediate products in the first half an hour', JOURNAL OF THE AUSTRALIAN CERAMIC SOCIETY, vol. 52, no. 1, pp. 177-182.

Macha, IJ, Grossin, D & Ben-Nissan, B 2016, 'Conversion of Marine Structures to Calcium Phosphate Materials: Mechanisms of Conversion Using Two Different Phosphate Solutions', Key Engineering Materials, vol. 696, pp. 36-39.
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Marine structure, coralline materials were converted to calcium phosphate using two different phosphate solutions. The aim was to study the conversion mechanisms under acidic and basic environment at moderate conditions of temperature. Crystal growth and morphology of converted corals were characterized by XRD and SEM respectively. The results suggested that under acidic conditions (H3PO4), dissolution and precipitation control and direct the crystal formation and morphology in which transition from plate like to rod like hydroxyapatite structure was favoured. Metastable phase such as monetite formed and transformed to HAp during reaction. During the first hour of the dissolution a monetite and hydroxyapatite mixture precipitates and then the full conversion to hydroxyapatite is observed. On the other hand, under basic conditions (NH4)2HPO4, just diffusional surface conversion of the calcium carbonate structure of coralline materials to hydroxyapatite and a very small amount of tri-calcium phosphate is observed. The mechanism can be classified as the solid-state topotactic ion-exchange reaction mechanism.

Macinnis-Ng, CMO, Zeppel, MJB, Palmer, AR & Eamus, D 2016, 'Seasonal variations in tree water use and physiology correlate with soil salinity and soil water content in remnant woodlands on saline soils', JOURNAL OF ARID ENVIRONMENTS, vol. 129, pp. 102-110.
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Maddahfar, M, Ramezani, M & Mostafa Hosseinpour-Mashkani, S 2016, 'Barium hexaferrite/graphene oxide: controlled synthesis and characterization and investigation of its magnetic properties', Applied Physics A, vol. 122, no. 8.
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Maes, WH, Baert, A, Huete, AR, Minchin, PEH, Snelgar, WP & Steppe, K 2016, 'A new wet reference target method for continuous infrared thermography of vegetations', Agricultural and Forest Meteorology, vol. 226-227, pp. 119-131.
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© 2016 Elsevier B.V.. Although infrared thermography for stress detection in plants is popular in scientific research, it is rarely used in continuous and automated applications. One of the main reasons for this is that the most precise method for generating wet reference targets, used for normalizing the leaf or canopy surface temperature for microclimatic conditions, requires manual wetting before each image capture. In this article, we present and evaluate a new type of wet reference target that remains wet while having an energy balance as similar as possible to that of the canopy. This reference target consists of a cloth knitted around a solid frame whose shape and dimensions mimic those of the leaves. The cloth remains wet by constantly absorbing water from a reservoir. The new reference target was evaluated on grapevine and kiwifruit plants in greenhouse and orchard conditions. In greenhouse conditions, measured stomatal conductance was consistently more highly correlated with the stomatal conductance index Ig when Ig was calculated with the new wet reference rather than the manually wetted reference target. Furthermore, the temperature difference between leaves and the new reference target remained stable for as long as measured, in contrast with the manually wetted leaves. Ig obtained with the new reference target method was also highly correlated with stomatal conductance (gs) of both crops in orchard conditions. A new empirical regression model to estimate gs from Ig in greenhouse conditions was introduced and evaluated. This regression model incorporates the background temperature, a parameter that needs to be included in thermographic measurements for obtaining correct surface temperatures, thus avoiding the need for any additional measurements. The same regression model can be applied on different days with differing conditions. The model performed better than other tested empirical models and provided unbiased estimates of gs on days wit...

Mahmodi, H & Hashim, MR 2016, 'Effects of post-deposition annealing on crystalline state of GeSn thin films sputtered on Si substrate and its application to MSM photodetector', Materials Research Express, vol. 3, no. 10, pp. 106403-106403.
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Ge1.xSnx alloy thin films were prepared by co-sputtering from Ge and Sn targets on a Si (100) substrate at room temperature, and were then heated at temperature ranging from 200 °C to 500 °C in N2 ambient to reduce the disorder and defects and increase the crystalline quality of the films. Images obtained by field emission scanning electron microscopy revealed that the as-grown and all annealed samples displayed a densely packed morphology. The atomic percent composition of Sn in the asgrown Ge1-xSnx film is 5.7 at%. Energy-dispersive X-ray spectroscopy results showed Sn surface segregation after heat treatment, as the Sn composition is reduced to 3.3 at%for the film annealed at 500 °C. The Raman analysis showed that the only observed phonon mode is attributed to Ge-Ge vibrations. The Raman spectra of as-sputtered and annealed films revealed their nanocrystallineamorphous nature. The samples annealed at lower temperature exhibited higher phonon intensity, indicating the improvement of crystallinity of the film. The optoelectronic characteristics of fabricated metal-semiconductor-metal photodetectors on the annealed sample at 200 °C and the as-sputtered sample were studied in the dark and under illumination. Compared with the as-sputtered one, the annealed sample showed lower dark current and higher current gain of 209. The results showed the potentiality of using the sputtering technique to produce GeSn layer for optoelectronics application.

Mahmodi, H, Hashim, MR & Hashim, U 2016, 'Formation of nanocrystalline GeSn thin film on Si substrate by sputtering and rapid thermal annealing', Superlattices and Microstructures, vol. 98, pp. 235-241.
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Nanocrystalline Ge1-xSnx thin films have been formed after rapid thermal annealing of sputtered GeSn layers. The alloy films were deposited onto the Silicon (100) substrate via low cost radio frequency magnetron sputtering. Then, the films were annealed by rapid thermal annealing at 350 °C, 400 °C, and 450 °C for 10 s. The morphological, structural, and optical properties of the layers were investigated with field emission scanning electron microscopy (FESEM), Energy-dispersive X-ray spectroscopy (EDX), Raman spectroscopy, and high-resolution X-ray diffraction (HR-XRD). The Raman analysis showed that the only observed phonon mode is attributed to Ge-Ge vibrations. Raman phonon intensities of GeSn thin films were enhanced with increasing the annealing temperature. The results clearly revealed that by increasing the annealing temperature the crystalline quality of the films were improved. The XRD measurements revealed the nanocrystalline phase formation in the annealed films with (111) preferred orientation. The results showed the potentiality of using the sputtering technique and rapid thermal anneal to produce crystalline GeSn layer.

Mahmood, A, Guo, W, Tabassum, H & Zou, R 2016, 'Metal‐Organic Framework‐Based Nanomaterials for Electrocatalysis', Advanced Energy Materials, vol. 6, no. 17, pp. 1600423-1600423.
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Metal‐organic frameworks (MOFs) with high surface area and tunable chemical structures have attracted tremendous attention. Recently, there has been increasing interest in deriving advanced materials from MOFs for electrochemical energy storage and conversion. This progress report highlights recent breakthroughs in electrocatalysis by using MOF‐based novel catalysts, such as in oxygen reduction and evolution, hydrogen evolution and carbon dioxide reduction. The advantages of preparing electrocatalysts from MOFs are introduced and discussed. Then, the development of MOF derived electrocatalysis‐active products, such as heteroatom‐doped carbon, metal oxide (MO), metal sulfide (MS), metal carbide (MC), metal phosphide (MP) and their hybrids with carbon, are summarized. The detailed functions of these materials in representative electrocatalysis systems are also reviewed. The demonstrated examples will provide understanding in preparing highly active and stable electrocatalysts. The progress report concludes with the future applications of MOF‐based materials in the field of electrocatalysis.

Mahmood, A, Zou, R, Wang, Q, Xia, W, Tabassum, H, Qiu, B & Zhao, R 2016, 'Nanostructured Electrode Materials Derived from Metal–Organic Framework Xerogels for High-Energy-Density Asymmetric Supercapacitor', ACS Applied Materials & Interfaces, vol. 8, no. 3, pp. 2148-2157.
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Mahmud, MAP, Lee, J, Kim, G, Lim, H & Choi, K-B 2016, 'Improving the surface charge density of a contact-separation-based triboelectric nanogenerator by modifying the surface morphology', Microelectronic Engineering, vol. 159, pp. 102-107.
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Main, BJ, Dunlop, RA & Rodgers, KJ 2016, 'The use of l-serine to prevent β-methylamino-l-alanine (BMAA)-induced proteotoxic stress in vitro', Toxicon, vol. 109, pp. 7-12.
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© 2015 Published by Elsevier Ltd. β-methylamino-l-alanine (BMAA), a non-protein amino acid synthesised by cyanobacteria, has been linked to a complex neurological disorder on Guam and more recently to other cases of sporadic ALS (sALS), however the mechanisms of BMAA toxicity are not completely understood. We have previously demonstrated that BMAA is misincorporated into newly synthesised proteins by human neuroblastoma cells and fibroblasts, resulting in the formation of autofluorescent material and the induction of apoptotic cell death. In the present study we show that BMAA at low levels does not cause an acute toxicity in neuroblastoma cells but increases the expression of the ER stress marker, C/EBP homologous protein (CHOP) and increases the activity of the pro-apoptotic enzyme caspase-3. We also observed an increase in the activity of the lysosomal cysteine proteases cathepsin B and L, characteristic of the accumulation of proteins in the lysosomal system. We were able to prevent these proteotoxic effects in neuroblastoma cells through co-treatment with l-serine suggesting that they resulted from incorporation of BMAA into proteins. Misincorporation provides a possible mechanism whereby BMAA could initiate misfolding, and the accumulation of aggregate-prone proteins in neurons. This build-up of misfolded proteins could explain the long latency period of the disease previously reported on Guam.

Maniam, S, Sandanayake, S, Izgorodina, EI & Langford, SJ 2016, 'Unusual Products from Oxidation of Naphthalene Diimides', Asian Journal of Organic Chemistry, vol. 5, no. 4, pp. 490-493.
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AbstractTransforming the naphthalene diimide (NDI) core into unusual aromatic systems has large potential for applications in which current NDI‐based systems show promise. Treatment of N,N‐dialkylNDIs under mild oxidizing conditions with ruthenium(III) chloride and sodium periodate affords the corresponding 1,4‐diones in good yield. Interestingly, while aliphatic substituents at the N‐imide positions allowed oxidation to take place easily, the presence of neutral, electron‐rich or electron‐deficient phenyl groups retarded the oxidation process under these reaction conditions. The chemistry of the 1,4‐dione is then explored through reduction and condensation reactions. In two examples, reaction of the 1,4‐dione with diamines gives an unusual, ring‐contracted product 20, which has a high quantum yield. Additionally, the 1,4‐dione can be converted into larger heterocycles such as 21 and 22 featuring an isoquinoline core. The 1,4‐diones and their products have been investigated by spectroscopy, cyclic voltammetry, theoretical studies, and X‐ray crystallography. The results obtained demonstrate the potential of the 1,4‐dione to serve as an invaluable precursor for NDI‐based research.

Mao, Y, Mathews, K & Gorrie, CA 2016, 'Temporal Response of Endogenous Neural Progenitor Cells Following Injury to the Adult Rat Spinal Cord', Frontiers in Cellular Neuroscience, vol. 10, no. MAR2016.
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© 2016 Mao, Mathews and Gorrie. A pool of endogenous neural progenitor cells (NPCs) found in the ependymal layer and the sub-ependymal area of the spinal cord are reported to upregulate Nestin in response to traumatic spinal cord injury (SCI). These cells could potentially be manipulated within a critical time period offering an innovative approach to the repair of SCI. However, little is known about the temporal response of endogenous NPCs following SCI. This study used a mild contusion injury in rat spinal cord and immunehistochemistry to determine the temporal response of ependymal NPCs following injury and their correlation to astrocyte activation at the lesion edge. The results from the study demonstrated that Nestin staining intensity at the central canal peaked at 24 h post-injury and then gradually declined over time. Reactive astrocytes double labeled by Nestin and glial fibrillary acidic protein (GFAP) were found at the lesion edge and commenced to form the glial scar from 1 week after injury. We conclude that the critical time period for manipulating endogenous NPCs following a spinal cod injury in rats is between 24 h when Nestin expression in ependymal cells is increased and 1 week when astrocytes are activated in large numbers.

Martin, AA, Lin, T, Toth, M, Westphal, AJ, Vicenzi, EP, Beeman, J & Silver, EH 2016, 'Exposure and analysis of microparticles embedded in silica aerogel keystones using NF₃‐mediated electron beam–induced etching and energy‐dispersive X‐ray spectroscopy', Meteoritics & Planetary Science, vol. 51, no. 7, pp. 1223-1232.
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AbstractIn 2006, NASA's Stardust spacecraft delivered to Earth dust particles collected from the coma of comet 81P/Wild 2, with the goal of furthering the understanding of solar system formation. Stardust cometary samples were collected in a low‐density, nanoporous silica aerogel making their study technically challenging. This article demonstrates the identification, exposure, and elemental composition analysis of particles analogous to those collected by NASA's Stardust mission using in‐situ SEM techniques. Backscattered electron imaging is shown by experimental observation and Monte Carlo simulation to be suitable for locating particles of a range of sizes relevant to Stardust (down to submicron diameters) embedded within silica aerogel. Selective removal of the silica aerogel encapsulating an embedded particle is performed by cryogenic NF3‐mediated electron beam–induced etching. The porous, low‐density nature of the aerogel results in an enhanced etch rate compared with solid material, making it an effective, nonmechanical method for the exposure of particles. After exposure, elemental composition of the particle was analyzed by energy‐dispersive X‐ray spectroscopy using a high spectral resolution microcalorimeter. Signals from fluorine contamination are shown to correspond to nonremoved silica aerogel and only in residual concentrations.

Marzagalli, R, Leggio, GM, Bucolo, C, Pricoco, E, Keay, KA, Cardile, V, Castorina, S, Salomone, S, Drago, F & Castorina, A 2016, 'Genetic blockade of the dopamine D3 receptor enhances hippocampal expression of PACAP and receptors and alters their cortical distribution', Neuroscience, vol. 316, pp. 279-295.
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Masiuk, SV, Shklyar, SV, Kukush, AG, Carroll, RJ, Kovgan, LN & Likhtarov, IA 2016, 'Estimation of radiation risk in presence of classical additive and Berkson multiplicative errors in exposure doses', Biostatistics, vol. 17, no. 3, pp. 422-436.
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Abstract In this paper, the influence of measurement errors in exposure doses in a regression model with binary response is studied. Recently, it has been recognized that uncertainty in exposure dose is characterized by errors of two types: classical additive errors and Berkson multiplicative errors. The combination of classical additive and Berkson multiplicative errors has not been considered in the literature previously. In a simulation study based on data from radio-epidemiological research of thyroid cancer in Ukraine caused by the Chornobyl accident, it is shown that ignoring measurement errors in doses leads to overestimation of background prevalence and underestimation of excess relative risk. In the work, several methods to reduce these biases are proposed. They are new regression calibration, an additive version of efficient SIMEX, and novel corrected score methods.

McCaughey, LC, Josts, I, Grinter, R, White, P, Byron, O, Tucker, NP, Matthews, JM, Kleanthous, C, Whitchurch, CB & Walker, D 2016, 'Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa', Biochemical Journal, vol. 473, no. 15, pp. 2345-2358.
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Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating its activity in vivo in a murine model of P. aeruginosa lung infection. In addition, we propose a mechanism of cell targeting and translocation for pyocin SD2 across the P. aeruginosa outer membrane. Pyocin SD2 is concentrated at the cell surface, via binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide (LPS), from where it can efficiently locate its outer membrane receptor FpvAI. This strategy of utilizing both the CPA and a protein receptor for cell targeting is common among pyocins as we show that pyocins S2, S5 and SD3 also bind to the CPA. Additional data indicate a key role for an unstructured N-terminal region of pyocin SD2 in the subsequent translocation of the pyocin into the cell. These results greatly improve our understanding of how pyocins target and translocate across the outer membrane of P. aeruginosa. This knowledge could be useful for the development of novel anti-pseudomonal therapeutics and will also support the development of pyocin SD2 as a therapeutic in its own right.

McCauley, JI, Meyer, BJ, Winberg, PC & Skropeta, D 2016, 'Parameters affecting the analytical profile of fatty acids in the macroalgal genus Ulva', Food Chemistry, vol. 209, pp. 332-340.
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The fatty acids (FA) of Ulva have potential to contribute to nutrition. However the large variability of FA profiles of Ulva species; thus the quality and quantity of FA in relation to nutrition is poorly defined. Herein we investigate the FA profile of 74 cultured Ulva samples crossing five culture regimes, six extraction regimes and four post-harvesting processes. This is compared alongside a comprehensive review of FA profiles of Ulva spp. With regard to the literature, Ulva is characterised by C16:0 (30.5±11.5%), C18:3 n-3 (14.5±6.3%), C18:4 n-3 (12.5±5.4%), C16:4 n-3 (8.9±4.8%) and C18:1 n-7 (10.1±4.0%). The investigated Ulva fell within the reported range of specific FA. High nutrient conditions showed the most desirable FA profile for health, along with the highest total FA content (56mgg(-1) dry weight equivalent) when extracted with an optimised protocol.

McElhone, RL, Meakin, GE, French, JC, Alexander, T & Morgan, RM 2016, 'Simulating forensic casework scenarios in experimental studies: The generation of footwear marks in blood', Forensic Science International, vol. 264, pp. 34-40.
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A study was designed to investigate the effects of external variables, including blood type, flooring surface, footwear tread depth and blood dryness, on the appearance of blood-based footwear marks, with particular reference to simulating a specific casework scenario. Results showed that footwear marks left in human blood tended to be of greater quality than those in equine blood, highlighting a potential issue in applying data generated with equine blood to human bloodstains in casework. Footwear tread effects were also dependent on blood type, but the type of flooring surface did not affect the appearance of the mark. Under some conditions, as the blood dried, the amount of detail retained from footwear contact decreased. These results provide the beginnings of an empirical evidence base to allow a more accurate interpretation of blood-based footwear marks in forensic casework. When applied to a disputed bloodstain in a specific case, these results also demonstrate the importance of such experiments in narrowing the range of explanations possible in the interpretation of forensic evidence.

McElroy, DJ, Doblin, MA, Murphy, RJ, Hochuli, DF & Coleman, RA 2016, 'A limited legacy effect of copper in marine biofilms', MARINE POLLUTION BULLETIN, vol. 109, no. 1, pp. 117-127.
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The effects of confounding by temporal factors remains understudied in pollution ecology. For example, there is little understanding of how disturbance history affects the development of assemblages. To begin addressing this gap in knowledge, marine biofilms were subjected to temporally-variable regimes of copper exposure and depuration. It was expected that the physical and biological structure of the biofilms would vary in response to copper regime. Biofilms were examined by inductively coupled plasma optical emission spectrometry, chlorophyll-a fluorescence and field spectrometry and it was found that (1) concentrations of copper were higher in those biofilms exposed to copper, (2) concentrations of copper remain high in biofilms after the source of copper is removed, and (3) exposure to and depuration from copper might have comparable effects on the photosynthetic microbial assemblages in biofilms. The persistence of copper in biofilms after depuration reinforces the need for consideration of temporal factors in ecology.

McNevin, D 2016, 'Preservation of and DNA Extraction from Muscle Tissue', Methods in Molecular Biology, vol. 1420, pp. 43-53.
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As well as protecting DNA for subsequent analysis, tissue preservation methods ideally should be safe, readily available, and easy to transport at relatively low cost. Formalin (formaldehyde solution), used extensively to preserve medical and museum specimens, irreparably damages DNA. We have found four tissue preservatives (solid salt, salt-saturated dimethyl sulfoxide (DMSO)-EDTA solution, ethanol solution, and ethanol-EDTA solution) that preserved muscle tissue at 35 °C for up to 1 month: full short tandem repeat (STR) profiles were obtained after preservation. In addition, salt-saturated DMSO-EDTA solution yielded full STR profiles from aliquots of the liquid preservative surrounding muscle tissue.

Medek, DE, Beggs, PJ, Erbas, B, Jaggard, AK, Campbell, BC, Vicendese, D, Johnston, FH, Godwin, I, Huete, AR, Green, BJ, Burton, PK, Bowman, DMJS, Newnham, RM, Katelaris, CH, Haberle, SG, Newbigin, E & Davies, JM 2016, 'Regional and seasonal variation in airborne grass pollen levels between cities of Australia and New Zealand', AEROBIOLOGIA, vol. 32, no. 2, pp. 289-302.
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Although grass pollen is widely regarded as the major outdoor aeroallergen source in Australia and New Zealand (NZ), no assemblage of airborne pollen data for the region has been previously compiled. Grass pollen count data collected at 14 urban sites in Australia and NZ over periods ranging from 1 to 17 years were acquired, assembled and compared, revealing considerable spatiotemporal variability. Although direct comparison between these data is problematic due to methodological differences between monitoring sites, the following patterns are apparent. Grass pollen seasons tended to have more than one peak from tropics to latitudes of 37°S and single peaks at sites south of this latitude. A longer grass pollen season was therefore found at sites below 37°S, driven by later seasonal end dates for grass growth and flowering. Daily pollen counts increased with latitude; subtropical regions had seasons of both high intensity and long duration. At higher latitude sites, the single springtime grass pollen peak is potentially due to a cooler growing season and a predominance of pollen from C3 grasses. The multiple peaks at lower latitude sites may be due to a warmer season and the predominance of pollen from C4 grasses. Prevalence and duration of seasonal allergies may reflect the differing pollen seasons across Australia and NZ. It must be emphasized that these findings are tentative due to limitations in the available data, reinforcing the need to implement standardized pollen-monitoring methods across Australasia. Furthermore, spatiotemporal differences in grass pollen counts indicate that local, current, standardized pollen monitoring would assist with the management of pollen allergen exposure for patients at risk of allergic rhinitis and asthma.

Mehta, B, Daniel, R, Phillips, C, Doyle, S, Elvidge, G & McNevin, D 2016, 'Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq', ELECTROPHORESIS, vol. 37, no. 21, pp. 2832-2840.
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Forensic DNA‐based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30–40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52‐plex, SNPforID 34‐plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.

Mehta, M, Satija, S & Garg, M 2016, 'Comparison Between HPLC and HPTLC Densitometry for the Determination of 11-keto-Beta-boswellic acid and 3- acetyl-11-keto-Beta-boswellic acid from Boswellia serrata Extract.', Indian Journal of Pharmaceutical Education and Research, vol. 50, no. 3, pp. 418-423.
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Menon, S, Alexander, K, Timms, P, Allan, JA & Huston, WM 2016, 'CXCL10, CXCL11, HLA-A and IL-1 beta are induced in peripheral blood mononuclear cells from women with Chlamydia trachomatis related infertility', PATHOGENS AND DISEASE, vol. 74, no. 1, pp. ftv099-ftv099.
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© FEMS 2015. All rights reserved. Chlamydia trachomatis infections can result in the development of serious sequelae such as pelvic inflammatory disease and tubal infertility. In this study, peripheral blood mononuclear cells from women who were undergoing or had recently undergone IVF treatment were cultured ex vivo with C. trachomatis to identify the immune responses associated with women who had serological evidence of a history of Chlamydia infection. Cytokines secreted into the supernatant from the cultures were measured using ELISA, and the level of IL-1β was found to be significantly higher in Chlamydia positive women than Chlamydia negative women. qRT-PCR analysis of the expression of 88 immune-related genes showed trends towards an upregulation of CXCL10, CXCL11 and HLA-A in Chlamydia positive women compared with Chlamydia negative women. These findings support that some women launch a more marked proinflammatory response upon infection with C. trachomatis and this may be associated with why C. trachomatis induces infertility in some infected women.

Menon, S, Stansfield, SH, Logan, B, Hocking, JS, Timms, P, Rombauts, L, Allan, JA & Huston, WM 2016, 'Development and evaluation of a multi-antigen peptide ELISA for the diagnosis of Chlamydia trachomatis-related infertility in women', Journal of Medical Microbiology, vol. 65, no. 9, pp. 915-922.
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Menon, S, Stansfield, SH, Walsh, M, Hope, E, Isaia, L, Righarts, AA, Niupulusu, T, Temese, SVA, Iosefa-Siitia, L, Auvaa, L, Tapelu, SA, Motu, MF, Suaalii-Sauni, T, Timms, P, Hill, PC & Huston, WM 2016, 'Sero-epidemiological assessment of Chlamydia trachomatis infection and sub-fertility in Samoan women', BMC Infectious Diseases, vol. 16, no. 1, pp. 1-7.
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In our recent village-based cross-sectional study, the prevalence of nucleic acid amplification technique (NAAT) diagnosed Chlamydia trachomatis (CT) in sexually active Samoan women was very high (36 %), and test positivity was associated with sub-fertility. We conducted a serological and epidemiological analysis in these participants to identify if serological data can provide further insight into the potential contribution of CT to sub-fertility in this population.Serological prediction of CT associated sub-fertility was conducted using a series of commercial tests. The correlation between fertility or sub-fertility, behavioral factors, and serologically predicted CT associated sub-fertility was determined.A positive antibody reaction against the Chlamydia Major Outer Membrane Protein (MOMP) was significantly associated with sub-fertility, with 50 % of infertile women being positive. Serum IgG and IgA antibodies against MOMP correlated with current infection measured by urine NAAT, suggesting longer term infections are common in this population. Chlamydia pneumoniae antibodies were frequently detected in this population (84 %), and unexpectedly, were significantly associated with sub-fertility.The high prevalence of chlamydial infection and of positive chlamydial sub-fertility results suggests that CT is an important and frequent contributory factor to sub-fertility in this population.

Merklein, M, Casas-Bedoya, A, Marpaung, D, Buttner, TFS, Pagani, M, Morrison, B, Kabakova, IV & Eggleton, BJ 2016, 'Stimulated Brillouin Scattering in Photonic Integrated Circuits: Novel Applications and Devices', IEEE Journal of Selected Topics in Quantum Electronics, vol. 22, no. 2, pp. 336-346.
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The last few years have seen major progress in harnessing on-chip photon-phonon interactions, leading to a wide range of demonstrations of new functionalities. Utilizing not only the optical response of a nonlinear waveguide - but also acoustic resonances - enables the realization of microwave devices with unprecedented performance, otherwise hard to achieve in all-optical processing schemes or electronically. Here, we overview on-chip stimulated Brillouin scattering (SBS) with special emphasis on microwave sources and microwave signal processing schemes. We review the different material platforms and structures for on-chip SBS, ranging from chalcogenide rib waveguides to hybrid silicon/silicon-nitride structures, high-Q photonic-phononic silica microresonators, and suspended silicon nanowires. We show that the paradigm shift in SBS research - from long length of fibers to chip-scale devices - is now moving toward fully integrated photonic-phononic CMOS chips.

Merklein, M, Stiller, B, Kabakova, IV, Mutugala, US, Vu, K, Madden, SJ, Eggleton, BJ & Slavík, R 2016, 'Widely tunable, low phase noise microwave source based on a photonic chip', Optics Letters, vol. 41, no. 20, pp. 4633-4633.
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Spectrally pure microwave sources are highly desired for several applications, ranging from wireless communication to next generation radar technology and metrology. Additionally, to generate very pure signals at even higher frequencies, these advanced microwave sources have to be compact, low in weight, and low energy consumption to comply with in-field applications. A hybrid optical and electronic cavity, known as an optoelectronic oscillator (OEO), has the potential to leverage the high bandwidth of optics to generate ultrapure high-frequency microwave signals. Here we present a widely tunable, low phase noise microwave source based on a photonic chip. Using on-chip stimulated Brillouin scattering as a narrowband active filter allows single-mode OEO operation and ultrawide frequency tunability with no signal degeneration. Furthermore, we show very low close-to-carrier phase noise. This Letter paves the way to a compact, fully integrated pure microwave source.

Messer, LF, Mahaffey, C, Robinson, CM, Jeffries, TC, Baker, KG, Isaksson, JB, Ostrowski, M, Doblin, MA, Brown, MV & Seymour, JR 2016, 'High levels of heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation', ISME JOURNAL, vol. 10, no. 6, pp. 1499-1513.
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© 2016 International Society for Microbial Ecology. Australia's tropical waters represent predicted 'hotspots' for nitrogen (N 2) fixation based on empirical and modelled data. However, the identity, activity and ecology of diazotrophs within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size-fractionated N 2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (δ-proteobacteria and γ-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N 2 fixation rates ranged from <1 to 91 nmol l -1 day -1, and size fractionation indicated that unicellular organisms dominated N 2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than in spring. Relative abundances of UCYN-A1 and γ-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia's tropical waters are indeed hotspots for N 2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N 2 fixation.

Midthune, D, Carroll, RJ, Freedman, LS & Kipnis, V 2016, 'Measurement error models with interactions', Biostatistics, vol. 17, no. 2, pp. 277-290.
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AbstractAn important use of measurement error models is to correct regression models for bias due to covariate measurement error. Most measurement error models assume that the observed error-prone covariate ($W$) is a linear function of the unobserved true covariate ($X$) plus other covariates ($Z$) in the regression model. In this paper, we consider models for $W$ that include interactions between $X$ and $Z$. We derive the conditional distribution of $X$ given $W$ and $Z$ and use it to extend the method of regression calibration to this class of measurement error models. We apply the model to dietary data and test whether self-reported dietary intake includes an interaction between true intake and body mass index. We also perform simulations to compare the model to simpler approximate calibration models.

Mirnaziry, SR, Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 2016, 'Stimulated Brillouin scattering in silicon/chalcogenide slot waveguides', Optics Express, vol. 24, no. 5, pp. 4786-4786.
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© 2016 Optical Society of America. We study slot waveguide geometries, comprising a combination of soft glasses and high-index guiding structures, for enhancing stimulated Brillouin scattering (SBS). We show that strong optical and acoustic mode confinement in these waveguides can lead to a substantial increase in SBS gain, comparable to or greater than recently proposed suspended silicon nanowire structures. We compute the optimal parameters of the structure and examine the physics of optical and acoustic confinement within slot waveguides. Finally, we compute the effects of linear and nonlinear loss mechanisms on optimum pump/Stokes powers and waveguide lengths.

Mitchell, AB, Mourad, B, Tovey, E, Buddle, L, Peters, M, Morgan, L & Oliver, BG 2016, 'Spirometry filters can be used to detect exhaled respiratory viruses', Journal of Breath Research, vol. 10, no. 4, pp. 046002-046002.
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© 2016 IOP Publishing Ltd. Respiratory viruses are very common in the community and contribute to the burden of illness for patients with chronic respiratory diseases, including acute exacerbations. Traditional sampling methods are invasive and problematic to repeat. Accordingly, we explored whether respiratory viruses could be isolated from disposable spirometry filters and whether detection of viruses in this context represented presence in the upper or lower respiratory tract. Discovery (n = 53) and validation (n = 49) cohorts were recruited from a hospital outpatient department during two different time periods. Spirometry mouthpiece filters were collected from all participants. Respiratory secretions were sampled from the upper and lower respiratory tract by nasal washing (NW), sputum, and bronchoalveolar lavage (BAL). All samples were examined using RT-PCR to identify a panel of respiratory viruses (rhinovirus, respiratory syncytial virus, influenza A, influenza B, parainfluenza virus 1, 2 & 3, and human metapneumovirus). Rhinovirus was quantified using qPCR. Paired filter-NW samples (n = 29), filter-sputum samples (n = 24), filter-BAL samples (n = 39) and filter-NW-BAL samples (n = 10) provided a range of comparisons. At least one virus was detected in any sample in 85% of participants in the discovery cohort versus 45% in the validation cohort. Overall, 72% of viruses identified in the paired comparator method matched those detected in spirometry filters. There was a high correlation between viruses identified in spirometry filters compared with viruses identified in both the upper and lower respiratory tract using traditional sampling methods. Our results suggest that examination of spirometry filters may be a novel and inexpensive sampling method for the presence of respiratory viruses in exhaled breath.

Mitchell, AB, Oliver, BGG & Glanville, AR 2016, 'Translational Aspects of the Human Respiratory Virome', American Journal of Respiratory and Critical Care Medicine, vol. 194, no. 12, pp. 1458-1464.
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© 2016 by the American Thoracic Society. Despite the dominant role of community-acquired respiratory viruses as etiological agents of disease, there has been little focus to date on the translation of rapidly developing diagnostic modalities, such as next-generation sequencing techniques in the examination of lower respiratory tract samples. When applied, these techniques should inform strategies to both understand the nexus between health and disease states of the respiratory virome, and drive a paradigm shift in how the practicing pulmonologist views the conceptual framework of respiratory infections. The lower respiratory tract was once thought to be a sanctuary site from microbiological colonization owing to the efficacy of upper airway-protective mechanisms and the host mucosal barrier function of the lower airways, combined with both innate and adaptive immune responses.As a small number of recent studies confirm, this is a naive vision of the lung, the viral component of which parallels recent revelations from respiratory microbiome studies. Hence, it is now timely to revise our thinking regarding the constituents, diversity, and changing nature of the respiratory virome in health and disease. One area worthy of focus is the interface between community-acquired respiratory viruses and the respiratory virome to better understand the dynamics in acute infection, as well as the factors that may lead to viral persistence and chronic disease. Given recent advances in metagenomics, the tools are now at hand to accomplish these goals.

Mitrovic, SM & Baldwin, DS 2016, 'Allochthonous dissolved organic carbon in river, lake and coastal systems: transport, function and ecological role', Marine and Freshwater Research, vol. 67, no. 9, pp. i-i.
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Moezzi, A, Cortie, M & McDonagh, A 2016, 'Transformation of zinc hydroxide chloride monohydrate to crystalline zinc oxide', DALTON TRANSACTIONS, vol. 45, no. 17, pp. 7385-7390.
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Moheimani, F, Hsu, AC-Y, Reid, AT, Williams, T, Kicic, A, Stick, SM, Hansbro, PM, Wark, PAB & Knight, DA 2016, 'The genetic and epigenetic landscapes of the epithelium in asthma', Respiratory Research, vol. 17, no. 1.
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© 2016 The Author(s). Asthma is a global health problem with increasing prevalence. The airway epithelium is the initial barrier against inhaled noxious agents or aeroallergens. In asthma, the airway epithelium suffers from structural and functional abnormalities and as such, is more susceptible to normally innocuous environmental stimuli. The epithelial structural and functional impairments are now recognised as a significant contributing factor to asthma pathogenesis. Both genetic and environmental risk factors play important roles in the development of asthma with an increasing number of genes associated with asthma susceptibility being expressed in airway epithelium. Epigenetic factors that regulate airway epithelial structure and function are also an attractive area for assessment of susceptibility to asthma. In this review we provide a comprehensive discussion on genetic factors; from using linkage designs and candidate gene association studies to genome-wide association studies and whole genome sequencing, and epigenetic factors; DNA methylation, histone modifications, and non-coding RNAs (especially microRNAs), in airway epithelial cells that are functionally associated with asthma pathogenesis. Our aims were to introduce potential predictors or therapeutic targets for asthma in airway epithelium. Overall, we found very small overlap in asthma susceptibility genes identified with different technologies. Some potential biomarkers are IRAKM, PCDH1, ORMDL3/GSDMB, IL-33, CDHR3 and CST1 in airway epithelial cells. Recent studies on epigenetic regulatory factors have further provided novel insights to the field, particularly their effect on regulation of some of the asthma susceptibility genes (e.g. methylation of ADAM33). Among the epigenetic regulatory mechanisms, microRNA networks have been shown to regulate a major portion of post-transcriptional gene regulation. Particularly, miR-19a may have some therapeutic potential.

Mohkam, M, Rasoul-Amini, S, Shokri, D, Berenjian, A, Rahimi, F, Sadraeian, M, Khalvati, B, Gholami, A & Ghasemi, Y 2016, 'Characterization and in vitro probiotic assessment of potential indigenous Bacillus strains isolated from soil rhizosphere', Minerva Biotecnologica, vol. 28, no. 1, pp. 19-28.
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BACKGROUND: Probiotics mainly Bacillus species can be advantageous to the host by promoting its intestinal balance. Attempts were made to isolate and identify Bacillus strains from rhizosphere environment. METHODS: The in vitro probiotic criteria were used for screening and characterizing potential Bacillus probiotics. Morphological, physiological and biochemical characteristics as well as 16S rRNA gene sequence analysis were utilized for identification of the isolates. Seven isolates were chosen based on withstanding to acidic condition (pH 2.5) and various bile salt concentrations (1-4%(w/v)). RESULTS: Isolates found to have the least antimicrobial activity against Listeria monocytogenes PTCC 1163, Staphylococcus aureus ATCC 1912 and Bacillus cereus PTCC 1015; however, no activity against Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 25922 was observed. The Bacillus Isolates showed different variation in auto-aggregation features and adhesion to hydrocarbons ranging from 60% to 90% and 10% to 60%, respectively. Excluding isolate 14 that exhibited resistance to penicillin and ampicillin, all the other Bacillus strains were sensitive to the tested antibiotics. All isolates showed relatively low cytotoxic effect on HepG2 cell line except strains 12 and 14. CONCLUSION: Taking together, among the investigated Bacillus isolates, strains 17 and S10 found to be the most promising candidates to fulfill in vitro probiotic specifications.

Molnar, A & Fu, S 2016, 'Techniques and Technologies for The Bioanalysis of Sativex ^® , Metabolites and Related Compounds', Bioanalysis, vol. 8, no. 8, pp. 829-845.
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Sativex® is an oromucosal spray indicated for the treatment of moderate-to-severe spasticity in multiple sclerosis and is also an effective analgesic for advanced cancer patients. Sativex contains Δ9-tetrahydrocannabinol (THC) and cannabidiol in an approximately 1:1 ratio. The increasing prevalence of medicinal cannabis products highlights the importance of reliable bioanalysis and re-evaluation of the interpretation of positive test results for THC, as legal implications may arise in workplace, roadside and sports drug testing situations. This article summarizes published research on the bioanalysis of THC and cannabidiol, with particular focus on Sativex. Common screening and confirmatory testing of blood, urine, oral fluid and hair samples are outlined. Correlations between matrices and current analytical pitfalls are also addressed.

Monahan, LG & Harry, EJ 2016, 'You Are What You Eat: Metabolic Control of Bacterial Division', TRENDS IN MICROBIOLOGY, vol. 24, no. 3, pp. 181-189.
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© 2015 Elsevier Ltd. Fluctuations in nutrient availability are a fact of life for bacterial cells in the 'wild'. To survive and compete, bacteria must rapidly modulate cell-cycle processes to accommodate changing nutritional conditions and concomitant changes in cell growth. Our understanding of how this is achieved has been transformed in recent years, with cellular metabolism emerging as a central player. Several metabolic enzymes, in addition to their normal catalytic functions, have been shown to directly modulate cell-cycle processes in response to changing nutrient levels. Here we focus on cell division, the final event in the bacterial cell cycle, and discuss recent compelling evidence connecting division regulation to nutritional status and metabolic activity.

Mondal, AK, Liu, H, Li, Z-F & Wang, G 2016, 'Multiwall carbon nanotube-nickel cobalt oxide hybrid structure as high performance electrodes for supercapacitors and lithium ion batteries', ELECTROCHIMICA ACTA, vol. 190, pp. 346-353.
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© 2015 Elsevier Ltd. All rights reserved. We developed a simple strategy to prepare a multiwall carbon nanotube-nickel cobalt oxide nanosheet hybrid structure by using a microwave method followed by subsequent calcination in air. The structure and morphology of the material are characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. When applied as electrode material in 2 M KOH electrolyte for supercapacitors, the multiwall carbon nanotube-nickel cobalt oxide nanosheet structure shows a high specific capacitance of 1395 F g-1 at a current density of 1 A g-1 and excellent cycling stability over 5000 cycles. As an anode material for lithium ion battery applications, the hybrid material presents a high reversible capacity of 904 mA h g-1, good rate capability and better cycling performance than nickel cobalt oxide nanosheets and pristine multiwall carbon nanotube. The improved performances of supercapacitors and lithium ion batteries could be accredited to the unique structural features, which support high electron conductivity and rapid ion/electron transport within the electrode and at the electrode/electrolyte interface, and also accommodate volume variation during charge-discharge cycling.

Mondal, AK, Liu, H, Xie, X, Kretschmer, K & Wang, G 2016, 'Hydrothermal Synthesis of Multiwalled Carbon Nanotube-Zinc Manganate Nanoparticles as Anode Materials for Lithium Ion Batteries', CHEMPLUSCHEM, vol. 81, no. 4, pp. 399-405.
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Mongin, M, Baird, ME, Tilbrook, B, Matear, RJ, Lenton, A, Herzfeld, M, Wild-Allen, K, Skerratt, J, Margvelashvili, N, Robson, BJ, Duarte, CM, Gustafsson, MSM, Ralph, PJ & Steven, ADL 2016, 'The exposure of the Great Barrier Reef to ocean acidification', Nature Communications, vol. 7, no. 1, pp. 1-8.
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AbstractThe Great Barrier Reef (GBR) is founded on reef-building corals. Corals build their exoskeleton with aragonite, but ocean acidification is lowering the aragonite saturation state of seawater (Ωa). The downscaling of ocean acidification projections from global to GBR scales requires the set of regional drivers controlling Ωa to be resolved. Here we use a regional coupled circulation–biogeochemical model and observations to estimate the Ωa experienced by the 3,581 reefs of the GBR, and to apportion the contributions of the hydrological cycle, regional hydrodynamics and metabolism on Ωa variability. We find more detail, and a greater range (1.43), than previously compiled coarse maps of Ωa of the region (0.4), or in observations (1.0). Most of the variability in Ωa is due to processes upstream of the reef in question. As a result, future decline in Ωa is likely to be steeper on the GBR than currently projected by the IPCC assessment report.

Moore, CE, Brown, T, Keenan, TF, Duursma, RA, van Dijk, AIJM, Beringer, J, Culvenor, D, Evans, B, Huete, A, Hutley, LB, Maier, S, Restrepo-Coupe, N, Sonnentag, O, Specht, A, Taylor, JR, van Gorsel, E & Liddell, MJ 2016, 'Australian vegetation phenology: new insights from satellite remote sensing and digital repeat photography', Biogeosciences Discussions, pp. 1-30.
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Abstract. Phenology is the study of periodic biological occurrences and can provide important insights into the influence of climatic variability and change on ecosystems. Understanding Australia’s vegetation phenology is a challenge due to its diverse range of ecosystems, from savannas and tropical rainforests to temperate eucalypt woodlands, semi-arid scrublands and alpine grasslands. These ecosystems exhibit marked differences in seasonal patterns of canopy development and plant life-cycle events, much of which deviates from the predictable seasonal phenological pulse of temperate deciduous and boreal biomes. Many Australian ecosystems are subject to irregular events (i.e., drought, flooding, cyclones and fire) that can alter ecosystem composition, structure and functioning just as much as seasonal change. We show how satellite remote sensing and ground-based digital repeat photography (i.e. phenocams) can be used to improve understanding of phenology in Australian ecosystems. First, we examine temporal variation in phenology at the continental scale using the Enhanced Vegetation Index (EVI), calculated from MODerate resolution Imaging Spectroradiomter (MODIS) data. Spatial gradients are revealed, ranging from regions with pronounced seasonality in canopy development (i.e., tropical savannas) to regions where seasonal variation is minimal (i.e., tropical rainforests) or high but irregular (i.e., arid ecosystems). Next, we use time series colour information extracted from phenocam imagery to illustrate a range of phenological signals in four contrasting Australian ecosystems. These include greening and senescing events in tropical savannas and temperate eucalypt understory, as well as strong seasonal dynamics of individual trees in a seemingly static evergreen rainforest. We also demonstrate how phenology links with ecosystem gross primary productivity (from eddy covariance) and discuss why these processes are linked in some ecosystems but not...

Moore, CE, Brown, T, Keenan, TF, Duursma, RA, van Dijk, AIJM, Beringer, J, Culvenor, D, Evans, B, Huete, A, Hutley, LB, Maier, S, Restrepo-Coupe, N, Sonnentag, O, Specht, A, Taylor, JR, van Gorsel, E & Liddell, MJ 2016, 'Reviews and syntheses: Australian vegetation phenology: new insights from satellite remote sensingand digital repeat photography', Biogeosciences, vol. 13, no. 17, pp. 5085-5102.
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Abstract. Phenology is the study of periodic biological occurrences and can provide important insights into the influence of climatic variability and change on ecosystems. Understanding Australia's vegetation phenology is a challenge due to its diverse range of ecosystems, from savannas and tropical rainforests to temperate eucalypt woodlands, semi-arid scrublands, and alpine grasslands. These ecosystems exhibit marked differences in seasonal patterns of canopy development and plant life-cycle events, much of which deviates from the predictable seasonal phenological pulse of temperate deciduous and boreal biomes. Many Australian ecosystems are subject to irregular events (i.e. drought, flooding, cyclones, and fire) that can alter ecosystem composition, structure, and functioning just as much as seasonal change. We show how satellite remote sensing and ground-based digital repeat photography (i.e. phenocams) can be used to improve understanding of phenology in Australian ecosystems. First, we examine temporal variation in phenology on the continental scale using the enhanced vegetation index (EVI), calculated from MODerate resolution Imaging Spectroradiometer (MODIS) data. Spatial gradients are revealed, ranging from regions with pronounced seasonality in canopy development (i.e. tropical savannas) to regions where seasonal variation is minimal (i.e. tropical rainforests) or high but irregular (i.e. arid ecosystems). Next, we use time series colour information extracted from phenocam imagery to illustrate a range of phenological signals in four contrasting Australian ecosystems. These include greening and senescing events in tropical savannas and temperate eucalypt understorey, as well as strong seasonal dynamics of individual trees in a seemingly static evergreen rainforest. We also demonstrate how phenology links with ecosystem gross primary productivity (from eddy covariance) and discuss why these processes are linked in some ecosystems but no...

Moores, N, Rogers, DI, Rogers, K & Hansbro, PM 2016, 'Reclamation of tidal flats and shorebird declines in Saemangeum and elsewhere in the Republic of Korea', Emu - Austral Ornithology, vol. 116, no. 2, pp. 136-146.
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© BirdLife Australia 2016. Saemangeum, in the Republic of Korea (ROK, commonly called South Korea) was one of the most important shorebird staging sites in the Yellow Sea. It supported at least 330000 shorebirds annually between 1997 and 2001, including ∼30% of the world population of Great Knots (Calidris tenuirostris) during both northward and southward migration. Construction of a 33-km long sea-wall was completed in April 2006. We show that shorebird numbers at Saemangeum and two adjacent wetlands decreased by 130000 during northward migration in the next two years and that all species have declined at Saemangeum since completion of the sea-wall. Great Knots were among the most rapidly affected species. Fewer than 5000 shorebirds were recorded at Saemangeum during northward migration in 2014. We found no evidence to suggest that most shorebirds of any species displaced from Saemangeum successfully relocated to other sites in the ROK. Instead, by 2011-13 nearly all species had declined substantially in the ROK since previous national surveys in 1998 and 2008, especially at more heavily reclaimed sites. It is likely that these declines were driven by increased mortality rather than movement to alternate staging sites given that other studies have shown concurrent declines in numbers and survival on the non-breeding grounds. This is the first study in the East Asian-Australasian Flyway to confirm declines of shorebirds at a range of geographical scales following a single reclamation project. The results indicate that if migratory shorebirds are displaced from major staging sites by reclamation they are probably unable to relocate successfully to alternate sites.

Moraes, MLL, da Silva, HDT, Blanes, L, Doble, P & Tavares, MFM 2016, 'Optimization of chemometric approaches for the extraction of isorhamnetin-3-O-rutinoside from Calendula officinalis L.', Journal of Pharmaceutical and Biomedical Analysis, vol. 125, pp. 408-414.
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Mostafa Hosseinpour-Mashkani, S, Maddahfar, M & Sobhani-Nasab, A 2016, 'Novel silver-doped CdMoO4: synthesis, characterization, and its photocatalytic performance for methyl orange degradation through the sonochemical method', Journal of Materials Science: Materials in Electronics, vol. 27, no. 1, pp. 474-480.
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Mowe, MAD, Abbas, F, Porojan, C, Mitrovic, SM, Lim, RP, Furey, A & Yeo, DCJ 2016, 'Roles of nitrogen and phosphorus in growth responses and toxin production (using LC-MS/MS) of tropical Microcystis ichthyoblabe and M. flos-aquae', Journal of Applied Phycology, vol. 28, no. 3, pp. 1543-1552.
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© 2015 Springer Science+Business Media Dordrecht In experiments investigating nutrient effects on tropical Microcystis, increasing nitrogen and phosphorus concentrations were found to have a significant positive effect on maximum cell yields of two strains of Microcystis ichthyoblabe (from Lower Peirce and Tengeh Reservoirs) and one strain of Microcystis flos-aquae isolated (Lower Peirce Reservoir) from Singapore. However, only increasing nitrogen concentration had a positive effect on growth rates of M. ichthyoblabe and M. flos-aquae from Lower Peirce Reservoir. MC-RR and MC-LR were produced by all three strains with MC-RR being the dominant variant. Phosphorus played an important role in MC production with increases in phosphorus from medium to high concentrations leading to decreases in MC-RR cell quotas for all three strains at the two highest nitrogen levels tested. The different growth and toxin production responses between M. ichthyoblabe strains could be due to location-specific differences.

Muhammad Umer Farooq, Ziyuan Gao, Sajid Butt, Kewei Gao, Xiaolu Pang, Hidayat Ullah Shah, Hasnain Mehdi Jafr, Asif Mahmod, Xigui Sun & Nasir Mahmood 2016, 'Enhanced Thermoelectric Transport Properties of La0.98Sr0.02CoO3-BiCuSeO Composite', J. of Electrical Engineering, vol. 4, no. 2.
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Muhammad Yousaf, Asif Mahmood, Yunsong Wang, Yijun Chen, Zhimin Ma & Ray P. S. Han 2016, 'Advancement in Layered Transition Metal Dichalcogenide Composites for Lithium and Sodium Ion Batteries', J. of Electrical Engineering, vol. 4, no. 2.
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Mullens, ED, Leslie, LM & Lamb, PJ 2016, 'Impacts of Gulf of Mexico SST Anomalies on Southern Plains Freezing Precipitation: ARW Sensitivity Study of the 28–30 January 2010 Winter Storm', Journal of Applied Meteorology and Climatology, vol. 55, no. 1, pp. 119-143.
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AbstractIce storms are an infrequent but significant hazard in the U.S southern Great Plains. Common synoptic profiles for freezing precipitation reveal advection of low-level warm moist air from the Gulf of Mexico (GOM), above a shallow Arctic air mass ahead of a midlevel trough. Because the GOM is the proximal basin and major moisture source, this study investigates impacts of varying GOM sea surface temperature (SST) on the thermodynamic evolution of a winter storm that occurred during 28–30 January 2010, with particular emphasis on the modulation of freezing precipitation. A high-resolution, nested ARW sensitivity study with a 3.3-km inner domain is performed, using six representations of GOM SST, including control, climatological mean, uniform ±2°C from control, and physically constrained upper- and lower-bound basin-average anomalies from a 30-yr dataset. The simulations reveal discernable impacts of SST on the warm-layer inversion, precipitation intensity, and low-level dynamics. Whereas total precipitation for the storm increased monotonically with SST, the freezing-precipitation response was more varied and nonlinear, with the greatest accumulation decreases occurring for the coolest SST perturbation, particularly at moderate precipitation rates. Enhanced precipitation and warm-layer intensity promoted by warmer SST were offset for the highest perturbations by deepening of the weak 850-hPa low circulation and faster eastward progression associated with enhanced baroclinicity and diabatic generation of potential vorticity. Air-parcel trajectories terminating within the freezing-precipitation region were examined to identify airmass sources and modification. These results suggest that GOM SST can affect the severity of concurrent ice-storm events in the southern Great Plains, with warmer basin SST potentially exacerbating the risk of damaging ice accumulations.

Mullens, ED, Leslie, LM & Lamb, PJ 2016, 'Synoptic Pattern Analysis and Climatology of Ice and Snowstorms in the Southern Great Plains, 1993–2011', Weather and Forecasting, vol. 31, no. 4, pp. 1109-1136.
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AbstractWinter storms in the southern United States can significantly impact infrastructure and the economy. In this study, National Centers for Environmental Information Storm Event Database and local climate summaries, are used to develop a spatial climatology of freezing precipitation (freezing rain and ice pellets) and snow over the southern Great Plains, 1993–2011. Principal component analysis is performed on the 500-hPa height field, at the approximate onset time of precipitation, for 33 freezing precipitation and 42 snow case studies, to differentiate common synoptic flow fields associated with precipitation type. The five leading patterns for each precipitation type are retained. Composites of temperature, moisture, pressure, and wind fields are constructed and extended 24 h before and after precipitation initiation to track the storm system evolution. Many 500-hPa flow fields are similar for both precipitation types. However, snow-dominant events have stronger and/or more frequent surface cyclone development. Freezing precipitation is associated with the southward propagation of an Arctic anticyclone well ahead of precipitation, weak or absent surface cyclone formation, and a more western trough axis. High-impact ice storms in the region often have slow-moving upper-level flow, persistent isentropic ascent over a surface quasi-stationary front with strongly positive moisture anomalies, and warm layer airmass trajectories originating over the Gulf of Mexico. The results here are based on a relatively small sample size. However, this work is intended to be useful for forecasters, in particular as a pattern recognition aid in predicting the evolution of precipitation within southern Great Plains winter storms.

Müller, S, Mitrovic, SM & Baldwin, DS 2016, 'Oxygen and dissolved organic carbon control release of N, P and Fe from the sediments of a shallow, polymictic lake', Journal of Soils and Sediments, vol. 16, no. 3, pp. 1109-1120.
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Purpose We examined potential causes of nutrient release from the sediments of a shallow polymictic reservoir that, unlike many other shallow lakes, had not received large amounts of nutrient loading. It was hypothesised that the sediments released greater amounts of nutrients under anoxic rather than oxic conditions and that nitrogen (N) and phosphorus (P) release was limited by the availability of different types of organic substrate. Materials and methods Sediment incubation experiments under oxic and anoxic conditions were conducted in summer and in winter. One anoxic incubation experiment with the addition of different types of dissolved organic substrate (glucose, acetate, formate and propionate) was carried out. Concentrations of nitrite and nitrate (NOx −-N), ammonium (NH4 +-N), soluble reactive P (srP) and iron (Fe(II)) were monitored in the supernatant of the incubation chambers over 28 days. Thermal stratification was monitored in situ for 17 months and sediment composition was analysed. Results and discussion NOx −-N concentration increased by 5.67±0.33 mg N l−1 in anoxic conditions but was much lower in oxic treatments. Release of srP was low in anoxic and oxic treatments (0.004±0.001 mg P l−1) but was stimulated by 0.027±0.015 mg P l−1 under additions of formate. Fe(II) release was mostly stimulated by glucose additions (25.59± 4.28 mg Fe l−1). P release was much lower than observed in eutrophic lakes. P release does not appear to be as a result of the reduction of Fe minerals and concurrent dissolution of orthophosphate, often reported as the most prevalent pathway for P release from anaerobic lake sediments. Conclusions Iron and P flux from lake sediments can be independent from each other and can be controlled by dissolved organic C. Further, the study confirms the role of oxygen availability in controlling nutrient release from the sediments.

Murray, SA, Farrell, H, Harwood, T & Zammit, A 2016, 'Is ciguatera moving south in Australia?', Harmful Algae News, vol. 54, pp. 5-6.

Murray, SA, Suggett, DJ, Doblin, MA, Kohli, GS, Seymour, JR, Fabris, M & Ralph, PJ 2016, 'Unravelling the functional genetics of dinoflagellates: a review of approaches and opportunities', Perspectives in Phycology, vol. 3, no. 1, pp. 37-52.
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Dinoflagellates occupy an extraordinarily diverse array of ecological niches. Their success stems from a suite of functional and ecological strategies, including the production of secondary metabolites with anti-predator or allelopathic impacts, nutritional flexibility, and the ability to form symbiotic relationships. Despite their ecological importance, we currently have a poor understanding of the genetic basis for many of these strategies, due to the complex genomes of dinoflagellates. Genomics and transcriptomic sequencing approaches are now providing the first insights into the genetic basis of some dinoflagellate functional traits, providing the opportunity for novel ecological experiments, novel methods for monitoring of harmful biotoxins, and allowing us to investigate the production of ecologically and economically important compounds such as the long chain polyunsaturated fatty acid, docosahexanoic acid and the climatically important metabolite, dimethylsulfoniopropionate. Despite these advances, we still generally lack the ability to genetically manipulate species, which would enable the confirmation of biosynthetic pathways and the development of novel bio-engineering applications. Here, we describe advances in understanding the genetic basis of dinoflagellate ecology, and propose biotechnological approaches that could be applied to further transform our understanding of this unique group of eukaryotes.

Musumeci, G, Loreto, C, Giunta, S, Rapisarda, V, Szychlinska, MA, Imbesi, R, Castorina, A, Annese, T, Castorina, S, Castrogiovanni, P & Ribatti, D 2016, 'Angiogenesis correlates with macrophage and mast cell infiltration in lung tissue of animals exposed to fluoro-edenite fibers', Experimental Cell Research, vol. 346, no. 1, pp. 91-98.
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© 2016 Elsevier Inc.Angiogenesis plays a crucial role in progression of pleural malignant mesothelioma. A significantly increased incidence of pleural mesothelioma has been attributed to exposure to fluoro-edenite, a fibrous amphibole extracted from a local stone quarry. In this study, we have investigated the expression of CD68-positive macrophages, tryptase-positive mast cells and CD31 positive areas, as expression of microvascular density, in lung tissue of sheeps exposed to fluoro-edenite fibers vs controls, by immunohistochemical, morphometric and Western blot analysis. The result have evidenced a significant increase in the expression of CD68-positive macrophages, tryptase-positive mast cells as well as a significant increase in microvascular density evaluated as CD31 positive areas in lung tissue of of sheeps exposed to fluoro-edenite fibers vs controls. These data confirmed the important role played by tumor microenvironment components, including macrophages and mast cells, in favour of angiogenesis in pleural mesothelioma induced by fluoro-edenite exposure.

Nguyen, KQ, Cuneo, P, Cunningham, SA, Krix, DW, Leigh, A & Murray, BR 2016, 'Ecological effects of increasing time since invasion by the exotic African olive (Olea europaea ssp. cuspidata) on leaf-litter invertebrate assemblages', Biological Invasions, vol. 18, no. 6, pp. 1689-1699.
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© 2016, Springer International Publishing Switzerland. Invasive African olive, Olea europaea ssp. cuspidata (Wall. ex G.Don) Cif., forms increasingly dense stands between initial and mature stages of invasion, leading to a progressive decline in native plant diversity. Here, we examined the response of leaf-litter invertebrates to increasing time since olive invasion. We compared invertebrate assemblages among early-stage olive (0–7 years since invasion, scattered olive shrubs and seedlings in native woodland), mature olive (>15 years, uniform olive stands dominated by multi-trunked trees) and uninvaded native grassy woodland habitats (both mature stands and edges) in a critically endangered ecological community of south-eastern Australia. Invertebrate species richness was significantly reduced in mature olive compared with early-stage olive and mature native woodland habitats. Species richness did not differ significantly between early-stage olive habitat and mature native woodland, demonstrating resistance in species richness to initial invasion. Invertebrate species composition of native woodlands differed significantly from both mature olive and early-stage olive habitats, demonstrating a lack of resistance in species composition to initial olive invasion. Compositional differences were principally driven by reduced abundances within Coleoptera, Hymenoptera and Polyxenida in mature olive habitat compared with mature native woodland. These changes were significantly correlated with an increase in bare ground, plant canopy cover and litter depth, and higher moisture and lower temperature within leaf litter, in mature olive habitat. Our findings show that negative ecological impacts of invasive African olive extend beyond plants to leaf-litter invertebrate assemblages and that significant impacts on invertebrate species assemblage composition occur early in the invasion process.

Nguyen, LT, Chen, H, Pollock, CA & Saad, S 2016, 'Sirtuins—mediators of maternal obesity‐induced complications in offspring?', The FASEB Journal, vol. 30, no. 4, pp. 1383-1390.
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Obesity is a complex metabolic disease, attributed to diverse and interactive genetic and environmental factors. The associated health consequences of obesity are pleiotropic, with individuals being more susceptible to chronic diseases such as type 2 diabetes mellitus, hypertension, and lipotoxicity-related chronic diseases. The contribution of maternal obesity to the offspring's predisposition to both obesity and its complications is increasingly recognized. Understanding the mechanisms underlying these "transmissible" effects is critical to develop therapeutic interventions to reduce the risk for "programmed" obesity. Sirtuins (SIRTs), particularly SIRT1 and SIRT3, are NAD(+)-dependent deacetylases that regulate metabolic balance and stress responses in both central and peripheral tissues, of which dysregulation is a well-established mediator for the development and effects of obesity. Nevertheless, their implication in the transmissible effects of maternal obesity across generations remains largely elusive. In this review, we examine multiple pathways and systems that are likely to mediate such effects, with particular emphasis on the role of SIRTs.-Nguyen, L. T., Chen, H., Pollock, C. A., Saad, S. Sirtuins-mediators of maternal obesity-induced complications in offspring?

Nguyen, T-K, Selvanayagam, R, Ho, KKK, Chen, R, Kutty, SK, Rice, SA, Kumar, N, Barraud, N, Duong, HTT & Boyer, C 2016, 'Co-delivery of nitric oxide and antibiotic using polymeric nanoparticles', Chemical Science, vol. 7, no. 2, pp. 1016-1027.
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The rise of hospital-acquired infections, also known as nosocomial infections, is a growing concern in intensive healthcare, causing the death of hundreds of thousands of patients and costing billions of dollars worldwide every year.

Nizalapur, S, Ho, KKK, Kimyon, O, Yee, E, Berry, T, Manefield, M, Cranfield, CG, Willcox, M, Black, DS & Kumar, N 2016, 'Synthesis and biological evaluation of N-naphthoyl-phenylglyoxamide-based small molecular antimicrobial peptide mimics as novel antimicrobial agents and biofilm inhibitors', ORGANIC & BIOMOLECULAR CHEMISTRY, vol. 14, no. 14, pp. 3623-3637.
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© The Royal Society of Chemistry 2016. Antimicrobial peptides (AMPs) are a key component of the human immune system. Synthetic AMP mimics represent a novel strategy to counteract the increasing incidence of antimicrobial resistance. Here, we describe the synthesis of novel glyoxamide derivatives via ring-opening reactions of N-hexanoyl, N-benzoyl and N-naphthoylisatins with N,N-dimethylethane-1,2-diamine and N,N-dimethylpropane-1,3-diamine. These were converted to both the hydrochloric acid (HCl) or quaternary ammonium iodide (MeI) salts and their antibacterial activity against Staphylococcus aureus was investigated by their zone-of-inhibition and minimum inhibitory concentration (MIC). The HCl salt 22b exhibited the lowest MIC of 16 μg mL-1, whereas the corresponding MeI salt 22c had a MIC of 39 μg mL-1. We also investigated the in vitro toxicity of active compounds against the MRC-5 normal human lung fibroblasts and their activity against established biofilm in S. aureus.

Nizalapur, S, Kimyon, Ö, Biswas, NN, Gardner, CR, Griffith, R, Rice, SA, Manefield, M, Willcox, M, Black, DS & Kumar, N 2016, 'Design, synthesis and evaluation of N-aryl-glyoxamide derivatives as structurally novel bacterial quorum sensing inhibitors', Organic & Biomolecular Chemistry, vol. 14, no. 2, pp. 680-693.
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Bacteria cooperatively regulate the expression of many phenotypes through a mechanism called quorum sensing (QS).

Nizio, KD, Perrault, KA, Troobnikoff, AN, Ueland, M, Shoma, S, Iredell, JR, Middleton, PG & Forbes, SL 2016, 'In vitrovolatile organic compound profiling using GC×GC-TOFMS to differentiate bacteria associated with lung infections: a proof-of-concept study', Journal of Breath Research, vol. 10, no. 2, pp. 026008-026008.
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© 2016 IOP Publishing Ltd. Chronic pulmonary infections are the principal cause of morbidity and mortality in individuals with cystic fibrosis (CF). Due to the polymicrobial nature of these infections, the identification of the particular bacterial species responsible is an essential step in diagnosis and treatment. Current diagnostic procedures are time-consuming, and can also be expensive, invasive and unpleasant in the absence of spontaneously expectorated sputum. The development of a rapid, non-invasive methodology capable of diagnosing and monitoring early bacterial infection is desired. Future visions of real-time, in situ diagnosis via exhaled breath testing rely on the differentiation of bacteria based on their volatile metabolites. The objective of this proof-of-concept study was to investigate whether a range of CF-associated bacterial species (i.e. Pseudomonas aeruginosa, Burkholderia cenocepacia, Haemophilus influenzae, Stenotrophomonas maltophilia, Streptococcus pneumoniae and Streptococcus milleri) could be differentiated based on their in vitro volatile metabolomic profiles. Headspace samples were collected using solid phase microextraction (SPME), analyzed using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GCGC-TOFMS) and evaluated using principal component analysis (PCA) in order to assess the multivariate structure of the data. Although it was not possible to effectively differentiate all six bacteria using this method, the results revealed that the presence of a particular pattern of VOCs (rather than a single VOC biomarker) is necessary for bacterial species identification. The particular pattern of VOCs was found to be dependent upon the bacterial growth phase (e.g. logarithmic versus stationary) and sample storage conditions (e.g. short-term versus long-term storage at -18 °C). Future studies of CF-associated bacteria and exhaled breath condensate will benefit from the approaches presented in t...

Nolan, M, Iwaszuk, A, Lucid, AK, Carey, JJ & Fronzi, M 2016, 'ChemInform Abstract: Design of Novel Visible Light Active Photocatalyst Materials: Surface Modified TiO₂', ChemInform, vol. 47, no. 35.
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AbstractReview: 119 refs.

Nolan, M, Iwaszuk, A, Lucid, AK, Carey, JJ & Fronzi, M 2016, 'Design of Novel Visible Light Active Photocatalyst Materials: Surface Modified TiO₂', Advanced Materials, vol. 28, no. 27, pp. 5425-5446.
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Work on the design of new TiO2based photocatalysts is described. The key concept is the formation of composite structures through the modification of anatase and rutile TiO2with molecular‐sized nanoclusters of metal oxides. Density functional theory (DFT) level simulations are compared with experimental work synthesizing and characterizing surface modified TiO2. DFT calculations are used to show that nanoclusters of metal oxides such as TiO2, SnO/SnO2, PbO/PbO2, ZnO and CuO are stable when adsorbed at rutile and anatase surfaces, and can lead to a significant red shift in the absorption edge which will induce visible light absorption; this is the first requirement for a useful photocatalyst. The origin of the red shift and the fate of excited electrons and holes are determined. For p‐block metal oxides the oxidation state of Sn and Pb can be used to modify the magnitude of the red shift and its mechanism. Comparisons of recent experimental studies of surface modified TiO2that validate our DFT simulations are described. These nanocluster‐modified TiO2structures form the basis of a new class of photocatalysts which will be useful in oxidation reactions and with a correct choice of nanocluster modified can be applied to other reactions.

O Rourke, MB & Djordjevic, SP 2016, 'The Renaissance of Microbiology: The Necessary Future for Matrix Assisted Laser Desorption Ionisation Mass Spectrometry Based Bio Typing', Journal of Microbial & Biochemical Technology, vol. 8, no. 4, pp. 373-374.
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O’Connor, JJ, Lecchini, D, Beck, HJ, Cadiou, G, Lecellier, G, Booth, DJ & Nakamura, Y 2016, 'Sediment pollution impacts sensory ability and performance of settling coral-reef fish', Oecologia, vol. 180, no. 1, pp. 11-21.
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© 2015, Springer-Verlag Berlin Heidelberg. Marine organisms are under threat globally from a suite of anthropogenic sources, but the current emphasis on global climate change has deflected the focus from local impacts. While the effect of increased sedimentation on the settlement of coral species is well studied, little is known about the impact on larval fish. Here, the effect of a laterite “red soil” sediment pollutant on settlement behaviour and post-settlement performance of reef fish was tested. In aquarium tests that isolated sensory cues, we found significant olfaction-based avoidance behaviour and disruption of visual cue use in settlement-stage larval fish at 50 mg L−1, a concentration regularly exceeded in situ during rain events. In situ light trap catches showed lower abundance and species richness in the presence of red soil, but were not significantly different due to high variance in the data. Prolonged exposure to red soil produced altered olfactory cue responses, whereby fish in red soil made a likely maladaptive choice for dead coral compared to controls where fish chose live coral. Other significant effects of prolonged exposure included decreased feeding rates and body condition. These effects on fish larvae reared over 5 days occurred in the presence of a minor drop in pH and may be due to the chemical influence of the sediment. Our results show that sediment pollution of coral reefs may have more complex effects on the ability of larval fish to successfully locate suitable habitat than previously thought, as well as impacting on their post-settlement performance and, ultimately, recruitment success.

Obata, K, Miura, T, Yoshioka, H, Huete, A & Vargas, M 2016, 'Spectral Cross-Calibration of VIIRS Enhanced Vegetation Index with MODIS: A Case Study Using Year-Long Global Data', Remote Sensing, vol. 8, no. 1, pp. 34-34.
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In this study, the Visible Infrared Imaging Radiometer Suite (VIIRS) Enhanced Vegetation Index (EVI) was spectrally cross-calibrated with the Moderate Resolution Imaging Spectroradiometer (MODIS) EVI using a year-long, global VIIRS-MODIS dataset at the climate modeling grid (CMG) resolution of 0.05°-by-0.05°. Our cross-calibration approach was to utilize a MODIS-compatible VIIRS EVI equation derived in a previous study [Obata et al., J. Appl. Remote Sens., vol.7, 2013] and optimize the coefficients contained in this EVI equation for global conditions. The calibrated/optimized MODIS-compatible VIIRS EVI was evaluated using another global VIIRS-MODIS CMG dataset of which acquisition dates did not overlap with those used in the calibration. The calibrated VIIRS EVI showed much higher compatibility with the MODIS EVI than the original VIIRS EVI, where the mean error (MODIS minus VIIRS) and the root mean square error decreased from −0.021 to −0.003 EVI units and from 0.029 to 0.020 EVI units, respectively. Error reductions on the calibrated VIIRS EVI were observed across nearly all view zenith and relative azimuth angle ranges, EVI dynamic range, and land cover types. The performance of the MODIS-compatible VIIRS EVI calibration appeared limited for high EVI values (i.e., EVI > 0.5) due likely to the maturity of the VIIRS dataset used in calibration/optimization. The cross-calibration methodology introduced in this study is expected to be useful for other spectral indices such as the normalized difference vegetation index and two-band EVI.

Ormerod, KL, Wood, DLA, Lachner, N, Gellatly, SL, Daly, JN, Parsons, JD, Dal’Molin, CGO, Palfreyman, RW, Nielsen, LK, Cooper, MA, Morrison, M, Hansbro, PM & Hugenholtz, P 2016, 'Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals', Microbiome, vol. 4, no. 1.
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© 2016 The Author(s). Open Access. Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name 'Candidatus Homeothermaceae,' using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of 'Ca. Homeothermaceae' to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and a-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: 'Ca. Homeothermaceae' representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis. Keywords: Gut microbiome, S24-7, Homeothermaceae, Population genomes, Metagenomics, Comparative genomics.

O'Rourke, MB & Padula, MP 2016, 'Analysis of formalin-fixed, paraffin-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval', BIOTECHNIQUES, vol. 60, no. 5, pp. 229-+.
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© 2016, Eaton Publishing Company. All rights reserved. Since emerging in the late 19th century, formaldehyde fixation has become a standard method for preservation of tissues from clinical samples. The advantage of formaldehyde fixation is that fixed tissues can be stored at room temperature for decades without concern for degradation. This has led to the generation of huge tissue banks containing thousands of clinically significant samples. Here we review techniques for proteomic analysis of formalin-fixed, paraffin-embedded (FFPE) tissue samples with a specific focus on the methods used to extract and break formaldehyde crosslinks. We also discuss an error-of-interpretation associated with the technique known as “antigen retrieval.” We have discovered that this term has been mistakenly applied to two disparate molecular techniques; therefore, we argue that a terminology change is needed to ensure accurate reporting of experimental results. Finally, we suggest that more investigation is required to fully understand the process of formaldehyde fixation and its subsequent reversal.

Paine, MRL, Pianegonda, NA, Huynh, TT, Manefield, M, MacLaughlin, SA, Rice, SA, Barker, PJ & Blanksby, SJ 2016, 'Evaluation of hindered amine light stabilisers and their N-chlorinated derivatives as antibacterial and antifungal additives for thermoset surface coatings', Progress in Organic Coatings, vol. 99, pp. 330-336.
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Palasuwan, A, Palasuwan, D, Mahittikorn, A, Chiabchalard, R, Combes, V & Popruk, S 2016, 'Subtype Distribution of Blastocystis in Communities along the Chao Phraya River, Thailand', The Korean Journal of Parasitology, vol. 54, no. 4, pp. 455-460.
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Palee, J, Dheeranupattana, S, Wangkarn, S, Pyne, SG & Ung, AT 2016, 'Effects of chitosan and salicylic acid on stemona alkaloid production in hydroponic culture of stemona curtisii Hook. f.', Chiang Mai Journal of Science, vol. 43, no. 5, pp. 1070-1076.
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The objective of this study was to investigate the effects of the elicitors, salicylic acid (SA) and chitosan, on the improvement of Stemona alkaloid production in hydroponic cultures of S. curtisii. In vitro plantlets were used as plant materials. The elicitors were added into the culture medium and samples of the roots and medium were collected on week 2 and 4 after the elicitor addition and then analyzed for Stemona alkaloid production by high performance liquid chromatography (HPLC). This study revealed that both SA and chitosan increased production of three Stemona alkaloids and that chitosan is better than SA for the enhancement of the production of these alkaloids. The elicitation by 20 mg L-1 of chitosan for 4 weeks induced highest amount of oxyprotostemonine (274.31 μg g-1 DW) stemocurtisine (35.46 μg g-1 DW) and stemocurtisinol (99.48μg g-1 DW), which were 1.9, 2.0 and 1.5 fold higher than that of the control, respectively.

Panth, N, Paudel, KR & Karki, R 2016, 'Phytochemical profile and biological activity of Juglans regia', Journal of Integrative Medicine, vol. 14, no. 5, pp. 359-373.
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© 2016 Journal of Integrative Medicine Editorial Office. E-edition published by Elsevier (Singapore) Pte Ltd. All rights reserved. Juglans regia Linn. (Juglandaceae), popularly known as English or Persian walnut, is a valuable medicinal plant with a potency to cure various diseases in traditional medicine. Since ancient time, different local ethnic groups have used various part of J. regia for a wide array of ailments including helminthiasis, diarrhea, sinusitis, stomach ache, arthritis, asthma, eczema, scrofula, skin disorders, diabetes mellitus, anorexia, thyroid dysfunction, cancer and infectious diseases. Biological activities of J. regia have been reported in several peer review journals and scientific attention is increasing. The present review attempts to provide comprehensive information on plant description, ethnobotanical use, toxicity, phytochemical profile, pharmacology, clinical studies and current research prospective of the J. regia. Currently, there is an immense interest on isolation/identification of active constituents from walnut and screening those active compounds for pharmacological activities. In addition, researchers are performing clinical trials as well as screening various solvent extracts or fractions of J. regia in several animal diseases models to identify promising therapeutic benefits. In the present work, we review the latest information based on published scientific investigations of J. regia.

Panth, N, Paudel, KR & Parajuli, K 2016, 'Reactive Oxygen Species: A Key Hallmark of Cardiovascular Disease', Advances in Medicine, vol. 2016, pp. 1-12.
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Cardiovascular diseases (CVDs) have been the prime cause of mortality worldwide for decades. However, the underlying mechanism of their pathogenesis is not fully clear yet. It has been already established that reactive oxygen species (ROS) play a vital role in the progression of CVDs. ROS are chemically unstable reactive free radicals containing oxygen, normally produced by xanthine oxidase, nicotinamide adenine dinucleotide phosphate oxidase, lipoxygenases, or mitochondria or due to the uncoupling of nitric oxide synthase in vascular cells. When the equilibrium between production of free radicals and antioxidant capacity of human physiology gets altered due to several pathophysiological conditions, oxidative stress is induced, which in turn leads to tissue injury. This review focuses on pathways behind the production of ROS, its involvement in various intracellular signaling cascades leading to several cardiovascular disorders (endothelial dysfunction, ischemia-reperfusion, and atherosclerosis), methods for its detection, and therapeutic strategies for treatment of CVDs targeting the sources of ROS. The information generated by this review aims to provide updated insights into the understanding of the mechanisms behind cardiovascular complications mediated by ROS.

Parkinson, KL & Booth, DJ 2016, 'Rapid growth and short life spans characterize pipefish populations in vulnerable seagrass beds', Journal of Fish Biology, vol. 88, no. 5, pp. 1847-1855.
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The life‐history traits of two species of pipefish (Syngnathidae) from seagrass meadows in New South Wales, Australia, were examined to understand whether they enhance resilience to habitat degradation. The spotted pipefish Stigmatopora argus and wide‐bodied pipefish Stigmatopora nigra exhibit some of the shortest life spans known for vertebrates (longevity up to 150 days) and rapid maturity (male S. argus 35 days after hatching (DAH) and male S. nigra at 16–19 DAH), key characteristics of opportunistic species. Growth rates of both species were extremely rapid (up to 2 mm day−1), with seasonal and sex differences in growth rate. It is argued that short life spans and high growth rates may be advantageous for these species, which inhabit one of the most threatened marine ecosystems on earth.

Parumasivam, T, Chan, JGY, Pang, A, Quan, DH, Triccas, JA, Britton, WJ & Chan, HK 2016, 'In Vitro Evaluation of Inhalable Verapamil-Rifapentine Particles for Tuberculosis Therapy', Molecular Pharmaceutics, vol. 13, no. 3, pp. 979-989.
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Parumasivam, T, Chan, JGY, Pang, A, Quan, DH, Triccas, JA, Britton, WJ & Chan, HK 2016, 'In vitro evaluation of novel inhalable dry powders consisting of thioridazine and rifapentine for rapid tuberculosis treatment', European Journal of Pharmaceutics and Biopharmaceutics, vol. 107, pp. 205-214.
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Patel, BS, Rahman, MM, Rumzhum, NN, Oliver, BG, Verrills, NM & Ammit, AJ 2016, 'Theophylline Represses IL-8 Secretion from Airway Smooth Muscle Cells Independently of Phosphodiesterase Inhibition. Novel Role as a Protein Phosphatase 2A Activator', American Journal of Respiratory Cell and Molecular Biology, vol. 54, no. 6, pp. 792-801.
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Copyright © 2016 by the American Thoracic Society. Theophylline is an old drug experiencing a renaissance owing to its beneficial antiinflammatory effects in chronic respiratory diseases, such as asthma and chronic obstructive pulmonary disease. Multiple modes of antiinflammatory action have been reported, including inhibition of the enzymes that degrade cAMP-phosphodiesterase (PDE).Using primary cultures of airway smooth muscle (ASM) cells, we recently revealed that PDE4 inhibitors can potentiate the antiinflammatory action of β2-agonists by augmenting cAMP-dependent expression of the phosphatase that deactivates mitogen-activated protein kinase (MAPK)-MAPK phosphatase (MKP)-1. Therefore, the aim of this study was to address whether theophylline repressed cytokine production in a similar, PDE-dependent, MKP-1-mediated manner. Notably, theophylline did not potentiate cAMP release from ASM cells treated with the long-acting β2-agonist formoterol. Moreover, theophylline (0.1-10 mM) did not increase formoterol-induced MKP-1 messenger RNA expression nor protein up-regulation, consistent with the lack of cAMP generation. However, theophylline (at 10 mM) was antiinflammatory and repressed secretion of the neutrophil chemoattractant cytokine IL-8, which is produced in response to TNF-α. Because theophylline's effectswere independent of PDE4 inhibition or antiinflammatory MKP-1, we then wished to elucidate the novel mechanisms responsible. We investigated the impact of theophylline on protein phosphatase (PP) 2A, a master controller of multiple inflammatory signaling pathways, and show that theophylline increases TNF-α-induced PP2A activity in ASM cells. Confirmatory results were obtained in A549 lung epithelial cells. PP2A activators have beneficial effects in ex vivo and in vivo models of respiratory disease. Thus, our study is the first to link theophylline with PP2A activation as a novel mechanism to control respiratory inflammation.

Paudel, KR, Karki, R & Kim, D-W 2016, 'Cepharanthine inhibits in vitro VSMC proliferation and migration and vascular inflammatory responses mediated by RAW264.7', Toxicology in Vitro, vol. 34, pp. 16-25.
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© 2015 Elsevier B.V. Pathogenesis of atherosclerosis involves vascular smooth muscle cell (VSMC) migration and proliferation followed by an inflammation mediated by activated macrophages in the tunica intima of blood vessels. Cepharanthine (CEP) belongs to bisbenzylisoquinoline alkaloids found in the plant Stephania cepharantha, which has been used for various diseases like cancer, alopecia areata, venomous snakebites, and malaria. In this study, we investigated whether CEP suppresses VSMC migration and proliferation and inhibits inflammatory mediator production in macrophage (RAW264.7). Our results showed that CEP possessed significant DPPH scavenging and metal chelating activities. It also markedly inhibited lipid peroxidation. Similarly, CEP suppressed the nitric oxide (NO) production and expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX-2) in RAW264.7 cells. Moreover, the level of prostaglandin E2 was also suppressed and the formation of macrophage derived foam cell was attenuated in RAW264.7 cells. Likewise, NO production in isolated peritoneal macrophage and VSMC migration in response to LPS stimulated RAW264.7 was also halted by CEP treatment. Also, VSMC migration induced by platelet-derived growth factor (PDGF-BB) was inhibited by CEP dose dependently. The anti-migratory effect of CEP on VSMCs was due to its inhibitory effect on metalloproteinase-9 (MMP-9) expression, preventing the degradation of extracellular matrix (ECM) component. Furthermore, CEP suppressed PDGF-BB induced VSMC proliferation by down-regulation of mitogen activated protein kinase (MAPK) signaling molecules. CEP also inhibited the translocation of NF-κB from cytosol to nucleus. Thus, our results suggest that CEP exerts potent anti-atherosclerotic effect through attenuation of inflammation, lipid peroxidation and VSMC migration and proliferation.

Paudel, KR, Lee, U-W & Kim, D-W 2016, 'Chungtaejeon, a Korean fermented tea, prevents the risk of atherosclerosis in rats fed a high-fat atherogenic diet', Journal of Integrative Medicine, vol. 14, no. 2, pp. 134-142.
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© 2016 Journal of Integrative Medicine Editorial Office. Objective Hypercholesterolemia is one of the well-established risk factors for cardiovascular mortality and morbidity in coronary heart disease. The aim of this study was to investigate the anti-atherogenic effect of Chungtaejeon (CTJ, a Korean fermented tea) aqueous extract on proliferation and migration of human aortic smooth muscle cells (HASMCs) in vivo and in vitro. Methods The authors used high-fat atherogenic diet (HFAD) to induce hyperlipidemia in Wistar rats in in vivo animal experiments and used HASMCs for in vitro cell experiments. For the in vitro cell experiment, the proliferation of asms was evaluated using the MTT assay. Similarly, the expression of matrix metalloproteinases (MMPs) in HASMCs was measured using gelatin zymography. Antimigratory activity of CTJ was revealed using the wound-healing model and Boyden's chamber assay. In the in vivo experiment, CTJ was administered in three different doses for 20 d from the initiation of the HFAD. After 20 d, the serum lipid profile and total lipid contents in liver were measured. Results Treatment with CTJ for 24 h dose-dependently inhibited the proliferation and migration of HASMCs and expression of MMP-2 in HASMCs. The oral administration of CTJ at concentrations of 200 and 400 mg/kg decreased the levels of low-density lipoprotein cholesterol, total serum cholesterol and hepatic cholesterol of HFAD-fed rats. Conclusion CTJ possessed strong antiproliferative, antimigratory, as well as lipid-lowering activities. Thus, CTJ can be considered as a therapeutic option in the treatment of high-fat diet-induced atherosclerosis.

Paudel, KR, Panth, N & Kim, D-W 2016, 'Circulating Endothelial Microparticles: A Key Hallmark of Atherosclerosis Progression', Scientifica, vol. 2016, pp. 1-9.
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The levels of circulating microparticles (MPs) are raised in various cardiovascular diseases. Their increased level in plasma is regarded as a biomarker of alteration in vascular function. The prominent MPs present in blood are endothelial microparticles (EMPs) described as complex submicron (0.1 to 1.0 μm) vesicles like structure, released in response to endothelium cell activation or apoptosis. EMPs possess both physiological and pathological effects and may promote oxidative stress and vascular inflammation. EMPs release is triggered by inducer like angiotensin II, lipopolysaccharide, and hydrogen peroxide leading to the progression of atherosclerosis. However, there are multiple physiological pathways for EMPs generation like NADPH oxidase derived endothelial ROS formation, Rho kinase pathway, and mitogen-activated protein kinases. Endothelial dysfunction is a key initiating event in atherosclerotic plaque formation. Atheroemboli, resulting from ruptured carotid plaques, is a major cause of stroke. Increasing evidence suggests that EMPs play an important role in the pathogenesis of cardiovascular disease, acting as a marker of damage, either exacerbating disease progression or triggering a repair response. In this regard, it has been suggested that EMPs have the potential to act as biomarkers of disease status. This review aims to provide updated information of EMPs in relation to atherosclerosis pathogenesis.

Paul, B, Hare, DJ, Bishop, DP, Paton, C, Nguyen, VT, Cole, N, Niedwiecki, MM, Andreozzi, E, Vais, A, Billings, JL, Bray, L, Bush, AI, McColl, G, Roberts, BR, Adlard, PA, Finkelstein, DI, Hellstrom, J, Hergt, JM, Woodhead, JD & Doble, PA 2016, 'Correction: Visualising mouse neuroanatomy and function by metal distribution using laser ablation-inductively coupled plasma-mass spectrometry imaging', Chemical Science, vol. 7, no. 10, pp. 6576-6576.
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Correction for ‘Visualising mouse neuroanatomy and function by metal distribution using laser ablation-inductively coupled plasma-mass spectrometry imaging’ by Bence Paul et al., Chem. Sci., 2015, 6, 5383–5393.

Pauszek, SJ, Eschbaumer, M, Brito, B, de Carvalho Ferreira, HC, Vu, LT, Phuong, NT, Hoang, BH, Tho, ND, Dong, PV, Minh, PQ, Long, NT, Dung, DH, Rodriguez, LL & Arzt, J 2016, 'Site-specific substitution (Q172R) in the VP1 protein of FMDV isolates collected from asymptomatic carrier ruminants in Vietnam', Virology Reports, vol. 6, pp. 90-96.
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© 2016 The epidemiological significance of asymptomatic persistent foot-and-mouth disease virus (FMDV) infection in carrier animals, specifically its ability to seed new clinical outbreaks, is undetermined, and consistent viral determinants of FMDV persistence have not been identified. We analyzed 114 FMDV O/ME-SA/PanAsia VP1 sequences from naturally infected animals in Vietnam, of which 31 were obtained from persistently infected carrier animals. A site-specific substitution was identified at VP1 residue 172 where arginine was present in all 31 of the carrier-associated viruses, whereas outbreak viruses typically contained glutamine. Additionally, we characterized multiple viruses from a single persistently infected animal that were collected over the course of eight months and at multiple distinct anatomic sites (larynx, dorsal soft palate and dorsal nasopharynx). This work sheds new light on naturally occurring viral mutations within the host and provides a basis for understanding the viral evolution and persistence mechanisms of FMDV.

Peng, D, Wu, C, Zhang, B, Huete, A, Zhang, X, Sun, R, Lei, L, Huang, W, Liu, L, Liu, X, Li, J, Luo, S & Fang, B 2016, 'The Influences of Drought and Land-Cover Conversion on Inter-Annual Variation of NPP in the Three-North Shelterbelt Program Zone of China Based on MODIS Data', PLOS ONE, vol. 11, no. 6, pp. e0158173-e0158173.
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© 2016, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Terrestrial ecosystems greatly contribute to carbon (C) emission reduction targets through photosynthetic C uptake.Net primary production (NPP) represents the amount of atmospheric C fixed by plants and accumulated as biomass. The Three-North Shelterbelt Program (TNSP) zone accounts for more than 40% of China's landmass. This zone has been the scene of several large-scale ecological restoration efforts since the late 1990s, and has witnessed significant changes in climate and human activities.Assessing the relative roles of different causal factors on NPP variability in TNSP zone is very important for establishing reasonable local policies to realize the emission reduction targets for central government. In this study, we examined the relative roles of drought and land cover conversion(LCC) on inter-annual changes of TNSP zone for 2001-2010. We applied integrated correlation and decomposition analyses to a Standardized Evapotranspiration Index (SPEI) and MODIS land cover dataset. Our results show that the 10-year average NPP within this region was about 420 Tg C. We found that about 60% of total annual NPP over the study area was significantly correlated with SPEI (p<0.05). The LCC-NPP relationship, which is especially evident for forests in the south-central area, indicates that ecological programs have a positive impact on C sequestration in the TNSP zone. Decomposition analysis generally indicated that the contributions of LCC, drought, and other Natural or Anthropogenic activities (ONA) to changes in NPP generally had a consistent distribution pattern for consecutive years. Drought and ONA contributed about 74% and 23% to the tota...

Perkins, G, Khatib, O, Peterson, M, Kallinen, A, Pham, T, Ung, A, Greguric, I & Pascali, G 2016, 'Microfluidic Implementation of Ru-Catalyzed Methylation of Amines Using CO2 as Carbon Source', Journal of Flow Chemistry, vol. 6, no. 4, pp. 302-308.
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Carbon dioxide chemistry is an area of continuing growth in recent times, due to socioeconomic and environmental reasons. Several methods have now been reported for obtaining N-methylation on primary and secondary amines directly from CO2. We have translated in two microfluidic setups (Slug Flow [SF] and Tube-in-Tube [TiT]) a ruthenium (Ru)-catalyzed process previously reported using a pressure vessel. Here, we demonstrate how the SF approach is more efficient but requires more input to reach a steady state, while the TiT system is less efficient but more tuneable.We have tested these processes on three model amines and two radiopharmaceutical precursors that are routinely used in 11C chemistry. The microfluidic processes tested are also potentially more efficient than the pressure vessel counterpart, in terms of amount of Ru catalyst needed (1% vs. 10%) and projected reaction completion time.

Pernice, M, Sinutok, S, Sablok, G, Commault, AS, Schliep, M, Macreadie, PI, Rasheed, MA & Ralph, PJ 2016, 'Molecular physiology reveals ammonium uptake and related gene expression in the seagrass Zostera muelleri', Marine Environmental Research, vol. 122, pp. 126-134.
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© 2016 Elsevier Ltd Seagrasses are important marine foundation species, which are presently threatened by coastal development and global change worldwide. The molecular mechanisms that drive seagrass responses to anthropogenic stresses, including elevated levels of nutrients such as ammonium, remains poorly understood. Despite the evidence that seagrasses can assimilate ammonium by using glutamine synthetase (GS)/glutamate synthase (glutamine-oxoglutarate amidotransferase or GOGAT) cycle, the regulation of this fundamental metabolic pathway has never been studied at the gene expression level in seagrasses so far. Here, we combine (i) reverse transcription quantitative real-time PCR (RT-qPCR) to measure expression of key genes involved in the GS/GOGAT cycle, and (ii) stable isotope labelling and mass spectrometry to investigate 15N-ammonium assimilation in the widespread Australian species Zostera muelleri subsp. capricorni (Z. muelleri). We demonstrate that exposure to a pulse of ammonium in seawater can induce changes in GS gene expression of Z. muelleri, and further correlate these changes in gene expression with 15N-ammonium uptake rate in above- and below-ground tissue.

Petersen, AC, Oneal, DC, Seibel, JR, Poel, K, Daum, CL, Djordjevic, SP & Minion, FC 2016, 'Cross reactivity among the swine mycoplasmas as identified by protein microarray', Veterinary Microbiology, vol. 192, pp. 204-212.
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© 2016 Elsevier B.V. Mycoplasmas are cell wall-less bacteria that infect a variety of animals in a species-specific manner. In swine, Mycoplasma hyopneumoniae is the most virulent and presents the most disease and economic problems to the swine industry. Serological assays are commonly used to assess colonization and disease, but antigenic cross-reactivity between M. hyopneumoniae and other mycoplasma species, most notably Mycoplasma hyorhinis, Mycoplasma hyosynoviae and Mycoplasma flocculare, is a concern. The extent of cross-reactivity has not been thoroughly investigated. These studies were designed to identify M. hyopneumoniae proteins that are recognized by rabbit hyperimmune sera raised against the other swine mycoplasmas. Our results indicate extensive cross-reactivity between M. flocculare and M. hyopneumoniae, which explains previous reports seen with ELISA assays. Only three of the thirty-nine M. hyopneumoniae proteins tested showed no cross reactivity with the other three swine mycoplasmas, mhp182 (42 kDa C-terminal fragment), mhp638 and mhp684 (C-terminal fragment). Two proteins, mhp384 and mhp511, were cross-reactive with hyperimmune sera generated against three of the four species. None of the anti-M. hyorhinis hyperimmune sera reacted to any of the M. hyopneumoniae proteins. These results suggest that inapparent M. flocculare infections could produce positive responses in M. hyopneumoniae serological assays due to cross-reactivity, and that M. hyosynoviae infections are less likely to do so and M. hyorhinis infections unlikely to affect assay results.

Petrou, K, Kranz, SA, Trimborn, S, Hassler, CS, Ameijeiras, SB, Sackett, O, Ralph, PJ & Davidson, AT 2016, 'Southern Ocean phytoplankton physiology in a changing climate', JOURNAL OF PLANT PHYSIOLOGY, vol. 203, pp. 135-150.
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© 2016 Elsevier GmbH The Southern Ocean (SO) is a major sink for anthropogenic atmospheric carbon dioxide (CO2), potentially harbouring even greater potential for additional sequestration of CO2 through enhanced phytoplankton productivity. In the SO, primary productivity is primarily driven by bottom up processes (physical and chemical conditions) which are spatially and temporally heterogeneous. Due to a paucity of trace metals (such as iron) and high variability in light, much of the SO is characterised by an ecological paradox of high macronutrient concentrations yet uncharacteristically low chlorophyll concentrations. It is expected that with increased anthropogenic CO2 emissions and the coincident warming, the major physical and chemical process that govern the SO will alter, influencing the biological capacity and functioning of the ecosystem. This review focuses on the SO primary producers and the bottom up processes that underpin their health and productivity. It looks at the major physico-chemical drivers of change in the SO, and based on current physiological knowledge, explores how these changes will likely manifest in phytoplankton, specifically, what are the physiological changes and floristic shifts that are likely to ensue and how this may translate into changes in the carbon sink capacity, net primary productivity and functionality of the SO.

Phetsang, W, Pelingon, R, Butler, MS, KC, S, Pitt, ME, Kaeslin, G, Cooper, MA & Blaskovich, MAT 2016, 'Fluorescent Trimethoprim Conjugate Probes To Assess Drug Accumulation in Wild Type and Mutant Escherichia coli', ACS Infectious Diseases, vol. 2, no. 10, pp. 688-701.
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Philp, M, Shimmon, R, Tahtouh, M & Fu, S 2016, 'Development and validation of a presumptive color spot test method for the detection of synthetic cathinones in seized illicit materials', Forensic Chemistry, vol. 1, pp. 39-50.
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Phong, VHN, Koottatep, T, Chapagain, SK, Panuvatvanich, A, Polprasert, C & Ahn, K-H 2016, 'Removal of acetaminophen from wastewater by constructed wetlands with Scirpus validus', Environmental Engineering Research, vol. 21, no. 2, pp. 164-170.
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Platt, ERM, Fowler, AM & Ord, TJ 2016, 'Land colonisation by fish is associated with predictable changes in life history', Oecologia, vol. 181, no. 3, pp. 769-781.
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© 2016 Springer-Verlag Berlin Heidelberg The colonisation of new environments is a central evolutionary process, yet why species make such transitions often remains unknown because of the difficulty in empirically investigating potential mechanisms. The most likely explanation for transitions to new environments is that doing so conveys survival benefits, either in the form of an ecological release or new ecological opportunity. Life history theory makes explicit predictions about how traits linked to survival and reproduction should change with shifts in age-specific mortality. We used these predictions to examine whether a current colonisation of land by fishes might convey survival benefits. We found that blenny species with more terrestrial lifestyles exhibited faster reproductive development and slower growth rates than species with more marine lifestyles; a life history trade off that is consistent with the hypothesis that mortality has become reduced in younger life stages on land. A plausible explanation for such a shift is that an ecological release or opportunity on land has conveyed survival benefits relative to the ancestral marine environment. More generally, our study illustrates how life history theory can be leveraged in novel ways to formulate testable predictions on why organisms might make transitions into novel environments.

Pokharel, D, Padula, M, Lu, J, Jaiswal, R, Djordjevic, S & Bebawy, M 2016, 'The Role of CD44 and ERM Proteins in Expression and Functionality of P-glycoprotein in Breast Cancer Cells', Molecules, vol. 21, no. 3, pp. 290-290.
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Multidrug resistance (MDR) is often attributed to the over-expression of P-glycoprotein (P-gp), which prevents the accumulation of anticancer drugs within cells by virtue of its active drug efflux capacity. We have previously described the intercellular transfer of P-gp via extracellular vesicles (EVs) and proposed the involvement of a unique protein complex in regulating this process. In this paper, we investigate the role of these mediators in the regulation of P-gp functionality and hence the acquisition of MDR following cell to cell transfer. By sequentially silencing the FERM domain-binding proteins, Ezrin, Radixin and Moesin (ERM), as well as CD44, which we also report a selective packaging in breast cancer derived EVs, we have established a role for these proteins, in particular Radixin and CD44, in influencing the P-gp-mediated MDR in whole cells. We also report for the first time the role of ERM proteins in the vesicular transfer of functional P-gp. Specifically, we demonstrate that intercellular membrane insertion is dependent on Ezrin and Moesin, whilst P-gp functionality is governed by the integrity of all ERM proteins in the recipient cell. This study identifies these candidate proteins as potential new therapeutic targets in circumventing MDR clinically.

Popic, TJ, Davila, YC & Wardle, GM 2016, 'Cheater or mutualist? Novel florivory interaction between nectar-rich Crotalaria cunninghamii and small mammals', AUSTRAL ECOLOGY, vol. 41, no. 4, pp. 390-398.
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© 2016 Ecological Society of Australia. Animals visit flowers to access resources and by moving pollen to conspecific individuals act as pollinators. While biotic pollinators can increase the seed set of plants, other flower visitors can reduce seed set directly by damaging vital reproductive organs and indirectly by affecting the way the plant interacts with subsequent flower visitors. It is, therefore, vital to understand the varied effects of all visitors and not only pollinators on plant fitness, including those visitors that are temporally or spatially rare. We document the first known case of flower visitation by small mammals to Crotalaria cunninghamii (Fabaceae), a plant species morphologically suited to bird pollination. During a rain-driven resource pulse in the Simpson Desert in 2011, the rodents Mus musculus (Muridae) and Pseudomys hermannsburgensis (Muridae) visited flowers to remove nectar by puncturing the calyx. We investigated the effects of this novel interaction on the reproductive output of C.cunninghamii. Compared with another recent resource pulse in 2007, plants flowering during mammal visitation had five times as many inflorescences per plant, 90% more flowers per inflorescence, and two to three times more nectar per flower, but this nectar was 30% less sugar rich. Concurrently, rodent plagues were up to three times larger during this rain-driven resource pulse than during a previous pulse in 2007. Up to 75% of flowers had evidence of small mammal florivory, but this was not necessarily destructive, as up to 90% of fruit had the remains of florivory. Through a series of exclusion experiments, we found that small mammal florivory did not directly reduce seed set. We conclude that rain-driven resource pulses led to a unique combination of events that facilitated the novel florivory interaction. Our findings emphasize the dynamic nature of biotic interactions and the importance of testing the role of all visitors to pollination services.

Porojan, C, Mitrovic, SM, Yeo, DCJ & Furey, A 2016, 'Overview of the potent cyanobacterial neurotoxin β-methylamino-L-alanine (BMAA) and its analytical determination', Food Additives & Contaminants: Part A, vol. 33, no. 10, pp. 1570-1586.
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Portbury, SD, Hare, DJ, Sgambelloni, C, Finkelstein, DI & Adlard, PA 2016, 'A time-course analysis of changes in cerebral metal levels following a controlled cortical impact', Metallomics, vol. 8, no. 2, pp. 193-200.
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A LA-ICP-MS time course study of changing metal concentrations following traumatic brain injury in mice.

Potgieter, CJ, Wei, R, Kipnis, V, Freedman, LS & Carroll, RJ 2016, 'Moment Reconstruction and Moment-Adjusted Imputation When Exposure Is Generated by a Complex, Nonlinear Random Effects Modeling Process', Biometrics, vol. 72, no. 4, pp. 1369-1377.
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Summary For the classical, homoscedastic measurement error model, moment reconstruction (Freedman et al., 2004, 2008) and moment-adjusted imputation (Thomas et al., 2011) are appealing, computationally simple imputation-like methods for general model fitting. Like classical regression calibration, the idea is to replace the unobserved variable subject to measurement error with a proxy that can be used in a variety of analyses. Moment reconstruction and moment-adjusted imputation differ from regression calibration in that they attempt to match multiple features of the latent variable, and also to match some of the latent variable's relationships with the response and additional covariates. In this note, we consider a problem where true exposure is generated by a complex, nonlinear random effects modeling process, and develop analogues of moment reconstruction and moment-adjusted imputation for this case. This general model includes classical measurement errors, Berkson measurement errors, mixtures of Berkson and classical errors and problems that are not measurement error problems, but also cases where the data-generating process for true exposure is a complex, nonlinear random effects modeling process. The methods are illustrated using the National Institutes of Health–AARP Diet and Health Study where the latent variable is a dietary pattern score called the Healthy Eating Index-2005. We also show how our general model includes methods used in radiation epidemiology as a special case. Simulations are used to illustrate the methods.

Poulos, DE, Gallen, C, Davis, T, Booth, DJ & Harasti, D 2016, 'Distribution and spatial modelling of a soft coral habitat in the Port Stephens–Great Lakes Marine Park: implications for management', Marine and Freshwater Research, vol. 67, no. 2, pp. 256-256.
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Habitat mapping is a useful method for understanding the complex spatial relationships that exist in the marine environment, and is used to evaluate the effectiveness of management strategies, particularly in regards to marine protected areas. This study explored the observed and predicted distribution of an uncommon soft coral species, Dendronephthya australis within the Port Stephens–Great Lakes Marine Park. Dendronephthya australis was mapped by video operated by a SCUBA diver towing a time synchronised GPS. A species distribution model was created to explore the possible occurrence of D. australis outside of the mapped area, using four environmental parameters: bathymetry, slope of seabed, velocity of tidal currents, and distance from estuary mouth. Dendronephthya australis colonies occurred along the southern shoreline in the Port Stephens estuary between Fly Point and Corlette Point, but no colonies were found within sanctuary (no-take) zones within the marine park. The model illustrated limited habitat suitability for D. australis within a larger section of the estuary, suggesting this species has specific environmental requirements survival. Owing to its current threats (anchor damage and fishing line entanglement), implications from these findings will assist future management and protection decisions, particularly in regard to its protection within a marine park.

Pouwels, SD, Hesse, L, Faiz, A, Lubbers, J, Bodha, PK, ten Hacken, NHT, van Oosterhout, AJM, Nawijn, MC & Heijink, IH 2016, 'Susceptibility for cigarette smoke-induced DAMP release and DAMP-induced inflammation in COPD', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 311, no. 5, pp. L881-L892.
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Cigarette smoke (CS) exposure is a major risk factor for chronic obstructive pulmonary disease (COPD). We investigated whether CS-induced damage-associated molecular pattern (DAMP) release or DAMP-mediated inflammation contributes to susceptibility for COPD. Samples, including bronchial brushings, were collected from young and old individuals, susceptible and nonsusceptible for the development of COPD, before and after smoking, and used for gene profiling and airway epithelial cell (AEC) culture. AECs were exposed to CS extract (CSE) or specific DAMPs. BALB/cByJ and DBA/2J mice were intranasally exposed to LL-37 and mitochondrial (mt)DAMPs. Functional gene-set enrichment analysis showed that CS significantly increases the airway epithelial gene expression of DAMPs and DAMP receptors in COPD patients. In cultured AECs, we observed that CSE induces necrosis and DAMP release, with specifically higher galectin-3 release from COPD-derived compared with control-derived cells. Galectin-3, LL-37, and mtDAMPs increased CXCL8 secretion in AECs. LL-37 and mtDAMPs induced neutrophilic airway inflammation, exclusively in mice susceptible for CS-induced airway inflammation. Collectively, we show that in airway epithelium from COPD patients, the CS-induced expression of DAMPs and DAMP receptors in vivo and the release of galectin-3 in vitro is exaggerated. Furthermore, our studies indicate that a predisposition to release DAMPs and subsequent induction of inflammation may contribute to the development of COPD.

Powell, KL, Stevens, V, Upton, DH, McCracken, SA, Simpson, AM, Cheng, Y, Tasevski, V, Morris, JM & Ashton, AW 2016, 'Role for the thromboxane A2 receptor β-isoform in the pathogenesis of intrauterine growth restriction', Scientific Reports, vol. 6, no. 1, pp. 1-15.
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AbstractIntrauterine growth restriction (IUGR) is a pathology of pregnancy that results in failure of the fetus to reach its genetically determined growth potential. In developed nations the most common cause of IUGR is impaired placentation resulting from poor trophoblast function, which reduces blood flow to the fetoplacental unit, promotes hypoxia and enhances production of bioactive lipids (TXA2 and isoprostanes) which act through the thromboxane receptor (TP). TP activation has been implicated as a pathogenic factor in pregnancy complications, including IUGR; however, the role of TP isoforms during pregnancy is poorly defined. We have determined that expression of the human-specific isoform of TP (TPβ) is increased in placentae from IUGR pregnancies, compared to healthy pregnancies. Overexpression of TPα enhanced trophoblast proliferation and syncytialisation. Conversely, TPβ attenuated these functions and inhibited migration. Expression of the TPβ transgene in mice resulted in growth restricted pups and placentae with poor syncytialisation and diminished growth characteristics. Together our data indicate that expression of TPα mediates normal placentation; however, TPβ impairs placentation and promotes the development of IUGR and represents an underappreciated pathogenic factor in humans.

Prabhala, P, Bunge, K, Ge, Q & Ammit, AJ 2016, 'Corticosteroid‐Induced MKP‐1 Represses Pro‐Inflammatory Cytokine Secretion by Enhancing Activity of Tristetraprolin (TTP) in ASM Cells', Journal of Cellular Physiology, vol. 231, no. 10, pp. 2153-2158.
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Exaggerated cytokine secretion drives pathogenesis of a number of chronic inflammatory diseases, including asthma. Anti‐inflammatory pharmacotherapies, including corticosteroids, are front‐line therapies and although they have proven clinical utility, the molecular mechanisms responsible for their actions are not fully understood. The corticosteroid‐inducible gene, mitogen‐activated protein kinase (MAPK) phosphatase 1 (MKP‐1, DUSP1) has emerged as a key molecule responsible for the repressive effects of steroids. MKP‐1 is known to deactivate p38 MAPK phosphorylation and can control the expression and activity of the mRNA destabilizing protein—tristetraprolin (TTP). But whether corticosteroid‐induced MKP‐1 acts via p38 MAPK‐mediated modulation of TTP function in a pivotal airway cell type, airway smooth muscle (ASM), was unknown. While pretreatment of ASM cells with the corticosteroid dexamethasone (preventative protocol) is known to reduce ASM synthetic function in vitro, the impact of adding dexamethasone after stimulation (therapeutic protocol) had not been explored. Whether dexamethasone modulates TTP in a p38 MAPK‐dependent manner in this cell type was also unknown. We address this herein and utilize an in vitro model of asthmatic inflammation where ASM cells were stimulated with the pro‐asthmatic cytokine tumor necrosis factor (TNF) and the impact of adding dexamethasone 1 h after stimulation assessed. IL‐6 mRNA expression and protein secretion was significantly repressed by dexamethasone acting in a temporally distinct manner to increase MKP‐1, deactivate p38 MAPK, and modulate TTP phosphorylation status. In this way, dexamethasone‐induced MKP‐1 acts via p38 MAPK to switch on the mRNA destabilizing function of TTP to repress pro‐inflammatory cytokine secretion from ASM cells. J. Cell. Physiol. 231: 2153–2158, 2016. © 2016 Wiley Periodicals, Inc.

Proctor, AKK, Ball, M, Freeman, P, Jenkins, C & Bogema, DR 2016, 'Prevalence of Theileria orientalis types in beef cattle herds on the North Coast of New South Wales', AUSTRALIAN VETERINARY JOURNAL, vol. 94, no. 4, pp. 117-120.
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© 2016 Australian Veterinary Association. Objective: To estimate the prevalence of Theileria orientalis infection for Chitose, Ikeda and Buffeli major piroplasm surface protein (MPSP) types at a herd- and animal-level in beef cattle in the North Coast Livestock Health and Pest Authority (NCLHPA) region of New South Wales (NSW). Methods: A total of 24 beef herds in the NCLHPA region containing more than 100 cattle were randomly selected. Blood samples were collected from five animals per herd and tested using Theileria PCR for Chitose, Buffeli and Ikeda. Samples were only taken from female cattle older than 2 years, born in the NCLHPA region and apparently healthy at the time of testing. Results: The herd-level prevalence for all MPSP types (Chitose, Ikeda and Buffeli) was 100%, with a 95% confidence interval of 86.3-99.9%. The mean prevalence at an animal level was 83.3%, 92.5% and 95.0% for Theileria Chitose, Buffeli and Ikeda, respectively. Quantitative PCR testing showed that 81.9% of animals had a low-level infection, while 17.0% had a moderate level of infection, and only 1.0% had a high level of infection. The majority of animals had a mixed infection of two or three MPSP types and few animals showed single infection. Conclusion: The results indicate endemicity of T. orientalis, especially the Ikeda type, in the NCLHPA region of Australia.

Qin, M, Brown, J, Padmadas, SS, Bohua, L, Jianan, Q & Falkingham, J 2016, 'Gender Inequalities in Employment and Wage-earning among Economic Migrants in Chinese Cities', Demographic Research, vol. 34, no. 6, pp. 175-202.
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© 2016 Min Qin et al. BACKGROUND: Recent trends show an unprecedented feminisation of migration in China, triggered by the increasing demand for cheap labour in big cities and the availability of women in the labour market. These trends corroborate the evidence that non-agricultural work and remittance from urban labour migrants have become the major sources of rural household income. OBJECTIVE: This paper investigates the extent of gender inequalities in job participation and wage earning among internal labour migrants in China. We hypothesize that female migrants in cities are economically more disadvantaged than male migrants in the job market. METHODS: We use data from the 2010 National Migrant Dynamics Monitoring Survey conducted in 106 cities representing all 31 provinces and geographic regions. The study applies the standard Heckman two-step Probit-OLS method to model job participation and wage- earning, separately for 59,225 males and 41,546 females aged 16-59 years, adjusting for demographic and social characteristics and potential selection effects. RESULTS: Female migrants have much lower job-participation and wage-earning potential than male migrants. Male migrants earn 26% higher hourly wages than their female counterparts. Decomposition analysis confirms potential gender discrimination, suggesting that 88% of the gender difference in wages (or 12% of female migrant wage) is due to discriminatory treatment of female migrants in the Chinese job market. Migrants with rural hukou status have a smaller chance of participation in the job market and they earn lower wages than those with urban hukou, regardless of education advantage. CONCLUSIONS: There is evidence of significant female disadvantage among internal labour migrants in the job market in Chinese cities. Household registration by urban and rural areas, as controlled by the hukou status, partly explains the differing job participation and wage earning among female labour migrants in urban China.

R. Marcelino, V, Cremen, MCM, Jackson, CJ, Larkum, AAW & Verbruggen, H 2016, 'Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii', Genome Biology and Evolution, vol. 8, no. 9, pp. 2939-2951.
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Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

Rahman, MM, Prabhala, P, Rumzhum, NN, Patel, BS, Wickop, T, Hansbro, PM, Verrills, NM & Ammit, AJ 2016, 'TLR2 ligation induces corticosteroid insensitivity in A549 lung epithelial cells: Anti-inflammatory impact of PP2A activators', The International Journal of Biochemistry & Cell Biology, vol. 78, pp. 279-287.
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© 2016 Elsevier Ltd Corticosteroids are effective anti-inflammatory therapies widely utilized in chronic respiratory diseases. But these medicines can lose their efficacy during respiratory infection resulting in disease exacerbation. Further in vitro research is required to understand how infection worsens lung function control in order to advance therapeutic options to treat infectious exacerbation in the future. In this study, we utilize a cellular model of bacterial exacerbation where we pretreat A549 lung epithelial cells with the synthetic bacterial lipoprotein Pam3CSK4 (a TLR2 ligand) to mimic bacterial infection and tumor necrosis factor α (TNFα) to simulate inflammation. Under these conditions, Pam3CSK4 induces corticosteroid insensitivity; demonstrated by substantially reduced ability of the corticosteroid dexamethasone to repress TNFα-induced interleukin 6 secretion. We then explored the molecular mechanism responsible and found that corticosteroid insensitivity induced by bacterial mimics was not due to altered translocation of the glucocorticoid receptor into the nucleus, nor an impact on the NF-κB pathway. Moreover, Pam3CSK4 did not affect corticosteroid-induced upregulation of anti-inflammatory MAPK deactivating phosphatase—MKP-1. However, Pam3CSK4 can induce oxidative stress and we show that a proportion of the MKP-1 produced in response to corticosteroid in the context of TLR2 ligation was rendered inactive by oxidation. Thus to combat inflammation in the context of bacterial exacerbation we sought to discover effective strategies that bypassed this road-block. We show for the first time that known (FTY720) and novel (theophylline) activators of the phosphatase PP2A can serve as non-steroidal anti-inflammatory alternatives and/or corticosteroid-sparing approaches in respiratory inflammation where corticosteroid insensitivity exists.

Rahman, MM, Prünte, L, Lebender, LF, Patel, BS, Gelissen, I, Hansbro, PM, Morris, JC, Clark, AR, Verrills, NM & Ammit, AJ 2016, 'The phosphorylated form of FTY720 activates PP2A, represses inflammation and is devoid of S1P agonism in A549 lung epithelial cells', Scientific Reports, vol. 6, no. 1, pp. 1-8.
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AbstractProtein phosphatase 2A (PP2A) activity can be enhanced pharmacologically by PP2A-activating drugs (PADs). The sphingosine analog FTY720 is the best known PAD and we have shown that FTY720 represses production of pro-inflammatory cytokines responsible for respiratory disease pathogenesis. Whether its phosphorylated form, FTY720-P, also enhances PP2A activity independently of the sphingosine 1-phosphate (S1P) pathway was unknown. Herein, we show that FTY720-P enhances TNF-induced PP2A phosphatase activity and significantly represses TNF-induced interleukin 6 (IL-6) and IL-8 mRNA expression and protein secretion from A549 lung epithelial cells. Comparing FTY720 and FTY720-P with S1P, we show that unlike S1P, the sphingosine analogs do not induce cytokine production on their own. In fact, FTY720 and FTY720-P significantly repress S1P-induced IL-6 and IL-8 production. We then examined their impact on expression of cyclooxygenase 2 (COX-2) and resultant prostaglandin E2 (PGE2) production. S1P did not increase production of this pro-inflammatory enzyme because COX-2 mRNA gene expression is NF-κB-dependent, and unlike TNF, S1P did not activate NF-κB. However, TNF-induced COX-2 mRNA expression and PGE2 secretion is repressed by FTY720 and FTY720-P. Hence, FTY720-P enhances PP2A activity and that PADs can repress production of pro-inflammatory cytokines and enzymes in A549 lung epithelial cells in a manner devoid of S1P agonism.

Rahman, MM, Rumzhum, NN, Hansbro, PM, Morris, JC, Clark, AR, Verrills, NM & Ammit, AJ 2016, 'Activating protein phosphatase 2A (PP2A) enhances tristetraprolin (TTP) anti-inflammatory function in A549 lung epithelial cells', Cellular Signalling, vol. 28, no. 4, pp. 325-334.
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© 2016. Chronic respiratory diseases are driven by inflammation, but some clinical conditions (severe asthma, COPD) are refractory to conventional anti-inflammatory therapies. Thus, novel anti-inflammatory strategies are necessary. The mRNA destabilizing protein, tristetraprolin (TTP), is an anti-inflammatory molecule that functions to induce mRNA decay of cytokines that drive pathogenesis of respiratory disorders. TTP is regulated by phosphorylation and protein phosphatase 2A (PP2A) is responsible for dephosphorylating (and hence activating) TTP, amongst other targets. PP2A is activated by small molecules, FTY720 and AAL(S), and in this study we examine whether these compounds repress cytokine production in a cellular model of airway inflammation using A549 lung epithelial cells stimulated with tumor necrosis factor α (TNFα) in vitro. PP2A activators significantly increase TNFα-induced PP2A activity and inhibit mRNA expression and protein secretion of interleukin 8 (IL-8) and IL-6; two key pro-inflammatory cytokines implicated in respiratory disease and TTP targets. The effect of PP2A activators is not via an increase in TNFα-induced TTP mRNA expression; instead we demonstrate a link between PP2A activation and TTP anti-inflammatory function by showing that specific knockdown of TTP with siRNA reversed the repression of TNFα-induced IL-8 and IL-6 mRNA expression and protein secretion by FTY720. Therefore we propose that PP2A activators affect the dynamic equilibrium regulating TTP; shifting the equilibrium from phosphorylated (inactive) towards unphosphorylated (active) but unstable TTP. PP2A activators boost the anti-inflammatory function of TTP and have implications for future pharmacotherapeutic strategies to combat inflammation in respiratory disease.

Raina, J-B, Tapiolas, D, Motti, CA, Foret, S, Seemann, T, Tebben, J, Willis, BL & Bourne, DG 2016, 'Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals', PeerJ, vol. 4, no. 8, pp. e2275-e2275.
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Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced byPseudovibriosp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities byPseudovibriosp., and prevented the growth of two previously identified coral pathogens,Vibrio coralliilyticusandV. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing ofPseudovibriosp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.

Rajan, A, Rogers, DJ, Ton-That, C, Zhu, L, Phillips, MR, Sundaram, S, Gautier, S, Moudakir, T, El-Gmili, Y, Ougazzaden, A, Sandana, VE, Teherani, FH, Bove, P, Prior, KA, Djebbour, Z, McClintock, R & Razeghi, M 2016, 'Wafer-scale epitaxial lift-off of optoelectronic grade GaN from a GaN substrate using a sacrificial ZnO interlayer', Journal of Physics D: Applied Physics, vol. 49, no. 31, pp. 315105-315105.
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© 2016 IOP Publishing Ltd. Full 2 inch GaN epilayers were lifted off GaN and c-sapphire substrates by preferential chemical dissolution of sacrificial ZnO underlayers. Modification of the standard epitaxial lift-off (ELO) process by supporting the wax host with a glass substrate proved key in enabling full wafer scale-up. Scanning electron microscopy and x-ray diffraction confirmed that intact epitaxial GaN had been transferred to the glass host. Depth-resolved cathodoluminescence (CL) analysis of the bottom surface of the lifted-off GaN layer revealed strong near-band-edge (3.33 eV) emission indicating a superior optical quality for the GaN which was lifted off the GaN substrate. This modified ELO approach demonstrates that previous theories proposing that wax host curling was necessary to keep the ELO etch channel open do not apply to the GaN/ZnO system. The unprecedented full wafer transfer of epitaxial GaN to an alternative support by ELO offers the perspective of accelerating industrial adoption of the expensive GaN substrate through cost-reducing recycling.

Raman, H, Raman, R, Coombes, N, Song, J, Prangnell, R, Bandaranayake, C, Tahira, R, Sundaramoorthi, V, Killian, A, Meng, J, Dennis, ES & Balasubramanian, S 2016, 'Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola', PLANT CELL AND ENVIRONMENT, vol. 39, no. 6, pp. 1228-1239.
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Optimum flowering time is the key to maximise canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify sixty-nine SNP markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional 5 SNPs were localised within 14 Kb of a previously identified QTL for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. GWAS analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modeled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programs. This article is protected by copyright. All rights reserved.

Redpath, GMI, Sophocleous, RA, Turnbull, L, Whitchurch, CB & Cooper, ST 2016, 'Ferlins Show Tissue‐Specific Expression and Segregate as Plasma Membrane/Late Endosomal or Trans‐Golgi/Recycling Ferlins', Traffic, vol. 17, no. 3, pp. 245-266.
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Ferlins are a family of transmembrane‐anchored vesicle fusion proteins uniquely characterized by 5–7 tandem cytoplasmic C2 domains, Ca2+‐regulated phospholipid‐binding domains that regulate vesicle fusion in the synaptotagmin family. In humans, dysferlin mutations cause limb‐girdle muscular dystrophy type 2B (LGMD2B) due to defective Ca2+‐dependent, vesicle‐mediated membrane repair and otoferlin mutations cause non‐syndromic deafness due to defective Ca2+‐triggered auditory neurotransmission. In this study, we describe the tissue‐specific expression, subcellular localization and endocytic trafficking of the ferlin family. Studies of endosomal transit together with 3D‐structured illumination microscopy reveals dysferlin and myoferlin are abundantly expressed at the PM and cycle to Rab7‐positive late endosomes, supporting potential roles in the late‐endosomal pathway. In contrast, Fer1L6 shows concentrated localization to a specific compartment of the trans‐Golgi/recycling endosome, cycling rapidly between this compartment and the PM via Rab11 recycling endosomes. Otoferlin also shows trans‐Golgi to PM cycling, with very low levels of PM otoferlin suggesting either brief PM residence, or rare incorporation of otoferlin molecules into the PM. Thus, type‐I and type‐II ferlins seg...

Rehman, AU, Szabó, M, Deák, Z, Sass, L, Larkum, A, Ralph, P & Vass, I 2016, 'Symbiodinium sp. cells produce light‐induced intra‐ and extracellular singlet oxygen, which mediates photodamage of the photosynthetic apparatus and has the potential to interact with the animal host in coral symbiosis', New Phytologist, vol. 212, no. 2, pp. 472-484.
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SummaryCoral bleaching is an important environmental phenomenon, whose mechanism has not yet been clarified. The involvement of reactive oxygen species (ROS) has been implicated, but direct evidence of what species are involved, their location and their mechanisms of production remains unknown.Histidine‐mediated chemical trapping and singlet oxygen sensor green (SOSG) were used to detect intra‐ and extracellular singlet oxygen (1O2) in Symbiodinium cultures.Inhibition of the Calvin–Benson cycle by thermal stress or high light promotes intracellular 1O2 formation. Histidine addition, which decreases the amount of intracellular 1O2, provides partial protection against photosystem II photoinactivation and chlorophyll (Chl) bleaching. 1O2 production also occurs in cell‐free medium of Symbiodinium cultures, an effect that is enhanced under heat and light stress and can be attributed to the excretion of 1O2‐sensitizing metabolites from the cells. Confocal microscopy imaging using SOSG showed most extracellular 1O2 around the cell surface, but it is also produced across the medium distant from the cells.We demonstrate, for the first time, both intra‐ and extracellular

Rehman, SF, Mansoor, Q, Farooqi, AA, Nazir, N, Kausar, R, Jabeen, N & Ismail, M 2016, 'Association between breast cancer and tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) gene 1595C/T SNP in a Pakistani population', Współczesna Onkologia, vol. 2, no. 2, pp. 185-187.
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AIM OF THE STUDY: TRAIL-mediated signalling has emerged as an extensively studied biological mechanism reported to differentially induce apoptosis in cancer cells. However, overwhelmingly increasing experimentally verified data is shedding light on resistance against TRAIL-induced apoptosis in cancer cells. Moreover, genetic and epigenetic mutations also exert effects on the functionality of TRAIL and its receptors. In this study we investigated the association between breast cancer and polymorphisms in tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) in a Pakistani Population. MATERIAL AND METHODS: Genotyping for TRAIL gene 1595 C/T polymorphism was done for 363 breast cancer patients and 193 age- and sex-matched healthy controls. DNA was extracted using standard organic methods. PCR-RFLP analysis was done for C/T polymorphism at position 1595 in exon 5 of the TRAIL gene using site-specific primers and restriction enzyme. The results were statistically evaluated by SPSS14. RESULTS: In this study, CC homozygotes were 46.3% in patients and 49.7% in controls, p = 0.729 with OR value 0.8705 (95% CI: 0.6137-1.2348). CT was statistically insignificant, p = 0.837 with OR value 0.9242 (95% CI: 0.6494-1.3154). However, the minor allele or risk allele genotype TT had a higher percentage among breast cancer patients (12.1%) than in the control group (6.7%). Since there was a statistically insignificant difference (p = 0.212, OR value 1.9098 with 95% CI 1.0019 to 3.6406) of TT genotype between the two groups, the contrastingly higher percentage of TT genotype in breast cancer patients seems to be a risk factor for the disease. Moreover, the frequency of minor allele T was also found to be higher in the patients (0.329) than in the controls (0.285). CONCLUSIONS: The TRAIL gene 1595 C/T SNP has a contradictory role in cancer development in different populations. In our population group although the percentage of homozygous risk allele TT was higher i...

Reimers, JR 2016, 'Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology', Australian Journal of Chemistry, vol. 69, no. 12, pp. 1331-1331.
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David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

Reimers, JR, Biczysko, M, Bruce, D, Coker, DF, Frankcombe, TJ, Hashimoto, H, Hauer, J, Jankowiak, R, Kramer, T, Linnanto, J, Mamedov, F, Müh, F, Rätsep, M, Renger, T, Styring, S, Wan, J, Wang, Z, Wang-Otomo, Z-Y, Weng, Y-X, Yang, C, Zhang, J-P, Freiberg, A & Krausz, E 2016, 'Challenges facing an understanding of the nature of low-energy excited states in photosynthesis', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1857, no. 9, pp. 1627-1640.
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© 2016 Elsevier B.V. While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.

Reimers, JR, Chi, Q, Ford, MJ, Halder, A, Hush, NS, Ulstrup, J & Zhang, J 2016, 'En ny historie om guld og svovl', Dansk Kemi, vol. 97, no. 8, pp. 20-23.
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- guld-svovlbindingen i thiolers adsorption på guldnanopartikler og plane guldoverfladerEn netop publiceret større australsk-dansk undersøgelse giver ny indsigt i, hvordan thioldækkede Au-overflader er opbygget. Det har betydning for design, syntese og dannelsesmekanismer for Au-nanopartikler og Au-overflader med skræddersyede fysiske og kemiske egenskaber

Reimers, JR, Ford, MJ & Goerigk, L 2016, 'Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism', Molecular Simulation, vol. 42, no. 6-7, pp. 494-510.
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© 2015 Taylor & Francis. The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual-Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual-Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future.

Reimers, JR, Ford, MJ, Halder, A, Ulstrup, J & Hush, NS 2016, 'Gold surfaces and nanoparticles are protected by Au(0)–thiyl species and are destroyed when Au(I)–thiolates form', Proceedings of the National Academy of Sciences, vol. 113, no. 11, pp. E1424-E1433.
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Significance Synthetic design strategies for gold surface protection and nanoparticle formation require knowledge of how protectant ligands bind. Sulfur compounds may protect gold surfaces using a weakly bound (physisorbed) form or a strongly bound (chemisorbed) one often assumed to be Au(I)–thiolate. However, chemical reaction conditions optimized for Au(I)–thiolate protection instead etch surfaces to produce molecular thin films. All experimental and calculated evidence indicates that chemisorbed surface species are actually bound mainly by strong van der Waals (aurophilic-like) forces. This understanding unifies gold–sulfur surface chemistry with that of all other ligands and also with that of gold compounds, forming the basis for future methodological developments. It is applied to predict intermediate species during the Brust–Schiffrin nanoparticle synthesis that are subsequently observed spectroscopically.

Reimers, JR, Panduwinata, D, Visser, J, Chin, Y, Tang, C, Goerigk, L, Ford, MJ, Baker, M, Sum, TJ, Coenen, MJJ, Hendriksen, BLM, Elemans, JAAW, Hush, NS & Crossley, MJ 2016, 'From Chaos to Order: Chain-Length Dependence of the Free Energy of Formation of Meso-tetraalkylporphyrin Self-Assembled Monolayer Polymorphs', The Journal of Physical Chemistry C, vol. 120, no. 3, pp. 1739-1748.
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© 2016 American Chemical Society. We demonstrate that systematic errors can be reduced and physical insight gained through investigation of the dependence of free energies for meso-tetraalkylporphyrin self-assembled monolayers (SAMs) polymorphism on the alkyl chain length m. These SAMs form on highly ordered pyrolytic graphite (HOPG) from organic solution, displaying manifold densities and atomic structures. SAMs with m = 11-19 are investigated experimentally while those with m = 6-28 are simulated using density-functional theory (DFT). It is shown that, for m = 15 or more, the alkyl chains crystallize to dominate SAM structure. Meso-tetraalkylporphyrin SAMs of length less than 11 have never been observed, a presumed effect of inadequate surface attraction. Instead, we show that free energies of SAM formation actually enhance as the chain length decreases. The inability to image regular SAMs stems from the appearance of many polymorphic forms of similar free energy, preventing SAM ordering. We also demonstrate a significant odd/even effect in SAM structure arising from packing anomalies. Comparison of the chain-length dependence of formation free energies allows the critical dispersion interactions between molecules, solvent, and substrate to be directly examined. Interpretation of the STM data combined with measured enthalpies indicates that Grimme's D3 explicit-dispersion correction and the implicit solvent correction of Floris, Tomasi and Pascual Ahuir are both quantitatively accurate and very well balanced to each other.

Ren, B, Tao, C, Swan, MA, Joachim, N, Martiniello-Wilks, R, Nassif, NT, O'Brien, BA & Simpson, AM 2016, 'Pancreatic Transdifferentiation and Glucose-Regulated Production of Human Insulin in the H4IIE Rat Liver Cell Line', INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 17, no. 4.
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© 2016 by the authors. Due to the limitations of current treatment regimes, gene therapy is a promising strategy being explored to correct blood glucose concentrations in diabetic patients. In the current study, we used a retroviral vector to deliver either the human insulin gene alone, the rat NeuroD1 gene alone, or the human insulin gene and rat NeuroD1 genes together, to the rat liver cell line, H4IIE, to determine if storage of insulin and pancreatic transdifferentiation occurred. Stable clones were selected and expanded into cell lines: H4IIEins (insulin gene alone), H4IIE/ND (NeuroD1 gene alone), and H4IIEins/ND (insulin and NeuroD1 genes). The H4IIEins cells did not store insulin; however, H4IIE/ND and H4IIEins/ND cells stored 65.5 ± 5.6 and 1475.4 ± 171.8 pmol/insulin/ 5 × 106 cells, respectively. Additionally, several β cell transcription factors and pancreatic hormones were expressed in both H4IIE/ND and H4IIEins/ND cells. Electron microscopy revealed insulin storage vesicles in the H4IIE/ND and H4IIEins/ND cell lines. Regulated secretion of insulin to glucose (0–20 mmol/L) was seen in the H4IIEins/ND cell line. The H4IIEins/ND cells were transplanted into diabetic immunoincompetent mice, resulting in normalization of blood glucose. This data shows that the expression of NeuroD1 and insulin in liver cells may be a useful strategy for inducing islet neogenesis and reversing diabetes.

Ren, S, Hure, A, Peel, R, D'Este, C, Abhayaratna, W, Tonkin, A, Hopper, I, Thrift, AG, Levi, C, Sturm, J, Durrheim, D, Hung, J, Briffa, T, Chew, DP, Anderson, P, Moon, L, McEvoy, M, Hansbro, P, Newby, D & Attia, J 2016, 'Rationale and design of a randomized controlled trial of pneumococcal polysaccharide vaccine for prevention of cardiovascular events: The Australian Study for the Prevention through Immunization of Cardiovascular Events (AUSPICE)', American Heart Journal, vol. 177, pp. 58-65.
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Research has shown that vaccination with Streptococcus pneumoniae reduced the extent of atherosclerosis in experimental animal models. It is thought that phosphorylcholine lipid antigens in the S. pneumoniae cell wall induce the production of antibodies that cross-react with oxidized low-density lipoprotein, a component of atherosclerotic plaques. These antibodies may bind to and facilitate the regression of the plaques. Available data provide evidence that similar mechanisms also occur in humans, leading to the possibility that pneumococcal vaccination protects against atherosclerosis. A systematic review and meta-analysis, including 8 observational human studies, of adult pneumococcal polysaccharide vaccination for preventing cardiovascular disease in people older than 65 years, showed a 17% reduction in the odds (odds ratio 0.83, 95% CI 0.71-0.97) of having an acute coronary syndrome event.The AUSPICE is a multicenter, randomized, placebo-controlled, double-blind, clinical trial to formally test whether vaccination with the pneumococcal polysaccharide vaccine protects against cardiovascular events (fatal and nonfatal acute coronary syndromes and ischemic strokes). Cardiovascular outcomes will be obtained during 4 to 5 years of follow-up, through health record linkage with state and national administrative data sets.This is the first registered randomized controlled trial (on US, World Health Organization, Australia and New Zealand trial registries) to be conducted to test whether vaccination with the pneumococcal polysaccharide vaccine will reduce cardiovascular events. If successful, vaccination can be readily extended to at-risk groups to reduce the risk of cardiovascular diseases.

Restrepo-Coupe, N, Huete, A, Davies, K, Cleverly, J, Beringer, J, Eamus, D, van Gorsel, E, Hutley, LB & Meyer, WS 2016, 'MODIS vegetation products as proxies of photosynthetic potential along a gradient of meteorologically and biologically driven ecosystem productivity', BIOGEOSCIENCES, vol. 13, no. 19, pp. 5587-5608.
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© 2016 Author(s). A direct relationship between gross ecosystem productivity (GEP) estimated by the eddy covariance (EC) method and Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices (VIs) has been observed in many temperate and tropical ecosystems. However, in Australian evergreen forests, and particularly sclerophyll and temperate woodlands, MODIS VIs do not capture seasonality of GEP. In this study, we re-evaluate the connection between satellite and flux tower data at four contrasting Australian ecosystems, through comparisons of GEP and four measures of photosynthetic potential, derived via parameterization of the light response curve: ecosystem light use efficiency (LUE), photosynthetic capacity (Pc), GEP at saturation (GEPsat), and quantum yield (α) with MODIS vegetation satellite products, including VIs, gross primary productivity (GPPMOD) leaf area index (LAIMOD), and fraction of photosynthetic active radiation (fPARMOD). We found that satellite-derived biophysical products constitute a measurement of ecosystem structure (e.g. leaf area index-quantity of leaves) and function (e.g. leaf level photosynthetic assimilation capacity-quality of leaves), rather than GEP. Our results show that in primarily meteorological-driven (e.g. photosynthetic active radiation, air temperature, and/or precipitation) and relatively aseasonal ecosystems (e.g. evergreen wet sclerophyll forests), there were no statistically significant relationships between GEP and satellite-derived measures of greenness. In contrast, for phenology-driven ecosystems (e.g. tropical savannas), changes in the vegetation status drove GEP, and tower-based measurements of photosynthetic activity were best represented by VIs. We observed the highest correlations between MODIS products and GEP in locations where key meteorological variables and vegetation phenology were synchronous (e.g. semi-arid Acacia woodlands) and low correlation at locations where they were asynchr...

Reyna Zeballos, JL & Meier, P 2016, 'Learning to Surf: Explaining the Flipped Classroom (FC) to Science Students Using an Analogy', American Journal of Educational Research, vol. 4, no. 17, pp. 1213-1216.
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Most of the literature in educational technology targets academics, educational designers, and policy makers. To date, there are no scholarly papers which help students to understand and ‘buy into’ educational technology. We expect students to engage with contemporary ways of teaching and learning, without fostering any attitudinal change. According to the current literature, Flipped Classrooms (FC) have become increasingly popular in higher education since 2012. Research done in this field has increased considerably in the last four years, judging by the number of scholarly published papers across different disciplines. A review of the literature indicated the implementation of FC suffers from several deficits, such as a rigorous and consistent approach, effective theoretical frameworks, and evaluation structures. Research is also pointing to the need to support students in transitioning from traditional classroom style to FC. To facilitate this transition, a communication strategy is required to help students adopt this model of learning. It is in the best interest of educators to ensure that students understand the rationale behind the FC. This paper outlines how the FC can be explained to science students using a ‘learning to surf’ analogy.

Reyna Zeballos, JL, Meier, P, Geronimo, F & Rodgers, K 2016, 'Implementing Digital Media Presentations as Assessment Tools for Pharmacology Students', American Journal of Educational Research, vol. 4, no. 14, pp. 983-991.
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At the Faculty of Science we introduced the use of digital presentations as assessment tools forthird-year pharmacology students. A cohort of 167 students self-allocated into groups of four and were assigned atopic related to the pharmacology lecture material. A one-hour lecture was delivered to discuss digital mediaprinciples (visual design, video composition, multimedia learning principles, etc.) and how to apply these to createdigital media projects. During practical classes, students developed a storyboard and received feedback and technicaladvice from tutors. Towards the end of the semester, students uploaded their preliminary presentations to a YouTubechannel and received feedback from lecturers, tutors, and peers before submitting the final version. A marking rubricwas developed and shared with students at the beginning of the semester. The study used a mixed-methods approachto evaluating the intervention. A comprehensive 35-step questionnaire was used, covering demographics, students’attitudes towards technology, digital media support, understanding of the assignment, and knowledge constructionand skills gained. It also contained five open-ended questions. A high response rate was achieved for the voluntarysurvey (97/167). Additionally, students reviewed contributions of group members using SPARKPlus, and the marksattained were used to triangulate the questionnaire responses. In summary, the data shows that students found theassignment was engaging, fostered learning and creativity, and that they gained additional skills relevant to theirfuture careers.

Reynolds, OL, Padula, MP, Zeng, R & Gurr, GM 2016, 'Silicon: Potential to Promote Direct and Indirect Effects on Plant Defense Against Arthropod Pests in Agriculture', Frontiers in Plant Science, vol. 7, no. June2016, pp. 1-13.
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© 2016 Reynolds, Padula, Zeng and Gurr. Silicon has generally not been considered essential for plant growth, although it is well recognized that many plants, particularly Poaceae, have substantial plant tissue concentrations of this element. Recently, however, the International Plant Nutrition Institute [IPNI] (2015), Georgia, USA has listed it as a “beneficial substance”. This reflects that numerous studies have now established that silicon may alleviate both biotic and abiotic stress. This paper explores the existing knowledge and recent advances in elucidating the role of silicon in plant defense against biotic stress, particularly against arthropod pests in agriculture and attraction of beneficial insects. Silicon confers resistance to herbivores via two described mechanisms: physical and biochemical/molecular. Until recently, studies have mainly centered on two trophic levels; the herbivore and plant. However, several studies now describe tri-trophic effects involving silicon that operate by attracting predators or parasitoids to plants under herbivore attack. Indeed, it has been demonstrated that silicon-treated, arthropod- attacked plants display increased attractiveness to natural enemies, an effect that was reflected in elevated biological control in the field. The reported relationships between soluble silicon and the jasmonic acid (JA) defense pathway, and JA and herbivore- induced plant volatiles (HIPVs) suggest that soluble silicon may enhance the production of HIPVs. Further, it is feasible that silicon uptake may affect protein expression (or modify proteins structurally) so that they can produce additional, or modify, the HIPV profile of plants. Ultimately, understanding silicon under plant ecological, physiological, biochemical, and molecular contexts will assist in fully elucidating the mechanisms behind silicon and plant response to biotic stress at both the bi- and tri-trophic levels.

Ribaux, O, Crispino, F, Delemont, O & Roux, C 2016, 'The progressive opening of forensic science toward criminological concerns', SECURITY JOURNAL, vol. 29, no. 4, pp. 543-560.
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© 2016 Macmillan Publishers Ltd. Technology is increasingly offering new means of human behavior traceability. This situation is challenging the standing, scope and role of forensic science in the criminal Justice System. At the same time, criminology is developing methodologies that encompass virtual worlds, and deal with the increasing quantity of accessible digital data reflecting criminal behaviors. Identifying how these concerns overlap begs the question: should we reconsider the articulation of many aspects of both forensic science and criminology? This article proposes a progressive and systematic modeling activity along five steps: (i) the expression of the investigative logic of forensic science; (ii) the use of theories in environmental criminology; (iii) a more systematic search for associations between traces and between crime situations; (iv) the search for studies in diverse areas of criminology that actually or potentially rely on forensic case data and (v) the suggestion of models and methods for framing the approach.

Rice, SA, Wuertz, S & Kjelleberg, S 2016, 'Next‐generation studies of microbial biofilm communities', Microbial Biotechnology, vol. 9, no. 5, pp. 677-680.
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SummaryAs we look into the future of microbial biofilm research, there is clearly an emerging focus on communities rather than populations. This represents an essential change in direction to more accurately understand how and why microorganisms assemble into communities, as well as the functional implications for such a life style. For example, current research studies shows that communities display emergent properties or functions that are not predicted from the individual single species populations, including elevated stress tolerance and resistance to antibiotics. Models for mixed species biofilms can be very simple, comprised only a handful of species or can be extremely species rich, with hundreds or thousands of species present. The future holds much promise for this area of research, where investigators will increasingly be able to resolve, at the molecular and biochemical levels, interspecies relationships and mechanisms of interaction. The outcome of these studies will greatly enhance our understanding of the ecological and evolutionary factors that drive community function in natural and engineered systems.

Richman, MB, Leslie, LM & Segele, ZT 2016, 'Classifying Drought in Ethiopia Using Machine Learning', Procedia Computer Science, vol. 95, pp. 229-236.
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Rinke, C, Low, S, Woodcroft, BJ, Raina, J-B, Skarshewski, A, Le, XH, Butler, MK, Stocker, R, Seymour, J, Tyson, GW & Hugenholtz, P 2016, 'Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics', PeerJ, vol. 4, no. 9, pp. e2486-e2486.
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High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

Roberts, BR, Doecke, JD, Rembach, A, Yévenes, LF, Fowler, CJ, McLean, CA, Lind, M, Volitakis, I, Masters, CL, Bush, AI & Hare, DJ 2016, 'Rubidium and potassium levels are altered in Alzheimer’s disease brain and blood but not in cerebrospinal fluid', Acta Neuropathologica Communications, vol. 4, no. 1, p. 119.
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Loss of intracellular compartmentalization of potassium is a biochemical feature of Alzheimer's disease indicating a loss of membrane integrity and mitochondrial dysfunction. We examined potassium and rubidium (a biological proxy for potassium) in brain tissue, blood fractions and cerebrospinal fluid from Alzheimer's disease and healthy control subjects to investigate the diagnostic potential of these two metal ions. We found that both potassium and rubidium levels were significantly decreased across all intracellular compartments in the Alzheimer's disease brain. Serum from over 1000 participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing (AIBL), showed minor changes according to disease state. Potassium and rubidium levels in erythrocytes and cerebrospinal fluid were not significantly different according to disease state, and rubidium was slightly decreased in Alzheimer's disease patients compared to healthy controls. Our data provides evidence that contrasts the hypothesized disruption of the blood-brain barrier in Alzheimer's disease, with the systemic decrease in cortical potassium and rubidium levels suggesting influx of ions from the blood is minimal and that the observed changes are more likely indicative of an internal energy crisis within the brain. These findings may be the basis for potential diagnostic imaging studies using radioactive potassium and rubidium tracers.

Rocha, AV, Rita Cardoso, B, Zavarize, B, Almondes, K, Bordon, I, Hare, DJ, Teixeira Favaro, DI & Franciscato Cozzolino, SM 2016, 'GPX1 Pro198Leu polymorphism and GSTM1 deletion do not affect selenium and mercury status in mildly exposed Amazonian women in an urban population', Science of The Total Environment, vol. 571, pp. 801-808.
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Mercury is potent toxicant element, but its toxicity can be reduced by forming a complex with selenium for safe excretion. Considering the impact of mercury exposure in the Amazon region and the possible interaction between these two elements, we aimed to assess the effects of Pro198Leu polymorphism to GPX1 and GSTM1 deletion, on mercury levels in a population from Porto Velho, an urban locality in the Brazilian Amazon region. Two hundred women from the capital city of Rondônia state were recruited for this study with 149 deemed suitable to participate. We assessed dietary intake using 24-hour recall. Selenium levels in plasma and erythrocytes were measured using hydride generation quartz tube atomic absorption spectroscopy and total hair mercury using cold vapor atomic absorption spectrometry. Oxidative stress parameters (GPx activity, oxygen radical absorbency capacity [ORAC] and malondialdehyde [MDA]) were also analyzed. All participants were genotyped for Pro198Leu polymorphism and GSTM1 deletion. We observed that this population presented high prevalence of selenium deficiency, and also low levels of mercury, likely due to food habits that did not include selenium-rich food sources or significant consumption of fish (mercury biomagnifiers) regularly. Univariate statistical analysis showed that Pro198Leu and GSTM1 genotypes did not affect selenium and mercury levels in this population. Pro198Leu polymorphism and GSTM1 deletion had no effect on mercury levels in mildly exposed people, suggesting these genetic variants impact mercury levels only in highly exposed populations.

Rogers, K, Boon, PI, Branigan, S, Duke, NC, Field, CD, Fitzsimons, JA, Kirkman, H, Mackenzie, JR & Saintilan, N 2016, 'The state of legislation and policy protecting Australia's mangrove and salt marsh and their ecosystem services', MARINE POLICY, vol. 72, pp. 139-155.
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Rohde, D & Wand, MP 2016, 'Semiparametric mean field variational bayes: General principles and numerical issues', Journal of Machine Learning Research, vol. 17, no. 172, pp. 1-47.
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We introduce the term semiparametric mean field variational Bayes to describe the relaxation of mean field variational Bayes in which some density functions in the product density restriction are pre-specified to be members of convenient parametric families. This notion has appeared in various guises in the mean field variational Bayes literature during its history and we endeavor to unify this important topic. We lay down a general framework and explain how previous relevant methodologies fall within this framework. A major contribution is elucidation of numerical issues that impact semiparametric mean field variational Bayes in practice.

Rohlfs, A-M, Mitrovic, SM, Williams, S & Coleman, D 2016, 'Can tributary in-flows improve the recovery of the dissolved organic carbon regime in a snowmelt river regulated by a large reservoir?', Marine and Freshwater Research, vol. 67, no. 9, pp. 1338-1338.
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Although tributary inputs can accelerate the recovery of many physical and chemical gradients below large reservoirs, their contribution to the dissolved organic carbon (DOC) regime in regulated rivers remains poorly studied. In some regulated tributaries, flow volumes can be manipulated, potentially influencing DOC supply to the main stem. The present study examines how tributary water diversion affects DOC supply to a snowmelt river regulated by large reservoirs. DOC concentration was measured at tributary and main stem sites, and tributary DOC export was estimated under different tributary flow-diversion scenarios. Significant, positive correlations between DOC concentration and discharge were absent directly below the dam, but were present in the unregulated tributary, and re-emerged below the tributary confluence. Irrespective of water-diversion practices, tributary in-flows reconnected the regulated main stem to a more variable DOC regime driven by catchment flushing processes. However, tributary water diversion dampened the tributary signal by reducing DOC pulse frequency and total DOC export to the regulated river. These aspects of the DOC regime may influence basal resource availability and ecosystem functioning in the regulated main stem. The present study illustrates how an ecologically valuable tributary function can be addressed and quantified to guide the management and rehabilitation of a regulated river system.

Rohlfs, A-M, Mitrovic, SM, Williams, S, Hitchcock, JN & Rees, GN 2016, 'Dissolved organic carbon delivery from managed flow releases in a montane snowmelt river', Aquatic Sciences, vol. 78, no. 4, pp. 793-807.
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Rollo, JL, Banihashemi, N, Vafaee, F, Crawford, JW, Kuncic, Z & Holsinger, RMD 2016, 'Unraveling the mechanistic complexity of Alzheimer's disease through systems biology', Alzheimer's & Dementia, vol. 12, no. 6, pp. 708-718.
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AbstractAlzheimer's disease (AD) is a complex, multifactorial disease that has reached global epidemic proportions. The challenge remains to fully identify its underlying molecular mechanisms that will enable development of accurate diagnostic tools and therapeutics. Conventional experimental approaches that target individual or small sets of genes or proteins may overlook important parts of the regulatory network, which limits the opportunity of identifying multitarget interventions. Our perspective is that a more complete insight into potential treatment options for AD will only be made possible through studying the disease as a system. We propose an integrative systems biology approach that we argue has been largely untapped in AD research. We present key publications to demonstrate the value of this approach and discuss the potential to intensify research efforts in AD through transdisciplinary collaboration. We highlight challenges and opportunities for significant breakthroughs that could be made if a systems biology approach is fully exploited.

Ros, M, Pernice, M, Le Guillou, S, Doblin, MA, Schrameyer, V & Laczka, O 2016, 'Colorimetric Detection of Caspase 3 Activity and Reactive Oxygen Derivatives: Potential Early Indicators of Thermal Stress in Corals', Journal of Marine Biology, vol. 2016, pp. 1-11.
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There is an urgent need to develop and implement rapid assessments of coral health to allow effective adaptive management in response to coastal development and global change. There is now increasing evidence that activation of caspase-dependent apoptosis plays a key role during coral bleaching and subsequent mortality. In this study, a “clinical” approach was used to assess coral health by measuring the activity of caspase 3 using a commercial kit. This method was first applied while inducing thermal bleaching in two coral species,Acropora milleporaandPocillopora damicornis. The latter species was then chosen to undergo further studies combining the detection of oxidative stress-related compounds (catalase activity and glutathione concentrations) as well as caspase activity during both stress and recovery phases. Zooxanthellae photosystem II (PSII) efficiency and cell density were measured in parallel to assess symbiont health. Our results demonstrate that the increased caspase 3 activity in the coral host could be detected before observing any significant decrease in the photochemical efficiency of PSII in the algal symbionts and/or their expulsion from the host. This study highlights the potential of host caspase 3 and reactive oxygen species scavenging activities as early indicators of stress in individual coral colonies.

Roushani, M, Hoseini, SJ, Azadpour, M, Heidari, V, Bahrami, M & Maddahfar, M 2016, 'Electrocatalytic oxidation behavior of NADH at Pt/Fe 3 O 4 /reduced-graphene oxide nanohybrids modified glassy carbon electrode and its determination', Materials Science and Engineering: C, vol. 67, pp. 237-246.
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Roy Chowdhury, P, Scott, M, Worden, P, Huntington, P, Hudson, B, Karagiannis, T, Charles, IG & Djordjevic, SP 2016, 'Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa', Open Biology, vol. 6, no. 3, pp. 150175-150175.
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Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn 6162 and Tn 6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn 6163 in GI2 carries a bla GES-5 – aacA4 – gcuE15 – aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antib...

Royce, SG, Nold, MF, Bui, C, Donovan, C, Lam, M, Lamanna, E, Rudloff, I, Bourke, JE & Nold-Petry, CA 2016, 'Airway Remodeling and Hyperreactivity in a Model of Bronchopulmonary Dysplasia and Their Modulation by IL-1 Receptor Antagonist', American Journal of Respiratory Cell and Molecular Biology, vol. 55, no. 6, pp. 858-868.
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© Copyright 2016 by the American Thoracic Society. Bronchopulmonary dysplasia (BPD) is a chronic disease of extreme prematurity that has serious long-term consequences including increased asthma risk. We earlier identified IL-1 receptor antagonist (IL-1Ra) as a potent inhibitor of murine BPD induced by combining perinatal inflammation (intraperitoneal LPS to pregnant dams) and exposure of pups to hyperoxia (fraction of inspired oxygen = 0.65). In this study, we determined whether airway remodeling and hyperresponsiveness similar to asthma are evident in this model, and whether IL-1Ra is protective. During 28-day exposure to air or hyperoxia, pups received vehicle or 10 mg/kg IL-1Ra by daily subcutaneous injection. Lungs were then prepared for histology and morphometry of alveoli and airways, or for real-time PCR, or inflated with agarose to prepare precision-cut lung slices to visualize ex vivo intrapulmonary airway contraction and relaxation by phase-contrast microscopy. In pups reared under normoxic conditions, IL-1Ra treatment did not affect alveolar or airway structure or airway responses. Pups reared in hyperoxia developed a severe BPD-like lung disease, with fewer, larger alveoli, increased subepithelial collagen, and increased expression of α-smooth muscle actin and cyclin D1. After hyperoxia, methacholine elicited contraction with similar potency but with an increased maximum reduction in lumen area (air, 44%; hyperoxia, 89%), whereas dilator responses to salbutamol were maintained. IL-1Ra treatment prevented hyperoxia-induced alveolar disruption and airway fibrosis but, surprisingly, not the increase in methacholine-induced airway contraction. The current study is the first to demonstrate ex vivo airway hyperreactivity caused by systemic maternal inflammation and postnatal hyperoxia, and it reveals further preclinical mechanistic insights into IL-1Ra as a treatment targeting key pathophysiological features of BPD.

Rumzhum, NN & Ammit, AJ 2016, 'Cyclooxygenase 2: its regulation, role and impact in airway inflammation', Clinical & Experimental Allergy, vol. 46, no. 3, pp. 397-410.
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SummaryCyclooxygenase 2 (COX‐2: official gene symbol – PTGS2) has long been regarded as playing a pivotal role in the pathogenesis of airway inflammation in respiratory diseases including asthma. COX‐2 can be rapidly and robustly expressed in response to a diverse range of pro‐inflammatory cytokines and mediators. Thus, increased levels of COX‐2 protein and prostanoid metabolites serve as key contributors to pathobiology in respiratory diseases typified by dysregulated inflammation. But COX‐2 products may not be all bad: prostanoids can exert anti‐inflammatory/bronchoprotective functions in airways in addition to their pro‐inflammatory actions. Herein, we outline COX‐2 regulation and review the diverse stimuli known to induce COX‐2 in the context of airway inflammation. We discuss some of the positive and negative effects that COX‐2/prostanoids can exert in in vitro and in vivo models of airway inflammation, and suggest that inhibiting COX‐2 expression to repress airway inflammation may be too blunt an approach; because although it might reduce the unwanted effects of COX‐2 activation, it may also negate the positive effects. Evidence suggests that prostanoids produced via COX‐2 upregulation show diverse actions (and herein we focus on prostaglandin E2 as a key example); these can be either beneficial or deleterious and their impact on respiratory disease can be dictated by local concentration and specific interaction with individual receptors. We propose that understanding the regulation of COX‐2 expression and associated receptor‐mediated functional outcomes may reveal number of critical steps amenable to pharmacological intervention. These may prove invaluable in our quest towards future development of novel anti‐inflammatory pharmacotherapeutic strategies for the treatment of airway diseases.

Rumzhum, NN & Ammit, AJ 2016, 'Prostaglandin E2 induces expression of MAPK phosphatase 1 (MKP-1) in airway smooth muscle cells', European Journal of Pharmacology, vol. 782, pp. 1-5.
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©2016 Published by Elsevier B.V. Prostaglandin E2 (PGE2) is a prostanoid with diverse actions in health and disease. In chronic respiratory diseases driven by inflammation, PGE2 has both positive and negative effects. An enhanced understanding of the receptor-mediated cellular signalling pathways induced by PGE2 may help us separate the beneficial properties from unwanted actions of this important prostaglandin. PGE2 is known to exert anti-inflammatory and bronchoprotective actions in human airways. To date however, whether PGE2 increases production of the anti-inflammatory protein MAPK phosphatase 1 (MKP-1) was unknown. We address this herein and use primary cultures of human airway smooth muscle (ASM) cells to show that PGE2 increases MKP-1 mRNA and protein upregulation in a concentration-dependent manner. We explore the signalling pathways responsible and show that PGE2-induces CREB phosphorylation, not p38 MAPK activation, in ASM cells. Moreover, we utilize selective antagonists of EP2 (PF-04418948) and EP4 receptors (GW 627368X) to begin to identify EP-mediated functional outcomes in ASM cells in vitro. Taken together with earlier studies, our data suggest that PGE2 increases production of the anti-inflammatory protein MKP-1 via cAMP/CREB-mediated cellular signalling in ASM cells and demonstrates that EP2 may, in part, be involved.

Rumzhum, NN, Patel, BS, Prabhala, P, Gelissen, IC, Oliver, BG & Ammit, AJ 2016, 'IL‐17A increases TNF‐α‐induced COX‐2 protein stability and augments PGE₂ secretion from airway smooth muscle cells: impact on β₂‐adrenergic receptor desensitization', Allergy, vol. 71, no. 3, pp. 387-396.
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AbstractBackgroundIL‐17A plays an important role in respiratory disease and is a known regulator of pulmonary inflammation and immunity. Recent studies have linked IL‐17A with exacerbation in asthma and COPD. We have shown that the enzyme cyclooxygenase‐2 (COX‐2) and its prostanoid products, prostaglandin E2 (PGE2) in particular, are key contributors in in vitro models of infectious exacerbation; however, the impact of IL‐17A was not known.Methods and ResultsWe address this herein and show that IL‐17A induces a robust and sustained upregulation of COX‐2 protein and PGE2 secretion from airway smooth muscle (ASM) cells. COX‐2 can be regulated at transcriptional, post‐transcriptional and/or post‐translational levels. We have elucidated the underlying molecular mechanisms responsible for the sustained upregulation of TNF‐α‐induced COX‐2 by IL‐17A in ASM cells and show that is not via increased COX‐2 gene expression. Instead, TNF‐α‐induced COX‐2 upregulation is subject to regulation by the proteasome, and IL‐17A acts to increase TNF‐α‐induced COX‐2 protein stability as confirmed by cycloheximide chase experiments. In this way, IL‐17A acts to amplify the COX‐2‐mediated effects of TNF‐α and greatly enhances PGE2 secretion from ASM cells.ConclusionAs PGE2 is a multifunctional prostanoid with diverse roles in respiratory disease, our studies demonstrate a novel function for IL‐17A in airway inflammation by showing for the first time that IL‐17A impacts on the COX‐2/PGE2 pathway, molecules known to contribute to disease exacerbation.

Rumzhum, NN, Rahman, MM, Oliver, BG & Ammit, AJ 2016, 'Effect of Sphingosine 1-Phosphate on Cyclo-Oxygenase-2 Expression, Prostaglandin E₂ Secretion, and β₂-Adrenergic Receptor Desensitization', American Journal of Respiratory Cell and Molecular Biology, vol. 54, no. 1, pp. 128-135.
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Copyright © 2016 by the American Thoracic Society. Tachyphylaxis of the β2-adrenergic receptor limits the efficacy of bronchodilatory β2-agonists in respiratory disease. Cellular studies in airway smooth muscle (ASM) have shown that inflammatory mediators and infectious stimuli reduce β2-adrenergic responsiveness in a cyclo-oxygenase (COX)-2-mediated, prostaglandin E2 (PGE2)-dependant manner. Herein, we show that sphingosine 1-phosphate (S1P), abioactive sphingolipid thatplays an important role in pathophysiology of asthma, also induces β2-adrenergic receptor desensitization in bronchial ASM cells and exerts hyporesponsiveness to β2-agonists. We treated ASM cells with S1P (1 μM) for up to 24 hours and then examined the temporal kinetics of COX-2 mRNA expression, protein up-regulation, and PGE2 secretion. S1P significantly enhanced COX-2 expression and PGE2 secretion, and this was repressed by the selective COX-2 inhibitor celecoxib, the corticosteroid dexamethasone, or small interfering RNA (siRNA) knockdown of COX-2 expression. In combination with another proinflammatory mediator found elevated in asthmatic airways, the cytokine TNF-α, we observed that S1P-induced COX-2 mRNA expression and protein up-regulation and PGE2 secretion from ASM cells were significantly enhanced. Notably, S1P induced heterologous β2-adrenergic desensitization, as measured by inhibition of cyclic adenosine monophosphate production in response to the short-acting β2-agonist, salbutamol, and the long-acting β2-agonist, formoterol. Taken together, these data indicate that S1P represses β2-adrenergic activity in ASM cells by increasing COX-2-mediated PGE2 production, and suggest that this bioactive sphingolipid found elevated in asthma may contribute to β2-adrenergic desensitization.

Russell, KE, Chung, KF, Clarke, CJ, Durham, AL, Mallia, P, Footitt, J, Johnston, SL, Barnes, PJ, Hall, SR, Simpson, KD, Starkey, MR, Hansbro, PM, Adcock, IM & Wiegman, CH 2016, 'The MIF Antagonist ISO-1 Attenuates Corticosteroid-Insensitive Inflammation and Airways Hyperresponsiveness in an Ozone-Induced Model of COPD', PLOS ONE, vol. 11, no. 1, pp. e0146102-e0146102.
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Copyright © 2016 Russell 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. Macrophage migration inhibitory factor (MIF) is an inflammatory cytokine associated with acute and chronic inflammatory disorders and corticosteroid insensitivity. Its expression in the airways of patients with chronic obstructive pulmonary disease (COPD), a relatively steroid insensitive inflammatory disease is unclear, however. Methods. Sputum, bronchoalveolar lavage (BAL) macrophages and serum were obtained from nonsmokers, smokers and COPD patients. To mimic oxidative stress-induced COPD, mice were exposed to ozone for six-weeks and treated with ISO-1, a MIF inhibitor, and/or dexamethasone before each exposure. BAL fluid and lung tissue were collected after the final exposure. Airway hyperresponsiveness (AHR) and lung function were measured using whole body plethysmography. HIF-1α binding to the Mif promoter was determined by Chromatin Immunoprecipitation assays. Results. MIF levels in sputum and BAL macrophages from COPD patients were higher than those from non-smokers, with healthy smokers having intermediate levels. MIF expression correlated with that of HIF-1α in all patients groups and in ozone-exposed mice. BAL cell counts, cytokine mRNA and protein expression in lungs and BAL, including MIF, were elevated in ozone-exposed mice and had increased AHR. Dexamethasone had no effect on these parameters in the mouse but ISO-1 attenuated cell recruitment, cytokine release and AHR. Conclusion MIF and HIF-1α levels are elevated in COPD BAL macrophages and inhibition of MIF function blocks corticosteroid-insensitive lung inflammation and AHR. Inhibition of MIF may provide a novel anti-inflammatory approach in COPD.

Ryan, LM, Wand, MP & Malecki, AA 2016, 'Bringing Coals to Newcastle', Significance, vol. 13, no. 6, pp. 32-37.
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Abstract Making effective public policy decisions is challenging at the best of times, but especially in the context of environmental regulation, which typically requires managing opposing interests and strong opinions from industry and private citizens. In this case study, Louise Ryan, Matt Wand and Alan Malecki show how statistical analysis can help resolve conflict and inform effective decision-making under uncertainty

Sablok, G, Mudunuri, SB, Edwards, D & Ralph, PJ 2016, 'Chloroplast genomics: Expanding resources for an evolutionary conserved miniature molecule with enigmatic applications', Current Plant Biology, vol. 7-8, pp. 34-38.
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© 2016 The Authors Chloroplast, methylation depreived uniparental organelle genome is the most studied organelle genome from the perspective of evolution and functional omics. Recent advances in organelle genome sequencing both in terms of genome or transcriptome sequencing has opened a wide range of opportunities to understand the transcriptional and translational role of the genes mainly involved in the light harvesting apparatus and the evolution of the inverted repeats across the lineage. However, as compared to the nuclear genome, limited resources are available in case of organelle genome. In this review, we discuss the recent advances in the chloroplast genomics and the resources that have been developed for understanding the evolution, repeat patterns, functional genomics of this miniature molecule with enigmatic applications.

Sablok, G, Pérez-Pulido, AJ, Do, T, Seong, TY, Casimiro-Soriguer, CS, La Porta, N, Ralph, PJ, Squartini, A, Muñoz-Merida, A & Harikrishna, JA 2016, 'PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers', Frontiers in Plant Science, vol. 7, pp. 1-9.
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© 2016 Sablok, Pérez-Pulido, Do, Seong, Casimiro-Soriguer, La Porta, Ralph, Squartini, Muñoz-Merida and Harikrishna. Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intrageneric differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www. bioinfocabd.upo.es/plantssr.

Sackett, O, Petrou, K, Reedy, B, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2016, 'Snapshot prediction of carbon productivity, carbon and protein content in a Southern Ocean diatom using FTIR spectroscopy', ISME JOURNAL, vol. 10, no. 2, pp. 416-426.
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© 2016 International Society for Microbial Ecology All rights reserved. Diatoms, an important group of phytoplankton, bloom annually in the Southern Ocean, covering thousands of square kilometers and dominating the region's phytoplankton communities. In their role as the major food source to marine grazers, diatoms supply carbon, nutrients and energy to the Southern Ocean food web. Prevailing environmental conditions influence diatom phenotypic traits (for example, photophysiology, macromolecular composition and morphology), which in turn affect the transfer of energy, carbon and nutrients to grazers and higher trophic levels, as well as oceanic biogeochemical cycles. The paucity of phenotypic data on Southern Ocean phytoplankton limits our understanding of the ecosystem and how it may respond to future environmental change. Here we used a novel approach to create a 'snapshot' of cell phenotype. Using mass spectrometry, we measured nitrogen (a proxy for protein), total carbon and carbon-13 enrichment (carbon productivity), then used this data to build spectroscopy-based predictive models. The models were used to provide phenotypic data for samples from a third sample set. Importantly, this approach enabled the first ever rate determination of carbon productivity from a single time point, circumventing the need for time-series measurements. This study showed that Chaetoceros simplex was less productive and had lower protein and carbon content during short-term periods of high salinity. Applying this new phenomics approach to natural phytoplankton samples could provide valuable insight into understanding phytoplankton productivity and function in the marine system.

Sadaf, T, John, P, Bhatti, A, Jahangir, S, Kiani, AK, Gill, FA & Malik, JM 2016, 'Lack of tumor necrosis factor alpha gene polymorphism ‐857c/t (rs1799724) association in Pakistani rheumatoid arthritis patients', International Journal of Rheumatic Diseases, vol. 19, no. 11, pp. 1119-1125.
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AbstractBackgroundRheumatoid arthritis (RA) is a common systemic autoimmune disease, influenced greatly by the pro‐inflammatory cytokine tumor necrosis factor‐ alpha (TNF‐α). Single nucleotide polymorphisms (SNPs) in regulatory regions of the TNF‐α gene play a significant role in disease development and pathogenesis. The aim of this study was to investigate the association of TNF‐α ‐857C/T (rs1799724) SNP with RA activity or severity in our Pakistani study group.MethodsThe study included 134 (116 women, 18 men) patients with RA and 134 ethnically matched healthy controls (108 women, 26 men). Each patient's disease activity was measured by Disease Activity Score of 28 joints. The genotypes were determined in all included individuals following allele‐specific polymerase chain reaction along with the prerequisite internal amplification controls. Statistical analysis including chi‐square/Fischer exact test and one‐way analysis of variance; nonparametric Kruskal–Wallis test was employed using Graphpad Prism 6 software for association study.ResultsThe prevalence of TNF‐α ‐857C/T (rs1799724) polymorphism was not differentially distributed between RA patients and...

Saeki, N, Kawanabe, T, Ying, H, Shimizu, M, Kojima, M, Abe, H, Okazaki, K, Kaji, M, Taylor, JM, Sakakibara, H, Peacock, WJ, Dennis, ES & Fujimoto, R 2016, 'Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage', BMC PLANT BIOLOGY, vol. 16.
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Safarchi, A, Octavia, S, Luu, LDW, Tay, CY, Sintchenko, V, Wood, N, Marshall, H, McIntyre, P & Lan, R 2016, 'Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study', Vaccine, vol. 34, no. 34, pp. 3967-3971.
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Molecular epidemiological data indicates that the resurgence of pertussis (whooping cough) in populations with high vaccine coverage is associated with genomic adaptation of Bordetella pertussis, the causative agent of the disease, to vaccine selection pressure. We have previously shown that in the period after the introduction of acellular pertussis vaccine (ACV), the majority of circulating strains in Australia switched to single nucleotide polymorphism (SNP) cluster I (carrying ptxP3/prn2), replacing SNP cluster II (carrying ptxP1/prn3). In this study, we carried out an in vivo competition assay using a mouse model infected with SNP cluster I and II B. pertussis strains from Australia. We found that the SNP cluster I strain colonised better than the SNP cluster II strain, in both naïve and immunised mice, suggesting that SNP cluster I strains had better fitness regardless of immunisation status of the host, consistent with SNP cluster I strains replacing SNP cluster II. Nevertheless, we found that ACV enhanced clearance of both SNP cluster I and II strains from the mouse respiratory tract.

Saleska, SR, Wu, J, Guan, K, Araujo, AC, Huete, A, Nobre, AD & Restrepo-Coupe, N 2016, 'Dry-season greening of Amazon forests', NATURE, vol. 531, no. 7594, pp. E4-E5.
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Sampson, JN, Matthews, CE, Freedman, LS, Carroll, RJ & Kipnis, V 2016, 'Methods to assess measurement error in questionnaires of sedentary behavior', Journal of Applied Statistics, vol. 43, no. 9, pp. 1706-1721.
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Santini, NS, Cleverly, J, Faux, R, Lestrange, C, Rumman, R & Eamus, D 2016, 'Xylem traits and water-use efficiency of woody species co-occurring in the Ti Tree Basin arid zone', TREES-STRUCTURE AND FUNCTION, vol. 30, no. 1, pp. 295-303.
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© 2015, Springer-Verlag Berlin Heidelberg. Key message: Species with low density of intact branches are likely to have higher growth rates than species with high density of intact branches, but at the cost of a lower water-use efficiency and larger sensitivity to xylem embolism. Abstract: The hydraulic niche separation theory proposes that species co-exist by having a range of traits to allow differential access to resources within heterogeneous environments. Here, we examined variation in branch xylem anatomy and foliar carbon stable isotopes (δ13C) as a measure of water-use efficiency (WUE) in seven co-occurring species, Acacia aneura, Acacia bivenosa, Corymbia opaca, Eucalyptus camaldulensis, Erythrinavespertilio, Hakea sp., and Psydrax latifolia, in an arid zone open Corymbia savanna on the Ti Tree Basin, Northern Territory, Australia. We test the following hypotheses: (1) Species with large conductive areas exhibit a low density of intact branches, while species with small conductive areas have a significantly higher density of intact branches. (2) Species with smaller conductive areas exhibit more enriched values of δ13C and therefore have larger WUE than those with larger conductive areas and (3) there is an inverse correlation between theoretical sapwood hydraulic conductivity and vessel implosion resistance. The results of this study demonstrated significant variation in density of intact branches, ranging from 0.38 to 0.80 g cm−3 and this variation was largely explained by variation in sapwood conductive area. Species with low conductive areas (P. latifolia, Hakea sp. and Acacia species) exhibited large values of WUE (r2 = 0.62, p < 0.05). These species are likely to be less vulnerable to cavitation by having small conductive areas and thicker fibre walls. We demonstrated a significant (r2 = 0.83, p = 0.004) negative correlation between theoretical sapwood hydraulic conductivity and vessel implosion resistance. These results are discussed in r...

Satija, S, Malik, S & Garg, M 2016, 'Development of a new, rapid, and sensitive validated high-performance thin-layer chromatographic method for the estimation of berberine inTinospora cordifolia', JPC - Journal of Planar Chromatography - Modern TLC, vol. 29, no. 3, pp. 209-215.
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Sayyadi, N, Care, A, Connally, RE, Try, AC, Bergquist, PL & Sunna, A 2016, 'A Novel Universal Detection Agent for Time-Gated Luminescence Bioimaging', Scientific Reports, vol. 6, no. 1.
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AbstractLuminescent lanthanide chelates have been used to label antibodies in time-gated luminescence (TGL) bioimaging. However, it is a challenging task to label directly an antibody with lanthanide-binding ligands and achieve control of the target ligand/protein ratios whilst ensuring that affinity and avidity of the antibody remain uncompromised. We report the development of a new indirect detection reagent to label antibodies with detectable luminescence that circumvents this problem by labelling available lysine residues in the linker portion of the recombinant fusion protein Linker-Protein G (LPG). Succinimide-activated lanthanide chelating ligands were attached to lysine residues in LPG and Protein G (without Linker) and the resulting Luminescence-Activating (LA-) conjugates were compared for total incorporation and conjugation efficiency. A higher and more efficient incorporation of ligands at three different molar ratios was observed for LPG and this effect was attributed to the presence of eight readily available lysine residues in the linker region of LPG. These Luminescence-Activating (LA-) complexes were subsequently shown to impart luminescence (upon formation of europium(III) complexes) to cell-specific antibodies within seconds and without the need for any complicated bioconjugation procedures. The potential of this technology was demonstrated by direct labelling of Giardia cysts and Cryptosporidium oocysts in TGL bioimaging.

Sayyadi, N, Justiniano, I, Connally, RE, Zhang, R, Shi, B, Kautto, L, Everest-Dass, AV, Yuan, J, Walsh, BJ, Jin, D, Willows, RD, Piper, JA & Packer, NH 2016, 'Sensitive Time-Gated Immunoluminescence Detection of Prostate Cancer Cells Using a TEGylated Europium Ligand', Analytical Chemistry, vol. 88, no. 19, pp. 9564-9571.
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Scajev, P, Malinauskas, T, Seniutinas, G, Arnold, MD, Gentle, A, Aharonovich, I, Gervinskas, G, Michaux, P, Hartley, JS, Mayes, ELH, Stoddart, PR & Juodkazis, S 2016, 'Light-induced reflectivity transients in black-Si nanoneedles', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 144, pp. 221-227.
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© 2015 Elsevier B.V. All rights reserved. The change in reflectivity of black-Si (b-Si) upon optical excitation was measured by the pump-probe technique using picosecond laser pulses at 532 (pump) and 1064 nm (probe) wavelengths. The specular reflection from the random pattern of plasma-etched b-Si nano-needles was dominated by the photo-excited free-carrier contribution to the reflectivity. The kinetics of the reflectivity were found to be consistent with surface structural and chemical analysis, performed by scanning and transmission electron microscopy, and spectroscopic ellipsometry. The surface recombination velocity on the b-Si needles was estimated to be ~10²cm/s. Metalization of b-Si led to much faster recombination and alteration of reflectivity. The reflectivity spectra of random b-Si surfaces with different needle lengths was modeled by a multi-step refractive index profile in the Drude formalism. The dip in the reflectivity spectra and the sign reversal in the differential reflectivity signal at certain b-Si needle sizes is explained by the model.

Scanes, E, Johnston, E, Cole, V, O’Connor, W, Parker, L & Ross, P 2016, 'Quantifying abundance and distribution of native and invasive oysters in an urbanised estuary', Aquatic Invasions, vol. 11, no. 4, pp. 425-436.
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Human activities have modified the chemical, physical and biological attributes of many of the world’s estuaries. Natural foreshores have been replaced by artificial habitats and non-indigenous species have been introduced by shipping, aquaculture, and as ornamental pets. In south east Australia, the native Sydney rock oyster Saccostrea glomerata is threatened by pollution, disease and competition from the invasive Pacific oyster Crassostrea gigas. This study assessed the abundance (as number m-2), size, and distribution of both invasive and native oyster species at 32 sites in the heavily urbanised Port Jackson Estuary, Australia. We tested the hypotheses that there would be: (1) a difference in the proportion of C. gigas and S. glomerata among locations; (2) a greater proportion of C. gigas on artificial compared to natural substrates; (3) a greater numbers of all oysters, with differing size characteristics, on artificial compared to natural substrates; and (4) that the abundance and size of all oysters would vary among locations along an environmental gradient. Environmental variables included distance from the estuary mouth and salinity. We found the abundance and size of all oysters differed among locations; smaller oysters occurred at greater abundances near the mouth of the estuary. Abundance was also higher on artificial, than on natural substrate. Habitat type, however, had no effect on which species of oyster was present. In contrast, distance from the estuary mouth strongly influenced the relative proportion of the two species. The invasive C. gigas comprised 16% of the oysters sampled, and up to 85% at some of the upper estuary sites. As predicted, C. gigas was more abundant at locations in the bay ends and upper channel of the estuary; it was also larger in size than the native S. glomerata. This is the first assessment of oyster distribution in Port Jackson and provides a solid base for monitoring changes in the estuarine distribution of ...

Schell, AW, Tran, TT, Takashima, H, Takeuchi, S & Aharonovich, I 2016, 'Non-linear excitation of quantum emitters in hexagonal boron nitride multiplayers', APL Photonics, vol. 1, no. 9, pp. 091302-091302.
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Two-photon absorption is an important non-linear process employed for high resolution bio-imaging and non-linear optics. In this work, we realize two-photon excitation of a quantum emitter embedded in a two-dimensional (2D) material. We examine defects in hexagonal boron nitride (hBN) and show that the emitters exhibit similar spectral and quantum properties under one-photon and two-photon excitation. Furthermore, our findings are important to deploy two-dimensional hexagonal boron nitride for quantum non-linear photonic applications.

Schmerl, NM, Gentle, AR, Quinton, JS, Smith, GB & Andersson, GG 2016, 'Surface and Near Surface Area Density of States for Magnetron-Sputtered ZnO and Al-ZnO: A MIES, UPS, and VBXPS Study Investigating Ultrahigh Vacuum Sputter Cleaning and UV Oxygen Plasma', The Journal of Physical Chemistry C, vol. 120, no. 29, pp. 15772-15784.
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Schneider, A, Steinberger, I, Herdean, A, Gandini, C, Eisenhut, M, Kurz, S, Morper, A, Hoecker, N, Rühle, T, Labs, M, Flügge, UI, Geimer, S, Schmidt, SB, Husted, S, Weber, APM, Spetea, C & Leister, D 2016, 'The Evolutionarily Conserved Protein PHOTOSYNTHESIS AFFECTED MUTANT71 is Required for Efficient Manganese Uptake at the Thylakoid Membrane in Arabidopsis', The Plant Cell, vol. 28, no. 4, pp. tpc.00812.2015-tpc.00812.2015.
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Schrameyer, V, Krämer, W, Hill, R, Jeans, J, Larkum, AWD, Bischof, K, Campbell, DA & Ralph, PJ 2016, 'Under high light stress two Indo-Pacific coral species display differential photodamage and photorepair dynamics', Marine Biology, vol. 163, no. 8.
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Schwendener, G, Moret, S, Cavanagh-Steer, K & Roux, C 2016, 'Can 'contamination' occur in body bags?-The example of background fibres in body bags used in Australia', FORENSIC SCIENCE INTERNATIONAL, vol. 266, pp. 517-526.
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Scott, JA, Totonjian, D, Martin, AA, Tran, TT, Fang, J, Toth, M, McDonagh, AM, Aharonovich, I & Lobo, CJ 2016, 'Versatile method for template-free synthesis of single crystalline metal and metal alloy nanowires', Nanoscale, vol. 8, no. 5, pp. 2804-2810.
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A versatile, template-free growth technique for single crystalline metal nanowires using gas or solution phase precursors.

Seoudi, RS, Dowd, A, Smith, BJ & Mechler, A 2016, 'Structural analysis of bioinspired nano materials with synchrotron far IR spectroscopy', Physical Chemistry Chemical Physics, vol. 18, no. 16, pp. 11467-11473.
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Synchrotron far-infrared spectroscopy was used in conjunction with density functional theory vibrational analysis to ascertain the core structure of self-assembled fibrous superstructures formed by unnatural β³-tripeptides.

Setzpfandt, F, Solntsev, AS & Sukhorukov, AA 2016, 'Nonlocal splitting of photons on a nonlinear chip', Optics Letters, vol. 41, no. 23, pp. 5604-5604.
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In spontaneous parametric downconversion (SPDC), a pump photon spontaneously splits into signal and idler photons in media with quadratic nonlinearity. This phenomenon is the most widely utilized source of entangled photons with multiple applications in quantum information technology. SPDC on a chip is usually treated as a local process, meaning that signal and idler photons are created in the same position at which the pump photon is destroyed. We reveal that this locality condition can be violated in an array of coupled waveguides. By utilizing higher-order modes of individual waveguides, it is possible to destroy a pump photon in one waveguide and to generate signal and idler photons in other waveguides. This phenomenon of nonlocal photon-pair generation opens new opportunities for the engineering of spatial photon entanglement.

Setzpfandt, F, Solntsev, AS, Titchener, J, Wu, CW, Xiong, C, Schiek, R, Pertsch, T, Neshev, DN & Sukhorukov, AA 2016, 'Tunable generation of entangled photons in a nonlinear directional coupler', Laser & Photonics Reviews, vol. 10, no. 1, pp. 131-136.
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AbstractThe on‐chip integration of quantum light sources has enabled the realization of complex quantum photonic circuits. However, for the practical implementation of such circuits in quantum information applications, it is crucial to develop sources delivering entangled quantum photon states with on‐demand tunability. Here we propose and experimentally demonstrate the concept of a widely tunable quantum light source based on spontaneous parametric down‐conversion in a simple nonlinear directional coupler. We show that spatial photon‐pair correlations and entanglement can be reconfigured on‐demand by tuning the phase difference between the pump beams and the phase mismatch inside the structure. We experimentally demonstrate the generation of split states, robust N00N states, various intermediate regimes and biphoton steering on a single chip. Furthermore we theoretically investigate other regimes allowing all‐optically tunable generation of all Bell states and flexible control of path‐energy entanglement. Such wide‐range capabilities of a structure comprised of just two coupled nonlinear waveguides are attributed to the intricate interplay between linear coupling and nonlinear phase matching. This scheme provides an important advance towards the realization of reconfigurable quantum circuitry.image

Shah, JS, Soon, PS & Marsh, DJ 2016, 'Comparison of Methodologies to Detect Low Levels of Hemolysis in Serum for Accurate Assessment of Serum microRNAs', PLOS ONE, vol. 11, no. 4, pp. e0153200-e0153200.
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Shahcheraghi, N, Keast, VJ, Gentle, AR, Arnold, MD & Cortie, MB 2016, 'Anomalously strong plasmon resonances in aluminium bronze by modification of the electronic density-of-states', Journal of Physics: Condensed Matter, vol. 28, no. 40, pp. 405501-405501.
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© 2016 IOP Publishing Ltd. We use a combination of experimental measurements and density functional theory calculations to show that modification of the band structure of Cu by additions of Al causes an unexpected enhancement of the dielectric properties. The effect is optimized in alloys with Al contents between 10 and 15 at.% and would result in strong localized surface plasmon resonances at suitable wavelengths of light. This result is surprising as, in general, alloying of Cu increases its DC resistivity and would be expected to increase optical loss. The wavelengths for the plasmon resonances in the optimized alloy are significantly blue-shifted relative to those of pure Cu and provide a new material selection option for the range 2.2-2.8 eV.

Shahid, M, El Saliby, I, McDonagh, A, Chekli, L, Tijing, LD, Kim, J-H & Shon, HK 2016, 'Adsorption and Photocatalytic Degradation of Methylene Blue Using Potassium Polytitanate and Solar Simulator', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 16, no. 5, pp. 4342-4349.
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Copyright © 2016 American Scientific Publishers All rights reserved. Solar photocatalytic degradation of organic water pollutants can be used to degrade toxic organic pollutants in water. In this study, potassium titanate nanofibres were synthesized by an aqueous peroxide route at high pH and examined as photocatalysts for photodegradation of methylene blue (MB) using a solar simulator. Initially, MB was adsorbed on the surface of potassium polytitanates to achieve adsorption equilibrium before the photocatalysts were illuminated using solar simulator. The results showed that potassium polytitanate nanofibres were effective adsorbents of MB and also facilitated its photocatalytic degradation. Sulphate ion evolution during photocatalysis confirmed that some mineralisation occurred and hence photo-oxidative degradation of MB took place. The optimum operational conditions for the photocatalytic degradation of MB were found at 0.05 g/L of photocatalyst load, 10 mg/L MB and pH 7. The stability and regeneration of the photocatalyst specimen was also studied for 3 degradation cycles using adsorption/photocatalysis model. Morphological structure analysis of potassium titanate showed nanocrystallines structure of longitudinally-oriented isolated fibre with a length up to several micrometres with diameters ranging from 10 to 20 nanometres.

Shahid, M, Tijing, LD, Saliby, IE, McDonagh, A, Kim, J-B, Kim, J-H & Shon, HK 2016, 'Adsorption Behavior of Pb(II) Onto Potassium Polytitanate Nanofibres', Journal of Nanoscience and Nanotechnology, vol. 16, no. 2, pp. 1916-1919.
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Copyright © 2016 American Scientific Publishers All rights reserved. Potassium polytitanate nanofibres prepared by a hydrothermal method were investigated for their possible application in removing toxic metals from aqueous solution. Particular attention was paid to employing the titanate as a novel effective adsorbent for the removal of Pb(II). Batch adsorption experiments demonstrated that the adsorption was influenced by various conditions such as solution pH, adsorbent dosage and initial Pb(II) concentration. The results showed that the adsorption rate was faster in the first 5 min and equilibrium was achieved after 180 min. The maximum amount of adsorption was detected at pH 5. Potassium titanate showed much higher adsorption capacity compared to P25. The kinetic studies indicated that the adsorption of Pb(II) onto titanate best fit the pseudo-second-order kinetic model. FTIR spectra revealed that the hydroxyl groups in titanate were responsible for Pb(II) adsorption. The principal mechanism of the adsorption of Pb(II) in the present study is attributed to both ion exchange and oxygen bonding. The adsorption-desorption results demonstrated that the titanate could be readily regenerated after adsorption. Therefore, the present titanate exhibits great potential for the removal of Pb(II) from wastewater.

Shanley, TW, Bonnie, F, Scott, J & Toth, M 2016, 'Role of Gas Molecule Complexity in Environmental Electron Microscopy and Photoelectron Yield Spectroscopy', ACS Applied Materials & Interfaces, vol. 8, no. 40, pp. 27305-27310.
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© 2016 American Chemical Society. Environmental scanning electron microscopy (ESEM) and environmental photoelectron yield spectroscopy (EPYS) enable electron imaging and spectroscopy of surfaces and interfaces in low-vacuum gaseous environments. The techniques are both appealing and limited by the range of gases that can be used to amplify electrons emitted from a sample and used to form images/spectra. However, to date only H2O and NH3 gases have been identified as highly favorable electron amplification media. Here we demonstrate that ethanol vapor (CH3CH2OH) is superior to both of these and attribute its performance to its molecular complexity and valence orbital structure. Our findings improve the present understanding of what constitutes a favorable electron amplification gas and will help expand the applicability and usefulness of the ESEM and EPYS techniques.

Shen, Z, Wang, G, Tian, H, Sunarso, J, Liu, L, Liu, J & Liu, S 2016, 'Bi-layer photoanode films of hierarchical carbon-doped brookite-rutile TiO 2 composite and anatase TiO 2 beads for efficient dye-sensitized solar cells', Electrochimica Acta, vol. 216, pp. 429-437.
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Shi, Y, Shi, B, Dass, AVE, Lu, Y, Sayyadi, N, Kautto, L, Willows, RD, Chung, R, Piper, J, Nevalainen, H, Walsh, B, Jin, D & Packer, NH 2016, 'Stable Upconversion Nanohybrid Particles for Specific Prostate Cancer Cell Immunodetection', Scientific Reports, vol. 6, no. 1, pp. 1-11.
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AbstractProstate cancer is one of the male killing diseases and early detection of prostate cancer is the key for better treatment and lower cost. However, the number of prostate cancer cells is low at the early stage, so it is very challenging to detect. In this study, we successfully designed and developed upconversion immune-nanohybrids (UINBs) with sustainable stability in a physiological environment, stable optical properties and highly specific targeting capability for early-stage prostate cancer cell detection. The developed UINBs were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS) and luminescence spectroscopy. The targeting function of the biotinylated antibody nanohybrids were confirmed by immunofluorescence assay and western blot analysis. The UINB system is able to specifically detect prostate cancer cells with stable and background-free luminescent signals for highly sensitive prostate cancer cell detection. This work demonstrates a versatile strategy to develop UCNPs based sustainably stable UINBs for sensitive diseased cell detection.

Shimoni, O, Shi, B, Adlard, PA & Bush, AI 2016, 'Delivery of Fluorescent Nanoparticles to the Brain', Journal of Molecular Neuroscience, vol. 60, no. 3, pp. 405-409.
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© 2016, Springer Science+Business Media New York. Nanotechnology applications in neuroscience promises to deliver significant scientific and technological breakthroughs, providing answers to unresolved questions regarding the processes occurring in the brain. In this perspective, we provide a short background on two distinct fluorescent nanoparticles and summarize several studies focussed on achieving delivery of these into the brain and their interaction with brain tissue. Furthermore, we discuss challenges and opportunities for further development of nanoparticle-based therapies for targeting delivery of drugs across the blood-brain barrier.

Siboni, N, Balaraju, V, Carney, R, Labbate, M & Seymour, JR 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7, no. APR.
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© 2016 Siboni, Balaraju, Carney, Labbate and Seymour. Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for th...

Simpson, JL, Baines, KJ, Horvat, JC, Essilfie, A, Brown, AC, Tooze, M, McDonald, VM, Gibson, PG & Hansbro, PM 2016, 'COPD is characterized by increased detection of Haemophilus influenzae, Streptococcus pneumoniae and a deficiency of Bacillus species', Respirology, vol. 21, no. 4, pp. 697-704.
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AbstractBackground and objectiveChronic obstructive pulmonary disease (COPD) is characterized by progressive airflow limitation and inflammation. Airway bacterial colonization is increased in COPD; however, the role of potentially pathogenic and non‐pathogenic bacteria in the pathogenesis of disease is unclear. This study characterized the presence of bacteria in a well‐characterized cohort of adults with COPD and healthy controls.MethodsAdults with COPD (n = 70) and healthy controls (n = 51) underwent clinical assessment and sputum induction. Sputum was dispersed, and total and differential cell counts were performed. Bacteria were cultured, identified and enumerated. Supernatants were assessed for neutrophil elastase (NE) and IL‐1β. Common respiratory pathogens were also determined using real‐time PCR.ResultsParticipants with COPD had a typical neutrophilic inflammatory profile. The total load of bacteria was increased in COPD and was associated with poorer respiratory health status, as measured by the St George's

Slavov, C, Schrameyer, V, Reus, M, Ralph, PJ, Hill, R, Büchel, C, Larkum, AWD & Holzwarth, AR 2016, '“Super-quenching” state protects Symbiodinium from thermal stress — Implications for coral bleaching', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1857, no. 6, pp. 840-847.
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The global rise in sea surface temperatures causes regular exposure of corals to high temperature and high light stress, leading to worldwide disastrous coral bleaching events (loss of symbiotic dinoflagellates (Symbiodinium) from reef-building corals). Our picosecond chlorophyll fluorescence experiments on cultured Symbiodinium clade C cells exposed to coral bleaching conditions uncovered the transformations of the alga's photosynthetic apparatus (PSA) that activate an extremely efficient non-photochemical 'super-quenching' mechanism. The mechanism is associated with a transition from an initially heterogeneous photosystem II (PSII) pool to a homogeneous 'spillover' pool, where nearly all excitation energy is transferred to photosystem I (PSI). There, the inherently higher stability of PSI and high quenching efficiency of P(700)(+) allow dumping of PSII excess excitation energy into heat, resulting in almost complete cessation of photosynthetic electron transport (PET). This potentially reversible 'super-quenching' mechanism protects the PSA against destruction at the cost of a loss of photosynthetic activity. We suggest that the inhibition of PET and the consequent inhibition of organic carbon production (e.g. sugars) in the symbiotic Symbiodinium provide a trigger for the symbiont expulsion, i.e. bleaching.

Smith, DG, Sajid, N, Rehn, S, Chandramohan, R, Carney, IJ, Khan, MA & New, EJ 2016, 'A library-screening approach for developing a fluorescence sensing array for the detection of metal ions', The Analyst, vol. 141, no. 15, pp. 4608-4613.
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A four-membered array based on fluorescent thiophenes is capable of distinguishing transition metal ions.

Smith, G, Gentle, A, Arnold, M & Cortie, M 2016, 'Nanophotonics-enabled smart windows, buildings and wearables', Nanophotonics, vol. 5, no. 1, pp. 55-73.
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AbstractDesign and production of spectrally smart windows, walls, roofs and fabrics has a long history, which includes early examples of applied nanophotonics. Evolving nanoscience has a special role to play as it provides the means to improve the functionality of these everyday materials. Improvement in the quality of human experience in any location at any time of year is the goal. Energy savings, thermal and visual comfort indoors and outdoors, visual experience, air quality and better health are all made possible by materials, whose “smartness” is aimed at designed responses to environmental energy flows. The spectral and angle of incidence responses of these nanomaterials must thus take account of the spectral and directional aspects of solar energy and of atmospheric thermal radiation plus the visible and color sensitivity of the human eye. The structures required may use resonant absorption, multilayer stacks, optical anisotropy and scattering to achieve their functionality. These structures are, in turn, constructed out of particles, columns, ultrathin layers, voids, wires, pure and doped oxides, metals, polymers or transparent conductors (TCs). The need to cater for wavelengths stretching from 0.3 to 35 μm including ultraviolet-visible, near-infrared (IR) and thermal or Planck radiation, with a spectrally and directionally complex atmosphere, and both being dynamic, means that hierarchical and graded nanostructures often feature. Nature has evolved to deal with the same energy flows, so biomimicry is sometimes a useful guide.

Smith, KF, Rhodes, L, Verma, A, Curley, BG, Harwood, DT, Kohli, GS, Solomona, D, Rongo, T, Munday, R & Murray, SA 2016, 'A new Gambierdiscus species (Dinophyceae) from Rarotonga, Cook Islands: Gambierdiscus cheloniae sp. nov', Harmful Algae, vol. 60, pp. 45-56.
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© 2016 Elsevier B.V. Ciguatera fish poisoning (CFP) has been reported for many years in Rarotonga, Cook Islands, and has had the world's highest reported incidence of this illness for the last 20 years. Following intensive sampling to understand the distribution of the causative organisms of CFP, an undescribed Gambierdiscus species was isolated from the Rarotongan lagoon. Gambierdiscus cheloniae sp. nov. has the common Gambierdiscus Kofoidian plate formula (except for a variability in the number of precingular plates in aberrant cells): Po, 3′, 6″ (7″), 6C?, 6 or 7S, 5′″, 1p and 2″″. The 2′ plate is hatchet shaped and the dorsal end of 1p is pointed and the relatively narrow 1p plate. Morphologically G. cheloniae is similar to the genetically closely related species G. pacificus, G. toxicus and G. belizeanus, although smaller (depth and length) than G. toxicus. The apical pore plate varies from those of G. belizeanus and G. pacificus, which are shorter and narrower, and from G. toxicus, which is larger. G. cheloniae also differs from G. pacificus in the shape of the 2′ plate. The description of this new species is supported by phylogenetic analyses using three different gene regions. G. cheloniae produced the putative maitotoxin-3 analogue, MTX-3, but neither maitotoxin or monitored ciguatoxin. Extracts of G. cheloniae were shown to be highly toxic to mice by intraperitoneal (i.p.) injection, although they were less toxic by gavage. It is possible that this species produces toxins other than putative MTX-3.

Smith, MJA, Kuhlmey, BT, de Sterke, CM, Wolff, C, Lapine, M & Poulton, CG 2016, 'Metamaterial control of stimulated Brillouin scattering', Optics Letters, vol. 41, no. 10, pp. 2338-2338.
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© 2016 Optical Society of America. Using full opto-acoustic numerical simulations, we demonstrate enhancement and suppression of the SBS gain in a metamaterial comprising a subwavelength cubic array of dielectric spheres suspended in a dielectric background material. We develop a general theoretical framework and present several numerical examples using technologically important materials. For As2 S3 spheres in silicon, we achieve a gain enhancement of more than an order of magnitude compared to pure silicon and for GaAs spheres in silicon, full suppression is obtained. The gain for As2 S3 glass can also be strongly suppressed by embedding silica spheres. The constituent terms of the gain coefficient are shown to depend in a complex way on the filling fraction. We find that electrostriction is the dominant effect behind the control of SBS in bulk media.

Smith, MJA, Wolff, C, de Sterke, CM, Lapine, M, Kuhlmey, BT & Poulton, CG 2016, 'Stimulated Brillouin scattering enhancement in silicon inverse opal waveguides', Optics Express, vol. 24, no. 22, pp. 25148-25148.
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© 2016 Optical Society of America. Silicon is an ideal material for on-chip applications, however its poor acoustic properties limit its performance for important optoacoustic applications, particularly for stimulated Brillouin scattering (SBS). We theoretically show that silicon inverse opals exhibit a strongly improved acoustic performance that enhances the bulk SBS gain coefficient by more than two orders of magnitude. We also design a waveguide that incorporates silicon inverse opals and which has SBS gain values that are comparable with chalcogenide glass waveguides. This research opens new directions for opto-acoustic applications in on-chip material systems.

Smith, MJA, Wolff, C, Martijn de Sterke, C, Lapine, M, Kuhlmey, BT & Poulton, CG 2016, 'Stimulated Brillouin scattering in metamaterials', Journal of the Optical Society of America B, vol. 33, no. 10, pp. 2162-2162.
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© 2016 Optical Society of America. We compute the stimulated Brillouin scattering (SBS) gain for a metamaterial comprising a cubic lattice of dielectric spheres suspended in a background dielectric material. Theoretical methods are presented to calculate the optical, acoustic, and optoacoustic parameters that describe the SBS properties of the material at long wavelengths. Using the electromagnetic and strain energy densities, we accurately characterize the optical and acoustic properties of the metamaterial. From a combination of energy density methods and perturbation theory, we recover the appropriate terms of the photoelastic tensor for the metamaterial. We demonstrate that electrostriction is not necessarily the dominant mechanism in the enhancement and suppression of the SBS gain coefficient in a metamaterial, and that other parameters, such as the Brillouin linewidth, can dominate instead. Examples are presented that exhibit an order of magnitude enhancement in the SBS gain as well as perfect suppression.

Smith, SM, Fox, RJ, Donelson, JM, Head, ML & Booth, DJ 2016, 'Predicting range-shift success potential for tropical marine fishes using external morphology', Biology Letters, vol. 12, no. 9, pp. 20160505-20160505.
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With global change accelerating the rate of species' range shifts, predicting which are most likely to establish viable populations in their new habitats is key to understanding how biological systems will respond. Annually, in Australia, tropical fish larvae from the Great Barrier Reef (GBR) are transported south via the East Australian Current (EAC), settling into temperate coastal habitats for the summer period, before experiencing near-100% mortality in winter. However, within 10 years, predicted winter ocean temperatures for the southeast coast of Australia will remain high enough for more of these so-called ‘tropical vagrants’ to survive over winter. We used a method of morphological niche analysis, previously shown to be an effective predictor of invasion success by fishes, to project which vagrants have the greatest likelihood of undergoing successful range shifts under these new climatic conditions. We find that species from the family of butterflyfishes (Chaetodontidae), and the moorish idol, Zanclus cornutus , are most likely to be able to exploit new niches within the ecosystem once physiological barriers to overwintering by tropical vagrant species are removed. Overall, the position of vagrants within the morphospace was strongly skewed, suggesting that impending competitive pressures may impact disproportionately on particular parts of the native community.

Sobhani-Nasab, A, Maddahfar, M & Hosseinpour-Mashkani, SM 2016, 'Ce(MoO4)2 nanostructures: Synthesis, characterization, and its photocatalyst application through the ultrasonic method', Journal of Molecular Liquids, vol. 216, pp. 1-5.
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Söderström, B, Mirzadeh, K, Toddo, S, von Heijne, G, Skoglund, U & Daley, DO 2016, 'Coordinated disassembly of the divisome complex in Escherichia coli', Molecular Microbiology, vol. 101, no. 3, pp. 425-438.
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SummaryThe divisome is the macromolecular complex that carries out cell division in Escherichia coli. Every generation it must be assembled, and then disassembled so that the sequestered proteins can be recycled. Whilst the assembly process has been well studied, virtually nothing is known about the disassembly process. In this study, we have used super‐resolution SIM imaging to monitor pairs of fluorescently tagged divisome proteins as they depart from the division septum. These simple binary comparisons indicated that disassembly occurs in a coordinated process that consists of at least five steps: [FtsZ, ZapA] ⇒ [ZipA, FtsA] ⇒ [FtsL, FtsQ] ⇒ [FtsI, FtsN] ⇒ [FtsN]. This sequence of events is remarkably similar to the assembly process, indicating that disassembly follows a first‐in, first‐out principle. A secondary observation from these binary comparisons was that FtsZ and FtsN formed division rings that were spatially separated throughout the division process. Thus the data indicate that the divisome structure can be visualized as two concentric rings; a proto‐ring containing FtsZ and an FtsN‐ring.

Sokulsky, LA, Collison, AM, Nightingale, S, Fevre, AL, Percival, E, Starkey, MR, Hansbro, PM, Foster, PS & Mattes, J 2016, 'TRAIL deficiency and PP2A activation with salmeterol ameliorates egg allergen-driven eosinophilic esophagitis', American Journal of Physiology-Gastrointestinal and Liver Physiology, vol. 311, no. 6, pp. G998-G1008.
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Food antigens are common inflammatory triggers in pediatric eosinophilic esophagitis (EoE). TNF-related apoptosis-inducing ligand (TRAIL) promotes eosinophilic inflammation through the upregulation of the E3 ubiquitin ligase Midline (MID)-1 and subsequent downregulation of protein phosphatase 2A (PP2A), but the role of this pathway in EoE that is experimentally induced by repeated food antigen challenges has not been investigated. Esophageal mucosal biopsies were collected from children with EoE and controls and assessed for TRAIL and MID-1 protein and mRNA transcript levels. Wild-type and TRAIL-deficient (Tnfsf10−/−) mice were administered subcutaneous ovalbumin (OVA) followed by oral OVA challenges. In separate experiments, OVA-challenged mice were intraperitoneally administered salmeterol or dexamethasone. Esophageal biopsies from children with EoE revealed increased levels of TRAIL and MID-1 and reduced PP2A activation compared with controls. Tnfsf10−/− mice were largely protected from esophageal fibrosis, eosinophilic inflammation, and the upregulation of TSLP, IL-5, IL-13, and CCL11 when compared with wild-type mice. Salmeterol administration to wild-type mice with experimental EoE restored PP2A activity and also prevented esophageal eosinophilia, inflammatory cytokine expression, and remodeling, which was comparable to the treatment effect of dexamethasone. TRAIL and PP2A regulate inflammation and fibrosis in experimental EoE, which can be therapeutically modulated by salmeterol.

Soleymani, S, Ireland, T & McNevin, D 2016, 'Effects of Plant Dyes, Watercolors and Acrylic Paints on the Colorfastness of Japanese Tissue Papers', Journal of the American Institute for Conservation, vol. 55, no. 1, pp. 56-70.
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Soliven, A, Foley, D, Pereira, L, Pravadali-Cekic, S, Dennis, GR, Cabrera, K, Ritchie, H, Edge, T & Shalliker, RA 2016, 'The performance of second generation silica monoliths, operating in parallel segmented flow mode', Microchemical Journal, vol. 124, pp. 657-661.
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Soliven, A, Pravadali-Cekic, S, Foley, D, Pereira, L, Dennis, GR, Cabrera, K, Ritchie, H, Edge, T & Shalliker, RA 2016, 'Using curtain flow second-generation silica monoliths to improve separations at pressures less than 400 bar', Microchemical Journal, vol. 127, pp. 68-73.
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Song, J, Su, D, Xie, X, Guo, X, Bao, W, Shao, G & Wang, G 2016, 'Immobilizing Polysulfides with MXene-Functionalized Separators for Stable Lithium–Sulfur Batteries', ACS Applied Materials & Interfaces, vol. 8, no. 43, pp. 29427-29433.
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Song, J, Sun, B, Ma, Z, Chen, Z, Shao, G & Wang, G 2016, 'Enhancement of the Rate Capability of LiFePO4 by a New Highly Graphitic Carbon-Coating Method', ACS APPLIED MATERIALS & INTERFACES, vol. 8, no. 24, pp. 15225-15231.
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Low lithium ion diffusivity and poor electronic conductivity are two major drawbacks for the wide application of LiFePO4 in high-power lithium ion batteries. In this work, we report a facile and efficient carbon-coating method to prepare LiFePO4/graphitic carbon composites by in situ carbonization of perylene-3,4,9,10-tetracarboxylic dianhydride during calcination. Perylene-3,4,9,10-tetracarboxylic dianhydride containing naphthalene rings can be easily converted to highly graphitic carbon during thermal treatment. The ultrathin layer of highly graphitic carbon coating drastically increased the electronic conductivity of LiFePO4. The short pathway along the [010] direction of LiFePO4 nanoplates could decrease the Li+ ion diffusion path. In favor of the high electronic conductivity and short lithium ion diffusion distance, the LiFePO4/graphitic carbon composites exhibit an excellent cycling stability at high current rates at room temperature and superior performance at low temperature (−20 °C).

Sorensen, A, Berry, C, Bruce, D, Gahan, ME, Hughes-Stamm, S & McNevin, D 2016, 'Direct-to-PCR tissue preservation for DNA profiling', International Journal of Legal Medicine, vol. 130, no. 3, pp. 607-613.
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Sornalingam, K, McDonagh, A & Zhou, JL 2016, 'Photodegradation of estrogenic endocrine disrupting steroidal hormones in aqueous systems: Progress and future challenges', Science of The Total Environment, vol. 550, pp. 209-224.
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© 2016 Elsevier B.V. This article reviews different photodegradation technologies used for the removal of four endocrine disrupting chemicals (EDCs): estrone (E1), 17β-estradiol (E2), estriol (E3) and 17α-ethinylestradiol (EE2). The degradation efficiency is greater under UV than visible light; and increases with light intensity up to when mass transfer becomes the rate limiting step. Substantial rates are observed in the environmentally relevant range of pH7-8, though higher rates are obtained for pH above the pKa (~10.4) of the EDCs. The effects of dissolved organic matter (DOM) on EDC photodegradation are complex with both positive and negative impacts being reported. TiO2 remains the best catalyst due to its superior activity, chemical and photo stability, cheap commercial availability, capacity to function at ambient conditions and low toxicity. The optimum TiO2 loading is 0.05-1gl-1, while higher loadings have negative impact on EDC removal. The suspended catalysts prove to be more efficient in photocatalysis compared to the immobilised catalysts, while the latter are considered more suitable for commercial scale applications. Photodegradation mostly follows 1st or pseudo 1st order kinetics. Photodegradation typically eradicates or moderates estrogenic activity, though some intermediates are found to exhibit higher estrogenicity than the parent EDCs; the persistence of estrogenic activity is mainly attributed to the presence of the phenolic moiety in intermediates.

Sorrell, TC, Juillard, P-G, Djordjevic, JT, Kaufman-Francis, K, Dietmann, A, Milonig, A, Combes, V & Grau, GER 2016, 'Cryptococcal transmigration across a model brain blood-barrier: evidence of the Trojan horse mechanism and differences between Cryptococcus neoformans var. grubii strain H99 and Cryptococcus gattii strain R265', Microbes and Infection, vol. 18, no. 1, pp. 57-67.
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Stark, D, Barratt, J, Chan, D & Ellis, JT 2016, 'Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel', CLINICAL MICROBIOLOGY REVIEWS, vol. 29, no. 3, pp. 553-580.
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© 2016, American Society for Microbiology. All Rights Reserved. Dientamoeba fragilis is a protozoan parasite of the human bowel, commonly reported throughout the world in association with gastrointestinal symptoms. Despite its initial discovery over 100 years ago, arguably, we know less about this peculiar organism than any other pathogenic or potentially pathogenic protozoan that infects humans. The details of its life cycle and mode of transmission are not completely known, and its potential as a human pathogen is debated within the scientific community. Recently, several major advances have been made with respect to this organism’s life cycle and molecular biology. While many questions remain unanswered, these and other recent advances have given rise to some intriguing new leads, which will pave the way for future research. This review encompasses a large body of knowledge generated on various aspects of D. fragilis over the last century, together with an update on the most recent developments. This includes an update on the latest diagnostic techniques and treatments, the clinical aspects of dientamoebiasis, the development of an animal model, the description of a D. fragilis cyst stage, and the sequencing of the first D. fragilis transcriptome.

Starkey, MR, Nguyen, DH, Brown, AC, Essilfie, A-T, Kim, RY, Yagita, H, Horvat, JC & Hansbro, PM 2016, 'Programmed Death Ligand 1 Promotes Early-LifeChlamydiaRespiratory Infection–Induced Severe Allergic Airway Disease', American Journal of Respiratory Cell and Molecular Biology, vol. 54, no. 4, pp. 493-503.
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Chlamydia infections are frequent causes of respiratory illness, particularly pneumonia in infants, and are linked to permanent reductions in lung function and the induction of asthma. However, the immune responses that protect against early-life infection and the mechanisms that lead to chronic lung disease are incompletely understood. In the current study, we investigated the role of programmed death (PD)-1 and its ligands PD-L1 and PD-L2 in promoting early-life Chlamydia respiratory infection, and infection-induced airway hyperresponsiveness (AHR) and severe allergic airway disease in later life. Infection increased PD-1 and PD-L1, but not PD-L2, mRNA expression in the lung. Flow cytometric analysis of whole lung homogenates identified monocytes, dendritic cells, CD4(+), and CD8(+) T cells as major sources of PD-1 and PD-L1. Inhibition of PD-1 and PD-L1, but not PD-L2, during infection ablated infection-induced AHR in later life. Given that PD-L1 was the most highly up-regulated and its targeting prevented infection-induced AHR, subsequent analyses focused on this ligand. Inhibition of PD-L1 had no effect on Chlamydia load but suppressed infection-induced pulmonary inflammation. Infection decreased the levels of the IL-13 decoy receptor in the lung, which were restored to baseline levels by inhibition of PD-L1. Finally, inhibition of PD-L1 during infection prevented subsequent infection-induced severe allergic airways disease in later life by decreasing IL-13 levels, Gob-5 expression, mucus production, and AHR. Thus, early-life Chlamydia respiratory infection-induced PD-L1 promotes severe inflammation during infection, permanent reductions in lung function, and the development of more severe allergic airway disease in later life.

Stehlik, S, Ondic, L, Berhane, AM, Aharonovich, I, Girard, HA, Arnault, J-C & Rezek, B 2016, 'Photoluminescence of nanodiamonds influenced by charge transfer from silicon and metal substrates', Diamond and Related Materials, vol. 63, pp. 91-96.
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© 2015 Elsevier B.V. All rights reserved. Photoluminescence of 5 nm detonation nanodiamonds (DNDs) is studied as a function of their surface treatment (hydrogenation/oxidation) and underlying substrate materials (silicon, gold, platinum, and nickel). The substrates affect DND photoluminescence emission spectrum and lifetime in the spectral range of 600-800 nm. The dependence is different for hydrogenated and oxidized DNDs. We attribute these effects to different electrostatic charging of DNDs on the substrates with different work functions (4.4 to 5.5 eV). We discuss the data based on naturally present NV centers, their phonon sideband, and surface-related non-radiative transitions.

Stelzer‐Braid, S, Tovey, ER, Willenborg, CM, Toelle, BG, Ampon, R, Garden, FL, Oliver, BG, Strachan, R, Belessis, Y, Jaffe, A, Reddel, HK, Crisafulli, D, Marks, GB & Rawlinson, WD 2016, 'Absence of back to school peaks in human rhinovirus detections and respiratory symptoms in a cohort of children with asthma', Journal of Medical Virology, vol. 88, no. 4, pp. 578-587.
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Much of what is known about the seasonality of human rhinovirus (hRV) infections has been learned from the study of acute asthma exacerbations presenting to emergency care, including those among children at the start of the school term. Much less is known about the patterns of hRVs in the community. In this study, viruses and day‐to‐day symptoms of asthma and colds were monitored twice weekly in 67 children with asthma aged 5–12 years, over a 15 month period in Sydney, Australia. Overall hRV was detected in 314/1232 (25.5%) of nasal wash samples and 142/1231 (11.5%) of exhaled breath samples; of these, 231 and 24 respectively were genotyped. HRVs were detected with similar prevalence rate throughout the year, including no peak in hRV prevalence following return to school. No peaks were seen in asthma and cold symptoms using twice‐weekly diary records. However, over the same period in the community, there were peaks in asthma emergency visits both at a large local hospital and in state‐wide hospitalizations, following both return to school (February) and in late autumn (May) in children of the same age. This study suggests that hRV infections are common throughout the year among children, and differences in virus prevalence alone may not account for peaks in asthma symptoms. J. Med. Virol. 88:578–587, 2016. © 2015 Wiley Periodicals, Inc.

Stenfeldt, C, Pacheco, JM, Brito, BP, Moreno-Torres, KI, Branan, MA, Delgado, AH, Rodriguez, LL & Arzt, J 2016, 'Transmission of Foot-and-Mouth Disease Virus during the Incubation Period in Pigs', Frontiers in Veterinary Science, vol. 3.
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Stuart, BH, Notter, SJ, Dent, B, Selvalatchmanan, J & Fu, S 2016, 'The formation of adipocere in model aquatic environments', International Journal of Legal Medicine, vol. 130, no. 1, pp. 281-286.
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An examination of the chemistry of adipocere formation in aquatic systems provides insight into how environmental factors affect the decomposition processes of human remains. Gas chromatography-mass spectrometry (GC-MS) and inductively coupled plasma-mass spectrometry (ICP-MS) have been employed to monitor the changes to the chemistry of adipocere formed in aquatic environments used to model seawater, river and chlorinated water systems. Seawater was shown to inhibit adipocere formation, and a distinctively different elemental composition was produced in this environment due to the high concentrations of salts. By comparison, river water has been shown to accelerate the formation of adipocere. Chlorinated water appears to significantly enhance adipocere formation, based on a comparison with established fatty acid concentration values. However, a competing reaction to form chlorohydrins in chlorinated water is believed to be responsible for the unusual findings in this environment. The application of the chemical characterisation of adipocere to an understanding of how this particular decomposition product forms in different water environments has been demonstrated, and there is potential to utilise this approach to identify the environment in which a body has been immersed.

Sturmberg, BCP, Chong, TK, Choi, D-Y, White, TP, Botten, LC, Dossou, KB, Poulton, CG, Catchpole, KR, McPhedran, RC & Martijn de Sterke, C 2016, 'Total absorption of visible light in ultrathin weakly absorbing semiconductor gratings', Optica, vol. 3, no. 6, pp. 556-556.
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© 2016 Optical Society of America. The perfect absorption of light in subwavelength thickness layers generally relies on exotic materials, metamaterials or thick metallic gratings. Here we demonstrate that total light absorption can be achieved in ultra-thin gratings composed of conventional materials, including relatively weakly-absorbing semiconductors, which are compatible with optoelectronic applications such as photodetectors and optical modulators. We fabricate a 41 nm thick antimony sulphide grating structure that has a measured absorptance of A = 99.3% at a visible wavelength of 591 nm, in excellent agreement with theory. We infer that the absorption within the grating is A = 98.7%, with only A = 0.6% within the silver mirror. A planar reference sample absorbs A = 7.7% at this wavelength.

Sturmberg, BCP, Dossou, KB, Lawrence, FJ, Poulton, CG, McPhedran, RC, Martijn de Sterke, C & Botten, LC 2016, 'EMUstack: An open source route to insightful electromagnetic computation via the Bloch mode scattering matrix method', Computer Physics Communications, vol. 202, pp. 276-286.
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© 2016 Elsevier B.V. We describe EMUstack, an open-source implementation of the Scattering Matrix Method (SMM) for solving field problems in layered media. The fields inside nanostructured layers are described in terms of Bloch modes that are found using the Finite Element Method (FEM). Direct access to these modes allows the physical intuition of thin film optics to be extended to complex structures. The combination of the SMM and the FEM makes EMUstack ideally suited for studying lossy, high-index contrast structures, which challenge conventional SMMs. Program summary: Program title: EMUstack. Catalogue identifier: AEZI_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEZI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: GNU General Public License, version 3. No. of lines in distributed program, including test data, etc.: 154301. No. of bytes in distributed program, including test data, etc.: 5308635. Distribution format: tar.gz. Programming language: Python, Fortran. Computer: Any computer with a Unix-like system with Python, a Fortran compiler and F2Py [1]. Also required are the following free libraries LAPACK and BLAS [2], UMFPACK [3]. Developed on 1.6 GHz Intel Core i7. Operating system: Any Unix-like system; developed on Ubuntu 14.04 (using Linux kernel 3.16). RAM: Problem dependent; specifically on the resolution of the FEM mesh and the number of modes included. The given example uses approximately 100 MB. Classification: 10. External routines: Required are the following free libraries LAPACK and BLAS [2], UMFPACK [3]. Optionally exploits additional commercial software packages: Intel MKL [4], Gmsh [5]. Nature of problem: Time-harmonic electrodynamics in layered media. Solution method: Finite element method and the scattering matrix method. Running time: Problem dependent (typically about 3 s per wavelength including plane wave orders ≤3). References: [1]P. Peterson, F2PY: A...

Su, D, Han Seo, D, Ju, Y, Han, Z, Ostrikov, K, Dou, S, Ahn, H-J, Peng, Z & Wang, G 2016, 'Ruthenium nanocrystal decorated vertical graphene nanosheets@Ni foam as highly efficient cathode catalysts for lithium-oxygen batteries', NPG Asia Materials, vol. 8, no. 7, pp. e286-e286.
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Su, D, Kretschmer, K & Wang, G 2016, 'Improved Electrochemical Performance of Na‐Ion Batteries in Ether‐Based Electrolytes: A Case Study of ZnS Nanospheres', Advanced Energy Materials, vol. 6, no. 2, pp. 1501785-1501785.
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Sodium‐ion batteries are considered as a promising technology for large‐scale energy storage applications, owing to their low cost. However, there are many challenges for developing sodium‐ion batteries with high capacity, long cycle life, and high‐rate capability. Herein, the development of high‐performance sodium‐ion batteries using ZnS nanospheres as anode material and an ether‐based electrolyte, which exhibit improved electrochemical performance over the pure alkyl carbonate electrolytes, is reported. ZnS nanospheres deliver a high specific capacity of 1000 mA h g−1 and high initial Columbic efficiency of 90%. Electrochemical testing and first‐principle calculations demonstrate that the ether‐based solvent can facilitate charge transport, reduce the energy barrier for sodium‐ion diffusion, and thus enhance electrochemical performances. Ex situ measurements (X‐ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS) mapping) reveal that ZnS nanospheres maintain structural integrity during the charge and discharge processes over 100 cycles. As anode material for sodium‐ion batteries, ZnS nanospheres deliver high reversible sodium storage capacity, high Coulombic efficiencies, and extended cycle life.

Su, J, Raghuwanshi, VS, Raverty, W, Garvey, CJ, Holden, PJ, Gillon, M, Holt, SA, Tabor, R, Batchelor, W & Garnier, G 2016, 'Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules', Scientific Reports, vol. 6, no. 1.
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AbstractNovel thin and smooth deuterated cellulose films were synthesised to visualize adsorbed bio-macromolecules using contrast variation neutron reflectivity (NR) measurements. Incorporation of varying degrees of deuteration into cellulose was achieved by growing Gluconacetobacter xylinus in deuterated glycerol as carbon source dissolved in growth media containing D2O. The derivative of deuterated cellulose was prepared by trimethylsilylation(TMS) in ionic liquid(1-butyl-3-methylimidazolium chloride). The TMS derivative was dissolved in toluene for thin film preparation by spin-coating. The resulting film was regenerated into deuterated cellulose by exposure to acidic vapour. A common enzyme, horseradish peroxidase (HRP), was adsorbed from solution onto the deuterated cellulose films and visualized by NR. The scattering length density contrast of the deuterated cellulose enabled accurate visualization and quantification of the adsorbed HRP, which would have been impossible to achieve with non-deuterated cellulose. The procedure described enables preparing deuterated cellulose films that allows differentiation of cellulose and non-deuterated bio-macromolecules using