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.

Macnamara, JR 2016, Organizational Listening: The Missing Essential in Public Communication, 1, Peter Lang Publishing, New York.
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Organizations including government departments and agencies, corporations, and non-government organizations claim they want and practice two-way communication, dialogue, and engagement with citizens, customers, employees, and other stakeholders and publics. But do they in reality? Voice—speaking up—is recognized as fundamental for democracy, representation, and social equity. But what if organizations are not listening? This book reports findings of a two-year, three-continent study that show that public and private sector organizations devote substantial and sometimes massive resources to construct an ‘architecture of speaking’ through advertising, PR and other public communication practices, but listen poorly, sporadically, and sometimes not all. Beyond identifying a ‘crisis of listening’, this landmark study proposes that organizations need to create an architecture of listening to regain trust and re-engage people whose voices are unheard or ignored. It presents a compelling case to show that organizational listening is essential for healthy democracy, organization legitimacy, business sustainability, and social equity and brings benefits to organizations, their stakeholders, and society.

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, 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' in Oceanography and Marine Biology - An Annual Review, CRC Press, pp. 387-412.
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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.

Barton, RW, Tatake, JG & Diwan, AR 2016, 'Nanoviricides: Targeted anti-viral nanomaterials' in Bawa, R, Audette, GF & Rubinstein, I (eds), Handbook of Clinical Nanomedicine: Nanoparticles, Imaging, Therapy and Clinical Applications, CRC Press, USA, pp. 1039-1052.
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Ben-Nissan, B, Choi, AH, Macha, IJ & Cazalbou, S 2016, 'Sol-gel Nanocoatings of Bioceramics' in Antoniac, IV (ed), Handbook of Bioceramics and Biocomposites, Springer International Publishing, Germany, pp. 735-756.
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© Springer International Publishing Switzerland 2016.The ability to produce homogeneous high-purity materials is of great interest to industrial and medical applications. In addition, the chemical and physical changes observed at the nanoscale and their influence on properties have been an important academic interest. The gel-structure transition plays a critical role in the formation as well as the current production of various types of sol-gel-derived materials such as nanopowders, nanofibers, nanocoatings, nanocomposites, and solid monoliths. It is the area of thin film coatings produced by sol-gel technology that this chapter covers. In particular, this chapter focuses on the basic synthesis and application methods to produce nanocoatings for biomedical applications. This chapter also attempts to answer some of the pertinent questions related to sol-gel processing and production methods and issues related to the fundamental understanding of the sol-gel process.

Care, A, Bergquist, PL & Sunna, A 2016, 'Solid-Binding Peptides: Immobilisation Strategies for Extremophile Biocatalysis in Biotechnology' in Biotechnology of Extremophiles:, Springer International Publishing, pp. 637-674.
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Choi, AH, Cazalbou, S & Ben-Nissan, B 2016, 'Biomimetics and Marine Materials in Drug Delivery and Tissue Engineering' in Antoniac, IV (ed), Handbook of Bioceramics and Biocomposites, Springer International Publishing, Germany, pp. 521-544.
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© Springer International Publishing Switzerland 2016. During the last two decades, biomimetics has provided mankind new directions for the utilization of natural organic and inorganic skeletons for novel drug delivery systems and new medical treatment approaches with unique designs ranging from the macro- to the nanoscale. The use of ready-made organic and inorganic marine skeletons has potentially created an opportunity of presenting one of the simplest cures to fundamental issues hampering the future development of regenerative medicine, dentistry, and orthopedics such as providing a richness of framework designs and devices and abundant and available sources of osteopromotive analogues and biomineralization proteins. Organic matrix and inorganic marine skeletons possess a habitat ideal for the proliferation of added mesenchymal stem cell populations and promoting clinically acceptable bone formation. It has been proven that self-sustaining musculoskeletal tissues can be supported by coral and marine sponge skeletons, and bone mineralization can be promoted by the extracts of spongin collagen and nacre seashell organic matrices. This idea is reinforced by the fact that bone morphogenetic protein molecules are produced by endodermal cells into the developing skeleton. Furthermore, the regenerative signaling proteins in bone therapeutics such as TGF and Wnt are also present in early marine sponge development and instrumental to the activation of stem cells in cnidarians. This chapter aims to give a brief background into the nature, morphology, and application of some of these structures in bone grafts, drug delivery, tissue engineering, and specific extracts such as proteins for regenerative medicine.

Commault, A & Weld, RJ 2016, 'Whole-cell Biosensors for Monitoring Bioremediation' in Lear, G (ed), Biofilms in Bioremediation, Caister Academic Press, Norfolk, United Kingdom, pp. 75-91.

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.

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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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), Pancreatic Islet Biology, 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 Systems Biology of Alzheimer's Disease, 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.

Holt, MK & Grills, AE 2016, 'Critical Issues in School-based Mental Health' in Holt, MK & Grills, AE (eds), Critical Issues in School-Based Mental Health: Evidence-Based Research, Practice, and Interventions, Routledge, pp. 1-4.
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Huete, A, Ponce-Campos, G, Zhang, Y, Restrepo-Coupe, N, Ma, X & Moran, MS 2016, 'Land Resources Monitoring, Modeling, and Mapping with Remote Sensing' in Thenkabail, PDPS (ed), Land Resources Monitoring, Modeling, and Mapping with Remote Sensing, CRC Press, Boca Raton, pp. 3-22.
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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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Macnamara, JR 2016, 'Socially integrating PR and operationalising an alternative approach' in L'Etang, J, McKike, D, Snow, N & Xifra, J (eds), The Routledge Handbook of Critical Public Relations, Routledge, London, pp. 335-348.
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This chapter contributes to critical thinking about public relations in two important ways. First, it reviews key literature and synthesizes the findings of several international research studies which reaffirm that claims made in the dominant paradigm of Excellence theory and other popular theories of PR and corporate communication for two-way interaction, dialogue, co-orientation, relationships, and even symmetry between organizations and their publics are largely illusory and require rethinking. Research involving a range or organizations shows that PR and ‘strategic communication’ are primarily implemented for dissemination of organization messages and persuasion and these approaches are continuing even in social media which explicitly advocate interactivity and sociality. Drawing on recent research and critical studies, this chapter calls for PR to facilitate the integration of organizations into society for mutual organization-public benefit, rather than contribute to power relations that privilege organizational interests. Second, in advocating a social integration model of public relations, this chapter takes an important step towards praxis, which Hegel, Marx and other founders of critical analysis advocated as part of criticism, by exploring how such an alternative model of PR might be operationalized. In doing so, it offers some answers to the critics’ critics by advancing critical thinking towards practice, as well as contributing to critical PR theory.

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.

Ralph, PJ, Hill, R, Doblin, MA & Davy, SK 2016, 'Theory and Application of Pulse Amplitude Modulated Chlorophyll Fluorometry in Coral Health Assessment' in Woodley, CM, Downs, CA, Bruckner, AW, Porter, JW & Galloway, SB (eds), Diseases of Coral, John Wiley & Sons, Inc, Hoboken, New Jersey, pp. 506-523.
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© 2016 John Wiley & Sons, Inc. Scleractinian corals exist in symbiosis with dinoflagellate alga (genus Symbiodinium), which provides access to nutrients by the host but also makes it makes the holobiont vulnerable to photosynthetic stress, providing an opportunity for rapid health assessment using chlorophyll a (chl-a) fluorescence techniques. Common photosynthetic stressors of corals are high irradiance, ultraviolet light, temperature extremes, chemical pollution and low salinity, which are further compounded by other major anthropogenic pressures on coral reefs. Coral Symbiodinium cells contain chlorophyll (chl) a, c2 and a range of accessory pigments. The chl-a within the pigment complex absorbs light maximally in the blue (peak at 440 nm) and red (peak at 678 nm) regions of the spectrum and re-emits light energy in the form of fluorescence, maximally in the red bandwidth (630 to 770 m with a peak at 680 nm). In vivo chl-a has a variable fluorescence yield that is dependent upon the wavelength of excitation irradiance and varies over time as a result of the complex interaction of the photosynthetic pathways (Kautsky effect). When a chloroplast captures a photon of energy, the chl a molecule is excited from its ground state to an excited state. There are three competing and complementary energy dissipation processes for that excited molecule: (i) driving photosynthesis via the electron transport chain leading to carbon fixation, (ii) heat dissipation, or (iii) returning to the ground state and re-emitting some of the energy as fluorescence. This is why chl a fluorescence can be used as a proxy for photochemistry (and energy dissipation). During periods of high incident irradiance, if the amount of absorbed light exceeds the maximum rate of electron transport, then the excess energy must be dissipated, or photodamage can occur. Pulse-amplitude modulated (PAM) fluorometry provides a versatile technique for monitoring and assessing zooxanthellae health. It measure...

Sullivan, C, Stuart, BH & Thomas, PS 2016, 'An Investigation of the Degradation of Polymeric Grave Goods in Soil Environments' in Kars, H & van den Eijkel, L (eds), Soil in Criminal and Environmental Forensics, Springer International Publishing, Germany, pp. 331-341.
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Plastic materials are a source of items that may be located in clandestine grave sites. Knowledge of their type and state of preservation or deterioration may provide a valuable resource for the identification of a victim or perpetrator. This study involves an examination of the effect of the nature of the soil environment on the structural properties of two common polymers, poly(vinyl chloride) and nylon, over a period of 18 months. These polymers represent common types of plastic sheeting and carpet material that may be used to wrap a body. Infrared spectroscopy and scanning electron microscopy have been used to monitor the structural changes that occur to these polymers in a soil environment and degradation mechanisms are proposed.

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), Green Roof Retrofit, John Wiley & Sons, Ltd, uk, pp. 158-188.
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Human populations are becoming increasingly urbanised and thus distanced, both physically and psychologically, from the sources of their food. Decentralizing 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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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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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, 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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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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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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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 result in the continued success of this species in Eastern Austr...

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, pp. 1-13.
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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 may increase competition, leading to species exclusion. I...

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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Ali, H, Kanodarwala, FK, Majeed, I, Stride, JA & Nadeem, MA 2016, 'La₂O₃ Promoted Pd/rGO Electro-catalysts for Formic Acid Oxidation', ACS Applied Materials & Interfaces, vol. 8, no. 47, pp. 32581-32590.
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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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Anantanawat, KJ, Glatz, R & Keller, MA 2016, 'Effect of induced tolerance toBttoxin on the egg size ofHelicoverpa armigeraand parasitism byTrichogramma pretiosum', Physiological Entomology, vol. 41, no. 3, pp. 267-273.
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© 2016 The Royal Entomological Society Larvae of Helicoverpa armigera (Hübner) can develop a form of Bt tolerance after exposure to sub-lethal doses of Bt-toxin subclass Cry1Ac. Increasing levels of tolerance are produced over generations of larval exposure, which are not related to DNA sequence changes, and are largely maternally transmitted. The characteristic of maternal transmission, combined with the importance of egg parasitoids to cotton pest management, raises questions about the effects of Bt tolerance/exposure on the eggs of H. armigera and on some key metrics of egg parasitism. In the present study, the effect of inducible tolerance on eggs of H. armigera and parasitism by Trichogramma pretiosum (Riley) is investigated. First, the volumes of eggs laid by susceptible and tolerant H. armigera females are compared. In addition, the effect of inducible tolerance on egg parasitism is determined by comparing parasitism success, the number of adult wasps emerged per host egg, and the proportion of male and female offspring emerged per host egg. The results obtained suggest that Cry1Ac-tolerance is associated with increased egg volume, even after just one generation of sub-lethal exposure. When tolerant H. armigera are freed from ongoing sub-lethal exposure, a corresponding decrease in egg volume is not detected. Although there is no difference in the percentage of eggs parasitized, there is an increase in the number of emergent parasitoids, especially males, from eggs laid by tolerant H. armigera. These results confirm that maternally-transmitted Bt tolerance is reflected in the phenotype of the eggs of tolerant offspring, which affects egg parasitism.

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 retirement behavior in the decumulation phase of Australian retirees with sequential family status subject to consumption, housing, investment, bequest and government provided means-tested Age Pension. We account for mortality risk and risky investment assets, and introduce a health proxy to capture the decreasing level of consumption for older retirees. Then we find optimal housing at retirement, and optimal consumption and optimal risky asset allocation depending on age and wealth. The model is solved numerically as a stochastic control problem, and is calibrated using the maximum likelihood method on empirical data of consumption and housing from the Australian Bureau of Statistics 2009-2010 Survey. The model fits the characteristics of the data well to explain the behavior of Australian retirees. The key findings are the following: First, the optimal policy is highly sensitive to means-tested Age Pension early in retirement but this sensitivity fades with age. Secondly, the allocation to risky assets shows a complex relationship with the means-tested Age Pension that disappears once minimum withdrawal rules are enforced. As a general rule, when wealth decreases the proportion allocated to risky assets increases, due to the Age Pension working as a buffer against investment losses. Finally, couples can be more aggressive with risky allocations due to their longer life expectancy compared with singles.

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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Abstract The molecular structure of bis(κ2S,Sʹ-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.

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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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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Despite the disparities in size and volume of marine and freshwater realms, a strikingly similar number ofspecies is found in each – with 15 150 Actinopterygian fishes in fresh water and 14 740 in the marine realm. Theirecological and societal values are widely recognized yet many marine and freshwater fishes increasingly risk local,regional or global extinction.2. 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 impactsof other stressors that threaten many marine and freshwater fishes.3. Isolated and fragmented habitats typically present the most challenging environments for small, specializedfreshwater and marine fishes, whereas overfishing is by far the greatest threat to larger marine and freshwaterspecies. Species that migrate within or between freshwater and marine realms may face high catchability inpredictable migration bottlenecks, and degradation of breeding habitat, feeding habitat or the interveningmigration corridors.4. Conservation reserves are vital to protect species-rich habitats, important radiations, and threatened endemicspecies. Integration of processes that connect terrestrial, freshwater and marine protected areas promises moreeffective conservation outcomes than disconnected reserves. Diadromous species in particular require moreattention in aquatic restoration and conservation planning across disparate government agencies.5. Human activities and stressors that increasingly threaten freshwater and marine fishes must be curbed toavoid a wave of extinctions. Freshwater recovery programmes range from plans for individual species torecovery of entire basin faunas. Reducing risks to threatened marine species in coastal habitats also requiresconservation actions at multiple scales. Most of the world's larger economically important fisheries are relativelywell-monitored and well-managed but there...

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.
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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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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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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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Bajpai, VK, Han, J-H, Nam, G-J, Majumder, R, Park, C, Lim, J, Paek, WK, Rather, IA & Park, Y-H 2016, 'Characterization and pharmacological potential of Lactobacillus sakei 1I1 isolated from fresh water fish Zacco koreanus', DARU Journal of Pharmaceutical Sciences, vol. 24, no. 1.
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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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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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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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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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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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Beelen, HPGJ, Raijmakers, LHJ, Donkers, MCF, Notten, PHL & Bergveld, HJ 2016, 'A comparison and accuracy analysis of impedance-based temperature estimation methods for Li-ion batteries', Applied Energy, vol. 175, pp. 128-140.
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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, 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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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 radiationuse 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 gCm 2 yr 1/ and the natural raised peat bog site having a very low GPP (820 gCm 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 benefi- ciaries 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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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.

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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Booker, JA, Ollendick, TH, Dunsmore, JC & Greene, RW 2016, 'Perceived Parent–Child Relations, Conduct Problems, and Clinical Improvement Following the Treatment of Oppositional Defiant Disorder', Journal of Child and Family Studies, vol. 25, no. 5, pp. 1623-1633.
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Our objective in this study was to examine the moderating influence of parent–child relationship quality (as viewed by the child) on associations between conduct problems and treatment responses for children with oppositional defiant disorder (ODD). To date, few studies have considered children’s perceptions of relationship quality with parents in clinical contexts even though extant studies show the importance of this factor in children’s behavioral adjustment in non-clinical settings. In this study, 123 children (ages 7–14 years, 61.8 % male, 83.7 % white) who fulfilled DSM-IV criteria for ODD received one of two psychosocial treatments: Parent Management Training or Collaborative and Proactive Solutions. In an earlier study, both treatments were found to be effective and equivalent in treatment outcomes. In the current study, pre-treatment maternal reports of conduct problems and pre-treatment child reports of relations with parents were used to predict outcomes in ODD symptoms and their severity following treatment. Elevated reports of children’s conduct problems were associated with attenuated reductions in both ODD symptoms and their severity. Perceived relationship quality with parents moderated the ties between conduct problems and outcomes in ODD severity but not the number of symptoms. Mother reports of elevated conduct problems predicted attenuated treatment response only when children viewed relationship quality with their parents as poorer. When children viewed the relationship as higher quality, they did not show an attenuated treatment response, regardless of reported conduct problems. The current findings underscore the importance of children’s perspectives in treatment response and reductions in externalizing child behaviors.

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, 100m along a reef edge. Given that the home range of both species is <1m2, 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.

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.
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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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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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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 the language $C^k(L)$, which consists of all words obtained by partitioning words from $L$ into $k$ factors and permuting them. We prove that the classes of ET0L and EDT0L languages are closed under the operators $C^k$. This both sharpens and 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 also show 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, 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.

Burton, MG, Whitchurch, CB, Turnbull, L, Rogers, K, Orth, R, Brien Simpson, NO, Gee, M, Clayton, AHA & Smith, TA 2016, 'Fluorescence Investigations on the Attack of Cell-Wall-Deficient Bacteria by Antimicrobial Peptides', Biophysical Journal, vol. 110, no. 3, pp. 79a-79a.
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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.

Caballo, VE, Salazar, IC, Arias, B, Calderero, M, Irurtia, MJ & Ollendick, TH 2016, 'The Social Anxiety Questionnaire for Children: Cross-Cultural Assessment with a New Self-Report Measure', Journal of Psychopathology and Behavioral Assessment, vol. 38, no. 4, pp. 695-709.
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This study describes a series of exploratory and confirmatory factor analyses that were conducted with the 44-item Social Anxiety Questionnaire for Children- 4th version (SAQ-CIV) to identify a reduced set of items that might be used to construct a new abbreviated instrument for measuring social anxiety in children and adolescents. The fourth version of the Social Anxiety Questionnaire for Children (SAQ-CIV) was administered to 12,801 non-clinical participants (ages 9 to 15 years) from 12 Latin American countries and Spain. Exploratory and confirmatory factor analysis supported a 6-factor structure of social anxiety in children, replicating a similar structure to that of adults (Caballo et al. in Behavioral Psychology/Psicología Conductual, 18(1), 5–34, 2010; Caballo et al. in Behavior Therapy, 43(2), 313–328, 2012): 1) Interactions with the opposite sex, 2) Criticism and embarrassment, 3) Speaking in public/Talking to teachers, 4) Assertive expression of annoyance and disgust, 5) Performing in public, and 6) Interactions with strangers. Each of the factors contains 4 items, yielding an abbreviated 24-item instrument, the Social Anxiety Questionnaire for Children (SAQ-C). The present results suggest this is a reliable, valid, and culturally sensitive instrument to assess social anxiety in youth.

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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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.
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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, pp. 1-16.
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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 corals living in reef-associated habitats and characterize the environme...

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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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.
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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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© 2015 John Wiley & Sons, Ltd. 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.

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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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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Increased 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 2 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. This article is protected by copyright. All rights reserved.

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, 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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Chatterjee, N, Chen, Y-H, Maas, P & Carroll, RJ 2016, 'Rejoinder', Journal of the American Statistical Association, vol. 111, no. 513, pp. 130-131.
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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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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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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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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 o f 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 (Na 15 Sn 4 ), which also deteriorated the conductivity. In contrast, the relatively weak interaction between Na 15 Sn 4 and graphitic carbon can maintain superior conductivity and structural stability for better cycling performance.

Chernomoretz, A, Stolovitzky, G, Labaj, PP, Graf, AB, Darling, A, Burke, C, Noushmehr, H, Moraes, MO, Dias-Neto, E, Guo, Y, Xie, Z, Lee, P, Shi, L, Ruiz-Perez, CA, Mercedes Zambrano, M, Siam, R, Ouf, A, Richard, H, Lafontaine, I, Wieler, LH, Semmler, T, Ahmed, N, Prithi-viraj, B, Nedunuri, N, Mehr, S, Banihashemi, K, Lista, F, Anselmo, A, Suzuki, H, Kuroda, M, Yamashita, R, Sato, Y, Kaminuma, E, Alpuche Aranda, CM, 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, Mason, CE, Eisen, J, Hirschberg, D & Hernandez, M 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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Cherukuru, N, Davies, PL, Brando, VE, Anstee, JM, Baird, ME, Clementson, LA & Doblin, MA 2016, 'Physical oceanographic processes influence bio-optical properties in the Tasman Sea', JOURNAL OF SEA RESEARCH, vol. 110, pp. 1-7.
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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, JP, Foley, M, Zhou, Z, Wong, W-Y, Gokoolparsadh, N, Arthur, JSC, Li, DY & Zheng, X 2016, 'Micro-CT Imaging Reveals Mekk3 Heterozygosity Prevents Cerebral Cavernous Malformations in Ccm2-Deficient Mice', PLOS ONE, vol. 11, no. 8, pp. e0160833-e0160833.
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Choi, JP, Zheng, Y, Handelsman, DJ & Simanainen, U 2016, 'Glandular epithelial AR inactivation enhances PTEN deletion-induced uterine pathology', Endocrine-Related Cancer, vol. 23, no. 5, pp. 377-390.
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Phosphatase and tensin homolog (PTEN) deletion induces uterine pathology, whereas androgen actions via androgen receptor (AR) support uterine growth and therefore may modify uterine cancer risk. We hypothesized that the androgen actions mediated via uterine glandular epithelial AR could modify PTEN deletion-induced uterine pathology. To test our hypothesis, we developed uterine glandular epithelium-specific PTEN and/or AR knockout mouse models comparing the uterine pathology among wild-type (WT), glandular epithelium-specific AR inactivation (ugeARKO), PTEN deletion (ugePTENKO), and the combined PTEN and AR knockout (ugePTENARKO) female mice. The double knockout restricted to glandular epithelium showed that AR inactivation enhanced PTEN deletion-induced uterine pathology with development of intraepithelial neoplasia by 20 weeks of age. In ugePTENARKO, 6/10 (60%) developed intraepithelial neoplasia, whereas 3/10 (30%) developed only glandular hyperplasia in ugePTENKO uterus. No uterine pathology was observed in WT (n=8) and ugeARKO (n=7) uteri. Uterine weight was significantly (P=0.002) increased in ugePTENARKO (374±97 mg (mean±s.e.)) compared with WT (97±6 mg), ugeARKO (94±12 mg), and ugePTENKO (205±33 mg). Estrogen receptor alpha (ERα) and P-AKT expression was modified by uterine pathology but did not differ between ugePTENKO and ugePTENARKO, suggesting that its expressions are not directly affected by androgens. However, progesterone receptor (PR) expression was reduced in ugePTENARKO compared to ugePTENKO uterus, suggesting that PR expression could be regulated by glandular epithelial AR inactivation. In conclusion, glandular epithelial AR inactivation (with persistent stromal AR action) enhanced PTEN deletion-induced uterine pathology possibly by downregulating PR expression in the uterus.

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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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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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.
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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.

Chua, L, Head, K, Thomas, P & Stuart, B 2016, 'Micro-characterisation of the colour palette of ceremonial objects from the Papua New Guinea Highlands: Transition from natural to synthetic pigments', Microchemical Journal, vol. 124, pp. 547-558.
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Chua, L, Maynard-Casely, HE, Thomas, PS, Head, K & Stuart, BH 2016, 'Characterisation of blue pigments from ceremonial objects of the Southern Highlands in Papua New Guinea using vibrational spectroscopy and X-ray diffraction', Vibrational Spectroscopy, vol. 85, pp. 43-47.
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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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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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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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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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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 non-peroxide 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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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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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.

Commault, AS, Lear, G, Bouvier, S, Feiler, L, Karacs, J & Weld, RJ 2016, 'Geobacter-dominated biofilms used as amperometric BOD sensors', Biochemical Engineering Journal, vol. 109, pp. 88-95.
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The biochemical oxygen demand (BOD) of a given water sample is typically measured using a conventional BOD5 assay, which requires 5 days of incubation at 20 °C of the sample with mixed communities of bacteria. The study presents a new type of BOD sensor using a Geobacter-dominated biofilm selected with ethanol as the sole carbon source. Ethanol selected for biofilms with a broader substrate usage than those selected with acetate, making them better for BOD biosensing applications. The biosensor was operated at room temperature with a voltage input of −0.08 V vs SHE (−0.36 V vs Ag/AgCl) and calibrated using several dilutions of synthetic wastewater with known BOD concentrations ranging from 174 mg/L to 1200 mg/L. The charge transferred by the biofilm over a reaction time of 17.5 h was linearly correlated (R2 = 0.96) with BOD. Once calibrated, the biosensor was used to measure the BOD of cow’s milk with a reproducibility of 94% and an error of only 7.4% compared to BOD5 values. In contrast to the 5 days incubation currently required by standard BOD methods our novel biosensor offers a rapid monitoring alternative for assessments of the BOD of dairy effluent.

Cong, Y, Shi, B, Lu, Y, Wen, S, Chung, R & Jin, D 2016, 'One-step Conjugation of Glycyrrhetinic Acid to Cationic Polymers for High-performance Gene Delivery to Cultured Liver Cell', Scientific Reports, vol. 6, no. 1, pp. 1-11.
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AbstractGene therapies represent a promising therapeutic route for liver cancers, but major challenges remain in the design of safe and efficient gene-targeting delivery systems. For example, cationic polymers show good transfection efficiency as gene carriers, but are hindered by cytotoxicity and non-specific targeting. Here we report a versatile method of one-step conjugation of glycyrrhetinic acid (GA) to reduce cytotoxicity and improve the cultured liver cell -targeting capability of cationic polymers. We have explored a series of cationic polymer derivatives by coupling different ratios of GA to polypropylenimine (PPI) dendrimer. These new gene carriers (GA-PPI dendrimer) were systematically characterized by UV-vis,1H NMR titration, electron microscopy, zeta potential, dynamic light-scattering, gel electrophoresis, confocal microscopy and flow cytometry. We demonstrate that GA-PPI dendrimers can efficiently load and protect pDNA, via formation of nanostructured GA-PPI/pDNA polyplexes. With optimal GA substitution degree (6.31%), GA-PPI dendrimers deliver higher liver cell transfection efficiency (43.5% vs 22.3%) and lower cytotoxicity (94.3% vs 62.5%, cell viability) than the commercial bench-mark DNA carrier bPEI (25kDa) with cultured liver model cells (HepG2). There results suggest that our new GA-PPI dendrimer are a promising candidate gene carrier for targeted liver cancer therapy.

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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Cooper, WA, Kraitsek, S, Selinger, CI, Tran, T, Kohonen-Corish, M, O'Toole, SA & Yu, B 2016, 'Targeted next generation sequencing in FFPE samples of NSCLC', Pathology, vol. 48, pp. S121-S121.
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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.

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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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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Aim Understanding 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. Location The Australian Arid Lands Botanic Garden, Port Augusta, South Australia. Methods Using 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. Results T50 was unrelated to macro-scale climate or latitude, whereas WT increased for species whose distributions extend into higher latitudes, a pattern hitherto not shown for terrestrial plants. We also found that species adapted to higher water availability in their native microhabitat had significantly lower T50 and WT than species from drier microhabitats. Main conclusions (1) Warming tolerance increased with latitude, but the strength of this relationship was related to the way WT was quantified, with Thab and latitude being linked. (2) T50 did not correlate with latitude, but both T50 and WT were strongly related to their microhabitats. Specifically, water availability is important, such that even within a desert biome, species associated with ‘wetter’ microhabitats, may be particularly vulnerable to heat stress. Thus, we show that local-scale patterns better capture plant physiological responses to temperatu...

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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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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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 singlemachine 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 Oðn2log nÞ 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.

Daley, DO, Skoglund, U & Söderström, B 2016, 'FtsZ does not initiate membrane constriction at the onset of division', Scientific Reports, vol. 6, no. 1.
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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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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.

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, 'Correction: Corrigendum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters', Scientific Data, vol. 3, no. 1.
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Scientific Data 3:160043 doi:10.1038/sdata.2016.43 (2016); Published 21 Jun 2016; Updated 6 Dec 2016 A series of errors in our database were brought to our attention by readers, and have been corrected in an updated version of this database, which is accessible via the AODN at the following link: https://portal.

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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Communal 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 nests annually, suggesting that there may be little plasticity in maternal nest-site selection. The impacts of climate change may therefore be es...

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 Jong, K, Vonk, JM, Faiz, A, van der Plaat, DA, Timens, W, Bossé, Y, Kromhout, H, Nedeljkovic, I, Postma, DS & Boezen, HM 2016, 'Novel Genetic Susceptibility Loci for FEV₁ in the Context of Occupational Exposure in Never-Smokers', American Journal of Respiratory and Critical Care Medicine, vol. 194, no. 6, pp. 769-772.
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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.

Delaigle, A & Wand, MP 2016, 'A Conversation with Peter Hall', Statistical Science, vol. 31, no. 2, pp. 275-304.
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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, 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 considered during e...

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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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.
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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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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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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.
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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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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, A, Hare, K & Roginskaya, M 2016, 'On $L^p$-improving measures', Revista Matemática Iberoamericana, vol. 32, no. 4, pp. 1211-1226.
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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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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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This paper discusses the problem of hedging not perfectly replicable contingent claims using the numeraire portfolio. The proposed concept of benchmarked risk min- ´ imization leads beyond the classical no-arbitrage paradigm. It provides in incomplete markets a generalization of the pricing under classical risk minimization, pioneered by Follmer, 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 numeraire portfolio ´ to identify the minimal possible price for a contingent claim. Furthermore, the resulting benchmarked (i.e., numeraire 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.

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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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.
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Dunsmore, JC, Booker, JA, Ollendick, TH & Greene, RW 2016, 'Emotion Socialization in the Context of Risk and Psychopathology: Maternal Emotion Coaching Predicts Better Treatment Outcomes for Emotionally Labile Children with Oppositional Defiant Disorder', Social Development, vol. 25, no. 1, pp. 8-26.
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We examined whether maternal emotion coaching at pretreatment predicted children's treatment response following a 12-week program addressing children's oppositional defiant disorder (ODD) symptoms. A total of 89 mother-child dyads participated. At pretreatment, mothers and children engaged in an emotion talk task. Mothers also reported their beliefs about emotions at pretreatment and their child's disruptive behavior symptoms, emotion regulation, and emotion lability/negativity at pre-, mid-, and post-treatment. Clinicians reported children's symptom severity at pre- and post-treatment. Children's emotion lability/negativity moderated effects of maternal emotion coaching on children's post-treatment ODD symptoms, with stronger benefits of emotion coaching for children high in emotion lability/negativity. Results suggest that emotion coaching may promote treatment response for children with ODD who are especially at risk due to their emotionality.

Duong, T, Mulmudi, HK, Shen, H, Wu, Y, Barugkin, C, Mayon, YO, Nguyen, HT, Macdonald, D, Peng, J, Lockrey, M, Li, W, Cheng, Y-B, White, TP, Weber, K & Catchpole, K 2016, 'Structural engineering using rubidium iodide as a dopant under excess lead iodide conditions for high efficiency and stable perovskites', Nano Energy, vol. 30, pp. 330-340.
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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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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 warmto- 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.Weuse 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.Weshow 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.

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 finitely generated 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 every finite normal subgroup, and $G=A_\mu$ if and only if $G$ is amenable. For non-amenable groups we show that $A_\mu$ is not always a normal subgroup, and can depend on the measure. We formulate some conjectures relating $A_\mu$ to the 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 or non-amenability in a finitely generated group by numerically estimating its asymptotic cogrowth rate. We identify two potential sources of error. We then propose a modification of the method that enables it to easily compute surprisingly accurate estimates for initial terms of the cogrowth sequence.

Evans, LA 2016, 'Magnetic Resonance Cryoporometry Analysis of Red Deer (Cervus elaphus) Antler Bone', JOURNAL OF THE AUSTRALIAN CERAMIC SOCIETY, vol. 52, no. 2, pp. 1-8.
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Deer antler is a unique example of mammalian long bone because it regenerates annually with an extremely rapid rate of growth. This study describes a low-field NMR technique combined with cryoporimetric calibration for the estimation of pore size distribution in antler bone from spin-spin (T2) relaxation data. Pore sizes determined by the NMR method have been compared with the more traditional methods of gas adsorption and mercury intrusion experiments. The NMR method has the advantage of being rapid, non-destructive and noninvasive. It is superior to image analysis because the whole sample is used rather than a cross-section. This technique is particularly useful for the determination of fine pore structure including pore dimensions at the nanometre level and may be applied to other bioceramic materials where pore size and interconnectivity of the pores is important.

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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Farrant, GK, Doré, H, Cornejo-Castillo, FM, Partensky, F, Ratin, M, Ostrowski, M, Pitt, FD, Wincker, P, Scanlan, DJ, Iudicone, D, Acinas, SG & Garczarek, L 2016, 'Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria', Proceedings of the National Academy of Sciences, vol. 113, no. 24, pp. E3365-E3374.
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Significance Metagenomics has become an accessible approach to study complex microbial communities thanks to the advent of high-throughput sequencing technologies. However, molecular ecology studies often face interpretation issues, notably due to the lack of reliable reference databases for assigning reads to the correct taxa and use of fixed cutoffs to delineate taxonomic groups. Here, we considerably refined the phylogeography of marine picocyanobacteria, responsible for about 25% of global marine productivity, by recruiting reads targeting a high-resolution marker from Tara Oceans metagenomes. By clustering lineages based on their distribution patterns, we showed that there is significant diversity at a finer resolution than the currently defined “ecotypes,” a diversity that is tightly controlled by environmental cues.

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.

Farrell, LJ, Oar, EL, Waters, AM, McConnell, H, Tiralongo, E, Garbharran, V & Ollendick, T 2016, 'Brief intensive CBT for pediatric OCD with E-therapy maintenance', Journal of Anxiety Disorders, vol. 42, pp. 85-94.
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Feng, S, Tan, CH, Cohen, Y & Rice, SA 2016, 'Isolation ofBdellovibrio bacteriovorusfrom 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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© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.It 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.

Feng, X, Zou, H, Xiang, H, Guo, X, Zhou, T, Wu, Y, Xu, W, Yan, P, Wang, C, Zhang, J-G & Yu, Y 2016, 'Ultrathin Li₄Ti₅O₁₂ Nanosheets as Anode Materials for Lithium and Sodium Storage', ACS Applied Materials & Interfaces, vol. 8, no. 26, pp. 16718-16726.
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Ferguson, IMC, Shareef, MZ, Burns, B & Reid, C 2016, 'A human cadaveric workshop: One solution to competence in the face of rarity', Emergency Medicine Australasia, vol. 28, no. 6, pp. 752-754.
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Competent performance of cricothyroidotomy, lateral canthotomy and resuscitative thoracostomy is an expected standard for Australasian emergency physicians, but infrequent exposure to these procedures could impair physician confidence, reducing the likelihood of their execution in a critical timeframe. Training to perform these procedures is a recognised challenge for non-surgeons, and cadaver-based training is one method of addressing this need. We describe a 1 day cadaver-based workshop for emergency medicine doctors and briefly report on its impact on physician confidence. This workshop appeared effective in increasing the confidence of emergency medicine physicians to carry out rarely performed life and sight-saving procedures and also provides an opportunity for senior clinicians to increase compliance with continuing profession development schemes.

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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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: erratum', Journal of the Optical Society of America B, vol. 33, no. 12, pp. 2587-2587.
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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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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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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 to environmental and burial variables wh...

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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Frölich, S & Wallach, M 2016, 'Use of fluorescent nanoparticles to investigate nutrient acquisition by developing Eimeria maxima macrogametocytes', Scientific Reports, vol. 6, no. 1, pp. 1-11.
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AbstractThe enteric disease coccidiosis, caused by the unicellular parasite Eimeria, is a major and reoccurring problem for the poultry industry. While the molecular machinery driving host cell invasion and oocyst wall formation has been well documented in Eimeria, relatively little is known about the host cell modifications which lead to acquisition of nutrients and parasite growth. In order to understand the mechanism(s) by which nutrients are acquired by developing intracellular gametocytes and oocysts, we have performed uptake experiments using polystyrene nanoparticles (NPs) of 40 nm and 100 nm in size, as model NPs typical of organic macromolecules. Cytochalasin D and nocodazole were used to inhibit, respectively, the polymerization of the actin and microtubules. The results indicated that NPs entered the parasite at all stages of macrogametocyte development and early oocyst maturation via an active energy dependent process. Interestingly, the smaller NPs were found throughout the parasite cytoplasm, while the larger NPs were mainly localised to the lumen of large type 1 wall forming body organelles. NP uptake was reduced after microfilament disruption and treatment with nocodazole. These observations suggest that E. maxima parasites utilize at least 2 or more uptake pathways to internalize exogenous material during the sexual stages of development.

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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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-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.

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.

Gao, H, Zhou, T, Zheng, Y, Liu, Y, Chen, J, Liu, H & Guo, Z 2016, 'Integrated Carbon/Red Phosphorus/Graphene Aerogel 3D Architecture via Advanced Vapor-Redistribution for High-Energy Sodium-Ion Batteries', Advanced Energy Materials, vol. 6, no. 21, pp. 1601037-1601037.
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Gao, L, Cui, Y, Vervuurt, RHJ, van Dam, D, van Veldhoven, RPJ, Hofmann, JP, Bol, AA, Haverkort, JEM, Notten, PHL, Bakkers, EPAM & Hensen, EJM 2016, 'High-Efficiency InP-Based Photocathode for Hydrogen Production by Interface Energetics Design and Photon Management', Advanced Functional Materials, vol. 26, no. 5, pp. 679-686.
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The solar energy conversion efficiency of photoelectrochemical (PEC) devices is usually limited by poor interface energetics, limiting the onset potential, and light reflection losses. Here, a three-pronged approach to obtain excellent performance of an InP-based photoelectrode for water reduction is presented. First, a buried p-n junction is fabricated, which shifts the valence band edge favorably with respect to the hydrogen redox potential. Photoelectron spectroscopy substantiates that the shift of the surface photovoltage is mainly determined by the buried junction. Second, a periodic array of InP nanopillars is created at the surface of the photoelectrode to substantially reduce the optical reflection losses. This device displays an unprecedented photocathodic power-saved efficiency of 15.8% for single junction water reduction. Third, a thin TiO protection layer significantly increases the stability of the InP-based photoelectrode. Careful design of the interface energetics based on surface photovoltage spectroscopy allows obtaining a PEC cell with stable record performance in water reduction. The efficiency of photoelectrochemical (PEC) water splitting devices is usually limited by interface energetics mismatch between the semiconductor and the electrolyte and insufficient light absorption. The highest photocathodic power-saved efficiency of 15.8% reported so far for single junction PEC water reduction is obtained through interface energetics design and photon management of an InP-based photoelectrode. + 2

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.
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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.
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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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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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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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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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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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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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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, Chen, H, Teh, R, McGrath, RT, Chen, J, Pollock, CA, Wong, MG & Saad, S 2016, 'Mouse Models of Diabetes, Obesity and Related Kidney Disease', PLOS ONE, vol. 11, no. 8, pp. e0162131-e0162131.
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Multiple rodent models have been used to study diabetic kidney disease (DKD). The purpose of the present study was to compare models of diabetes and obesity-induced metabolic syndrome and determine differences in renal outcomes. C57BL/6 male mice were fed either normal chow or high fat diet (HFD). At postnatal week 8, chow-fed mice were randomly assigned to low-dose streptozotocin (STZ, 55 mg/kg/day, five consecutive days) or vehicle control, whereas HFD-fed mice were given either one high-dose of STZ (100 mg/kg) or vehicle control. Intraperitoneal glucose tolerance tests were performed at Week 14, 20 and 30. Urinary albumin to creatinine ratio (ACR) and serum creatinine were measured, and renal structure was assessed using Periodic Acid Schiff (PAS) staining at Week 32. Results showed that chow-fed mice exposed to five doses of STZ resembled type 1 diabetes mellitus with a lean phenotype, hyperglycaemia, microalbuminuria and increased serum creatinine levels. Their kidneys demonstrated moderate tubular injury with evidence of tubular dilatation and glycogenated nuclear inclusion bodies. HFD-fed mice resembled metabolic syndrome as they were obese with dyslipidaemia, insulin resistance, and significantly impaired glucose tolerance. One dose STZ, in addition to HFD, did not worsen metabolic features (including fasting glucose, non esterified fatty acid, and triglyceride levels). There were significant increases in urinary ACR and serum creatinine levels, and renal structural changes were predominantly related to interstitial vacuolation and tubular dilatation in HFD-fed mice.

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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Gloag, ES, Turnbull, L, Javed, MA, Wang, H, Gee, ML, Wade, SA & Whitchurch, CB 2016, 'Stigmergy co-ordinates multicellular collective behaviours during Myxococcus xanthus surface migration', Scientific Reports, vol. 6, no. 1.
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AbstractSurface translocation by the soil bacterium Myxococcus xanthus is a complex multicellular phenomenon that entails two motility systems. However, the mechanisms by which the activities of individual cells are coordinated to manifest this collective behaviour are currently unclear. Here we have developed a novel assay that enables detailed microscopic examination of M. xanthus motility at the interstitial interface between solidified nutrient medium and a glass coverslip. Under these conditions, M. xanthus motility is characterised by extensive micro-morphological patterning that is considerably more elaborate than occurs at an air-surface interface. We have found that during motility on solidified nutrient medium, M. xanthus forges an interconnected furrow network that is lined with an extracellular matrix comprised of exopolysaccharides, extracellular lipids, membrane vesicles and an unidentified slime. Our observations have revealed that M. xanthus motility on solidified nutrient medium is a stigmergic phenomenon in which multi-cellular collective behaviours are co-ordinated through trail-following that is guided by physical furrows and extracellular matrix materials.

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. PM10 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). PM10-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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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.

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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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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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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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.

Halldorsdottir, T & Ollendick, TH 2016, 'Long-term outcomes of brief, intensive CBT for specific phobias: The negative impact of ADHD symptoms.', Journal of Consulting and Clinical Psychology, vol. 84, no. 5, pp. 465-471.
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Objectives: The objectives were twofold: (a) examine long-term treatment effects in youth receiving 1-session treatment (OST) or educational support (EST) for a specific phobia (SP) and (b) examine the differential predictive and moderation effects of attention-deficit/hyperactivity disorder (ADHD) symptoms on immediate and long-term outcomes following the interventions. Method: Eighty-three children (ages 6-15, 47% female, 89% White) with a SP were randomly assigned to receive OST or EST. Follow up assessments occurred at 1 week, 6 months, 1 year, and 4 years. Hierarchical linear growth modeling (HLGM) was used to explore the association of parent-reported ADHD symptoms, the 2 treatment conditions (i.e., OST vs. EST), and the trajectory of change in the severity of the SP from pretreatment to the 4-year follow-up. Age, conduct problems and learning problems were controlled for in all analyses. Results: A greater immediate reduction in severity rating of the SP was observed in the OST compared to EST, whereas the trajectory of long-term outcomes was similar across conditions over time. Higher levels of ADHD symptoms predicted poor immediate and long-term treatment outcomes across treatment conditions. ADHD symptoms, however, did not moderate the relationship between treatment condition and immediate or long-term treatment outcomes. Conclusions: The results of the study need to be interpreted in light of several study limitations. However, if confirmed, the findings suggest that anxious youth with comorbid ADHD symptoms are less likely to benefit from brief, intensive psychotherapy and may require either longer, standard CBT treatment or adjunctive pharmacotherapy.

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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Hamidian, M, Holt, KE, Pickard, D & Hall, RM 2016, 'A smallAcinetobacterplasmid carrying thetet39tetracycline resistance determinant', Journal of Antimicrobial Chemotherapy, vol. 71, no. 1, pp. 269-271.
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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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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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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.

Harikesh, PC, Mulmudi, HK, Ghosh, B, Goh, TW, Teng, YT, Thirumal, K, Lockrey, M, Weber, K, Koh, TM, Li, S, Mhaisalkar, S & Mathews, N 2016, 'Rb as an Alternative Cation for Templating Inorganic Lead-Free Perovskites for Solution Processed Photovoltaics', CHEMISTRY OF MATERIALS, vol. 28, no. 20, pp. 7496-7504.
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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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Hassan, KA, Cain, AK, Huang, T, Liu, Q, Elbourne, LDH, Boinett, CJ, Brzoska, AJ, Li, L, Ostrowski, M, Nhu, NTK, Nhu, TDH, Baker, S, Parkhill, J & Paulsen, IT 2016, 'Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii', mBio, vol. 7, no. 5.
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ABSTRACT Multidrug efflux pumps provide clinically significant levels of drug resistance in a number of Gram-negative hospital-acquired pathogens. These pathogens frequently carry dozens of genes encoding putative multidrug efflux pumps. However, it can be difficult to determine how many of these pumps actually mediate antimicrobial efflux, and it can be even more challenging to identify the regulatory proteins that control expression of these pumps. In this study, we developed an innovative high-throughput screening method, combining transposon insertion sequencing and cell sorting methods (TraDISort), to identify the genes encoding major multidrug efflux pumps, regulators, and other factors that may affect the permeation of antimicrobials, using the nosocomial pathogen Acinetobacter baumannii . A dense library of more than 100,000 unique transposon insertion mutants was treated with ethidium bromide, a common substrate of multidrug efflux pumps that is differentially fluorescent inside and outside the bacterial cytoplasm. Populations of cells displaying aberrant accumulations of ethidium were physically enriched using fluorescence-activated cell sorting, and the genomic locations of transposon insertions within these strains were determined using transposon-directed insertion sequencing. The relative abundance of mutants in the input pool compared to the selected mutant pools indicated that the AdeABC, AdeIJK, and AmvA efflux pumps are the major ethidium efflux systems in A. baumannii . Furthermore, the method identified a new transcriptional regulator that controls expression of amvA . In addition to the identification of efflux pumps and their regulators, TraDISort iden...

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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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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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.
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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.
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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.

Ho, YYW, Evans, DM, Montgomery, GW, Henders, AK, Kemp, JP, Timpson, NJ, St. Pourcain, B, Heath, AC, Madden, PAF, Loesch, DZ, McNevin, D, Daniel, R, Davey-Smith, G, Martin, NG & Medland, SE 2016, 'Common Genetic Variants Influence Whorls in Fingerprint Patterns', Journal of Investigative Dermatology, vol. 136, no. 4, pp. 859-862.
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Hogendoorn, K, Anantanawat, K & Collins, C 2016, 'Cap removal by honey bees leads to higher pollen rewards from grapevine flowers', Apidologie, vol. 47, no. 5, pp. 671-678.
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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.
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Homaira, N, Sheils, J, Stelzer-Braid, S, Lui, K, Oie, J-L, 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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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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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.
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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.

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.

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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Huang, Y-H, Hwang, FJ & Lu, H-C 2016, 'An effective placement method for the single container loading problem', Computers & Industrial Engineering, vol. 97, pp. 212-221.
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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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Hunt, A, Thomas, P, James, D, David, B, Geneste, J-M, Delannoy, J-J & Stuart, B 2016, 'The characterisation of pigments used in X-ray rock art at Dalakngalarr 1, central-western Arnhem Land', Microchemical Journal, vol. 126, pp. 524-529.
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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, 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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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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Genetic 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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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 initially ...

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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Irga, PJ & Torpy, FR 2016, 'Indoor air pollutants in occupational buildings in a sub-tropical climate: Comparison among ventilation types (vol 98, pg 190, 2016)', BUILDING AND ENVIRONMENT, vol. 100, pp. 227-227.
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Irga, PJ, Armstrong, B, King, WL, Burchett, M & Torpy, FR 2016, 'Correspondence Between Urban Bird Roosts and the Presence of Aerosolised Fungal Pathogens', Mycopathologia, vol. 181, no. 9-10, pp. 689-699.
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Irga, PJ, Burchett, MD, O’Reilly, G & Torpy, FR 2016, 'Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment', Urban Ecosystems, vol. 19, no. 2, pp. 885-898.
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Many street trees in urban areas are deciduous and drop leaves during autumn. These leaves are a potential growing substrate for fungi, which when aerosolized and inhaled, can lead to allergy along with more serious diseases. This investigation assessed the potential contribution of fallen leaves to the diversity of airborne fungal propagules during autumn. The senescent leaves of five deciduous tree species prevalent in urban environments were subject to a manipulative experiment in which their phyllospheric fungi were aerosolized, cultured and identified. Aerosolized fungi were compared with fungi detected from direct observation of the phyllosphere. Thirty-nine fungal genera were identified across the plant species sampled, of which twenty-eight were present in corresponding air samples. Significant differences were observed amongst the fungal genera growing on the leaves of the different trees, however few differences were found in the composition of fungal spores that were aerosolized. The dominant genera that were aerosolized were: Penicillium, Cladosporium, Alternaria, Chaetomium, Botrytis and Trichothecium. Some of these fungi are known to produce allergy and other symptoms in humans. As these fungal genera have been commonly identified in autumn air samples in other studies, it is likely that the phyllospheric fungi present on deciduating leaves contribute to the aeromycota of urban areas.

James, SA, Hare, DJ, Jenkins, NL, de Jonge, MD, Bush, AI & McColl, G 2016, 'Erratum: φXANES: In vivo imaging of metal-protein coordination environments', Scientific Reports, vol. 6, no. 1.
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Scientific Reports 6: Article number: 20350; published online: 10 February 2016; updated: 21 March 2016 In this Article, the online methods were omitted. The online methods should read: Strains Wild type C. elegans (strain N2) were obtained from the Caenorhabditis Genetics Center (University of Minnesota), and ftn-2(ok404) and the ferritin null ftn-2(ok404); ftn-1(ok3625) (strain GMC005) have been previously described 1 .

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.

Jarnicki, AG, Schilter, H, Liu, G, Wheeldon, K, Essilfie, A-T, 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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Jarrett, MA, Wolff, JC, Davis, TE, Cowart, MJ & Ollendick, TH 2016, 'Characteristics of Children With ADHD and Comorbid Anxiety', Journal of Attention Disorders, vol. 20, no. 7, pp. 636-644.
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Objective: The following comorbid subgroups of ADHD have been proposed: ADHD Only, ADHD + anxiety disorders (ANX), ADHD + oppositional defiant disorder/conduct disorder (ODD/CD), and ADHD + ODD/CD + ANX. The current study examined a subset of these groups. Method: A total of 134 children and adolescents ( M age = 9.92; range = 6-17) from a clinic-referred sample ( n = 407) were grouped based on a semistructured diagnostic interview: ADHD only ( n = 41), ADHD + ANX ( n = 31), and ANX Only ( n = 62). Results: Findings supported greater parent-reported anxiety symptoms in anxiety groups, and greater parent- and teacher-reported attention problems in ADHD groups. ADHD groups performed worse on a continuous performance test, whereas ADHD + ANX performed worse on working memory than ADHD Only. ADHD + ANX reported more physical anxiety symptoms than ADHD Only. Conclusion: Comorbid anxiety should be considered in ADHD assessment and treatment.

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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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, pp. 1-17.
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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 insights into the simultaneous influence of natural and anthropogenic drivers on the structure and...

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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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.
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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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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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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.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.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).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, 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, pp. 1-11.
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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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AbstractBackgroundThis 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).MethodsAfter 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.ResultsThe 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.ConclusionsThe rise of CAM as a social and clinical phenomenon necessitates consideration of further inclusion of these topics in the medical curriculum, if future physicians are to be able to fully discharge their role as care providers in an increasingly medically pluralistic world. However, the inclusion of CAM needs to b...

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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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.
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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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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.-Kapetanovic, R., Bokil, N. J., Achard, M. E. S., Ong, C.-L. Y., Peters, K. M., Stocks, C. J., Phan, M.-D., Monteleone, M., Schroder, K., Irvine, K. M., Saunders, B. M., Walker, M. J., Stacey, K. J., McEwan, A. G., Schembri, M. A., Sweet, M. J. Salmonella employs multiple mechanisms to subvert the TLR-inducible zinc-mediated antimicrobial response of human macrophages.

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.
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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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Kelvin Lee, KW, Hoong Yam, JK, 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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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 Medicine published 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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Khuu, A, Chadwick, S, Spindler, X, Lam, R, Moret, S & Roux, C 2016, 'Authors' response to comments on 'Evaluation of one-step luminescent cyanoacrylate fuming''', FORENSIC SCIENCE INTERNATIONAL, vol. 268, pp. E25-E26.
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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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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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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 requires robust, stable solid state single photon sources. However, most existing sources cease to function above cryogenic or room temperature due to thermal ionization or strong phonon coupling which impede their emissive and quantum properties. Here we present an efficient single photon source based on a defect in a van der Waals crystal that is optically stable and operates at elevated temperatures of up to 800 K. The quantum nature of the source and the photon purity are maintained upon heating to 800 K and cooling back to room temperature. Our report of a robust high temperature solid state single photon source constitutes a significant step to-wards practical, integrated quantum technologies for real-world environments.

Kim, ASI & Wand, MP 2016, 'The explicit form of expectation propagation for a simple statistical model', Electronic Journal of Statistics, vol. 10, no. 1, pp. 550-581.
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© 2016, Institute of Mathematical Statistics. All rights reserved. We derive the explicit form of expectation propagation for approximate deterministic Bayesian inference in a simple statistical model. The model corresponds to a random sample from the Normal distribution. The explicit forms, and their derivation, allow a deeper understanding of the issues and challenges involved in practical implementation of expectation propagation for statistical analyses. No auxiliary approximations are used: we follow the expectation propagation prescription exactly. A simulation study shows expectation propagation to be more accurate than mean field variational Bayes for larger sample sizes, but at the cost of considerably more algebraic and computational effort.

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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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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Kim, T-H, Zaslawski, C, Kwon, S & Kang, JW 2016, 'Korean Medicine in General Practice: Current Status, Challenges, and Vision in Clinical Evidence', EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 2016.
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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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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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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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© 2015, The International Biometric Society. Semicontinuous 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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© 2016 by the authors. 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/m 2 , R = 0.68). The average total above-ground biomass was 23.95 ± 10.38 g·DW/m 2 . 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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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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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, 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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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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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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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.

Kyng, T, Konstandatos, O & Bienek, T 2016, 'Valuation of employee stock options using the exercise multiple approach and life tables', INSURANCE MATHEMATICS & ECONOMICS, vol. 68, pp. 17-26.
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Labeeuw, L, Khey, J, Bramucci, AR, Atwal, H, de la Mata, AP, Harynuk, J & Case, RJ 2016, 'Indole-3-Acetic Acid Is Produced by Emiliania huxleyi Coccolith-Bearing Cells and Triggers a Physiological Response in Bald Cells', Frontiers in Microbiology, vol. 7.
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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. 155, pp. 1-14.
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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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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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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.

Ledovskikh, AV, Danilov, DL, Vliex, M & Notten, PHL 2016, 'Modeling and experimental verification of the thermodynamic properties of hydrogen storage materials', International Journal of Hydrogen Energy, vol. 41, no. 6, pp. 3904-3918.
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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.
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Lee, CYY & Wand, MP 2016, 'Streamlined mean field variational Bayes for longitudinal and multilevel data analysis', Biometrical Journal, vol. 58, no. 4, pp. 868-895.
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Streamlined mean field variational Bayes algorithms for efficient fitting and inference in large models for longitudinal and multilevel data analysis are obtained. The number of operations is linear in the number of groups at each level, which represents a two orders of magnitude improvement over the naïve approach. Storage requirements are also lessened considerably. We treat models for the Gaussian and binary response situations. Our algorithms allow the fastest ever approximate Bayesian analyses of arbitrarily large longitudinal and multilevel datasets, with little degradation in accuracy compared with Markov chain Monte Carlo. The modularity of mean field variational Bayes allows relatively simple extension to more complicated scenarios.

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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Lee, H-H, Paudel, KR, Jeong, J, Wi, A-J, Park, W-S, Kim, D-W & Oak, M-H 2016, 'Antiatherogenic Effect ofCamellia japonicaFruit Extract in High Fat Diet-Fed Rats', Evidence-Based Complementary and Alternative Medicine, vol. 2016, 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 japonicais 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 ofC. japonicafruit 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, 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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Lepère, C, Ostrowski, M, Hartmann, M, Zubkov, MV & Scanlan, DJ 2016, 'In situassociations between marine photosynthetic picoeukaryotes and potential parasites - a role for fungi?', Environmental Microbiology Reports, vol. 8, no. 4, pp. 445-451.
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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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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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Li, D, Danilov, DL, Gao, L, Yang, Y & Notten, PHL 2016, 'Degradation Mechanisms of the Graphite Electrode in C₆/LiFePO₄Batteries Unraveled by a Non-Destructive Approach', Journal of The Electrochemical Society, vol. 163, no. 14, pp. A3016-A3021.
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© 2016 The Electrochemical Society. All rights reserved. C6/LiFePO4 (LFP) batteries have been cycled at various temperatures (20 and 60°C) and State-of-Charge (SoC) ranges (0-30, 35-65, 70-100% and 0-100%). Electromotive force (emf) curves have regularly been determined by regression extrapolation of the measured voltage discharge curves. A non-destructive approach to quantitatively determine the graphite electrode decay has been proposed on the basis of dVEMF/dQ curves. It is concluded that the graphite inaccessibility is more pronounced at lower SoC (0-30%) than at higher SoC. The graphite electrode decay at 35-65%, 70-100% and 0-100% is identified to be negligible at moderated temperatures but becomes significant at elevated temperatures. The graphite electrode degradation has been confirmed by XPS and Raman spectroscopy, supporting the conclusions drawn from the dVEMF/dQ results. A model is proposed to explain the various graphite degradation mechanisms.

Li, D, Danilov, DL, Xie, J, Raijmakers, L, Gao, L, Yang, Y & Notten, PHL 2016, 'Degradation Mechanisms of C6/LiFePO4 Batteries: Experimental Analyses of Calendar Aging', Electrochimica Acta, vol. 190, pp. 1124-1133.
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The capacity loss and material decay of C /LiFePO (LFP) batteries have been investigated under various storage conditions in dependence of State-of-Charge (SoC) and temperature. The electromotive force (EMF) curves, which are regularly determined by mathematical extrapolation of the measured voltage discharge curves, are used to investigate the aging mechanisms during storage. The irreversible capacity loss, which is accurately determined on the basis of the maximum storage capacity estimated from the EMF curves, increases as a function of temperature and SoC. The cyclable Li-ion loss during storage is considered to be the main source of the irreversible capacity loss. Strikingly, the inaccessibility of graphite is observed during storage at 60 °C. The graphite capacity decay has been quantitatively determined by non-destructive analyses on the basis of dV /dQ curves. Deposition of Fe on the graphite electrode has experimentally been confirmed by X-ray photoelectron spectroscopy (XPS). The increasing graphite inaccessibility is shown to be the consequence of Fe dissolution from the cathode and the subsequent deposition onto the anode. 6 4 EMF

Li, D, L. Danilov, D, Gao, L, Yang, Y & Notten, PHL 2016, 'Degradation Mechanisms of C6/LiFePO4 Batteries: Experimental Analyses of Cycling-induced Aging', Electrochimica Acta, vol. 210, pp. 445-455.
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© 2016 Elsevier Ltd. Electromotive force (EMF) voltage curves are regularly determined to facilitate in-depth understanding of aging mechanisms of C6/LiFePO4 batteries during cycling. The irreversible capacity losses under various cycling conditions and temperatures are accurately obtained from the extrapolated EMF curves and are found to increase with cycle number and time. A new mathematical extrapolation method is proposed to distinguish between calendar ageing and cycling-induced ageing. The capacity losses due to calendar aging are obtained by extrapolating the total irreversible capacity losses to zero cycle number. It is found that calendar ageing increases logarithmically in time. On the other hand, cycling-induced ageing is accurately determined by extrapolating the capacity losses to zero time. In this case the capacity losses are found to increase linearly with cycle number. It is furthermore found that iron dissolution from the cathode at 60 °C and the subsequent deposition onto the anode enhances significantly the SEI formation on the graphite electrode and, consequently, battery ageing. Interestingly, the graphite electrode decay has been quantified in much more detail, by analyzing the dVEMF/dQ curves. The analyses show that the electrode decay can be related to both the structural deterioration and the inter-layer surface blockage of the graphite electrode, as has also been experimentally confirmed by Raman and XPS spectroscopy.

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 (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.

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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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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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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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, BMT, Hwang, FJ & Kononov, AV 2016, 'Relocation scheduling subject to fixed processing sequences', Journal of Scheduling, vol. 19, no. 2, pp. 153-163.
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© 2015 Springer Science+Business Media New York This study addresses a relocation scheduling problem that corresponds to resource-constrained scheduling on two parallel dedicated machines where the processing sequences of jobs assigned to the machines are given and fixed. Subject to the resource constraints, the problem is to determine the starting times of all jobs for each of the six considered regular performance measures, namely, the makespan, total weighted completion time, maximum lateness, total weighted tardiness, weighted number of tardy jobs, and number of tardy jobs. By virtue of the proposed dynamic programming framework, the studied problem for the minimization of makespan, total weighted completion time, or maximum lateness can be solved in (Formula presented.) time, where (Formula presented.) and (Formula presented.) are the numbers of jobs on the two machines. The simplified case with a common job processing time can be solved in (Formula presented.) time. For the objective function of total weighted tardiness or weighted number of tardy jobs, this problem is proved to be NP-hard in the ordinary sense, and the case with a common job processing length is solvable in (Formula presented.) time. The studied problem for the minimization of number of tardy jobs is solvable in (Formula presented.) time. The solvability of the common-processing-time problems can be generalized to the m-machine cases, where (Formula presented.).

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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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, 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, 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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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 biofilm population size and structure are now...

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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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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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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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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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).

Lu, JF, Pokharel, D, Padula, MP & Bebawy, M 2016, 'A novel method to detect translation of membrane proteins following microvesicle intercellular transfer of nucleic acids', Journal of Biochemistry, vol. 160, no. 5, pp. 281-289.
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Microvesicles (MVs) serve as vectors of nucleic-acid dissemination and are important mediators of intercellular communication. However, the functionality of packaged nucleic acids on recipient cells following transfer of MV-cargo has not been clearly elucidated. This limitation is attributed to a lack of methodology available in assessing protein translation following homotypic intercellular transfer of nucleic-acids. Using surface peptide shaving we have demonstrated that MVs derived from human leukaemic cells transfer functional P-glycoprotein transcripts, conferring drug-efflux capacity to recipient cells. We demonstrate expression of newly synthesized protein using Western blot. Furthermore, we show functionality of translated P-gp protein in recipient cells using Calcein-AM dye exclusion assays on flow cytometry. Newly synthesized 170 kDa P-gp was detected in recipient cells after co-culture with shaven MVs and these proteins were functional, conferring drug-efflux. This is the first demonstration of functionality of transferred nucleic-acids between human homotypic cells as well as the translation of the cancer multidrug-resistance protein in recipient cells following intercellular transfer of its transcript. This study supports the significant role of MV's in the transfer of deleterious traits in cancer populations and describes a new paradigm in mechanisms governing the acquisition of traits in cancer cell populations.

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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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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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, 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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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, 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.

Macnamara, J 2016, 'Multiple intelligences and minds as attributes to reconfigure PR-A critical analysis', PUBLIC RELATIONS REVIEW, vol. 42, no. 2, pp. 249-257.
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The fields of business and management with which public relations interacts and in which it is often located are rife with concepts, models and theories on leadership, performance, and effectiveness. Recently these have turned attention to alleged multiple forms of intelligence, such as Howard Gardner’s claims for eight types of intelligence, which have been expanded by others to as many as 150. Gardner also proposed that humans have five minds and claimed that application of these diverse intelligences and minds can enhance human interactions and relationships. This article critically reviews the potential of these concepts and theories to reconfigure PR, identifying some useful insights, but also raising fundamental theoretical questions.

Macnamara, J 2016, 'Organizational listening: Addressing a major gap in public relations theory and practice', Journal of Public Relations Research, vol. 28, no. 3-4, pp. 146-169.
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An extensive body of literature theorizes public relations as two-way communication, dialogue, and relationships between organizations and their publics. While there are alternative views including public relations as advocacy, most theories emphasize dialogue, co-orientation, and relationships incorporating satisfaction, trust, and control mutuality – even to the extent of symmetry. Critical perspectives propose a ‘sociocultural turn’ that further emphasizes stakeholders’ and societal interests. This analysis draws on a three-country study that reveals a major theory-practice gap and proposes a significant expansion of public relations theory in relation to listening to realize normative notions of public relations and give effect to claims of dialogue and engagement.

Macnamara, J 2016, 'The Continuing Convergence of Journalism and PR', Journalism & Mass Communication Quarterly, vol. 93, no. 1, pp. 118-141.
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The influence of public relations (PR) on media content has been shown to be substantial, and research indicates that it is growing through new media practices. However, the interrelationship between journalism and PR remains obscured by paradoxical discourses and stereotypes such as “spin doctors.” This article identifies gaps in the literature and current understandings, and reports findings from in-depth interviews with senior editors, journalists, and PR practitioners in several countries that provide new insights into how the fields of practice interact which not only debunk some myths but also expose a need for improved transparency and standards to ensure ethical media practice.

Macnamara, J 2016, 'The Work and ‘Architecture of Listening’: Addressing Gaps in Organization-Public Communication', International Journal of Strategic Communication, vol. 10, no. 2, pp. 133-148.
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Listening is extensively discussed in relation to interpersonal communication, in therapeutic contexts such as counselling and, to some extent, in the context of intra-organizational communication conducted as part of human resources management. However, listening is surprisingly and problematically overlooked in the large body of literature on organization-public communication including government, political, corporate, and marketing communication and related practices such as public relations. Based on critical analysis of relevant literature and primary research among 36 organizations in three countries, this analysis identifies a ‘crisis of listening’ in organization-public communication and proposes strategies to address gaps in theory and practice including attention to the work of listening and the creation of an architecture of listening in organizations, which can offer significant stakeholder, societal, and organizational benefits.

Macnamara, J, Lwin, M, Adi, A & Zerfass, A 2016, '‘PESO’ media strategy shifts to ‘SOEP’: Opportunities and ethical dilemmas', Public Relations Review, vol. 42, no. 3, pp. 377-385.
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It is well established that the internet, and particularly the unprecedented growth of social media, are changing the mediascape and media practices in advertising and marketing, public relations, and journalism. Some of these changes are leading to convergence of genre and practices as well as the much-discussed convergence of technologies of media. This analysis focuses on the first two of these types of convergence, drawing on data from the first Asia-Pacific Communication Monitor, a survey of 1,200 PR and communication practitioners in 23 Asia-Pacific countries. The findings reveal major shifts from the traditional paid, earned, shared, owned (PESO) model of media use by organizations to an emerging ‘SOEP model’ (shared, owned, earned, paid). This affords new opportunities for practitioners, but also poses practical and ethical dilemmas.

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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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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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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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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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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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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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.
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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 NF ₃ ‐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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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.

Mayers, TJ, Bramucci, AR, Yakimovich, KM & Case, RJ 2016, 'A Bacterial Pathogen Displaying Temperature-Enhanced Virulence of the Microalga Emiliania huxleyi', Frontiers in Microbiology, vol. 7.
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Mazard, S, Penesyan, A, Ostrowski, M, Paulsen, I & Egan, S 2016, 'Tiny Microbes with a Big Impact: The Role of Cyanobacteria and Their Metabolites in Shaping Our Future', Marine Drugs, vol. 14, no. 5, pp. 97-97.
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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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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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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.

Meakin, GE & Jamieson, A 2016, 'A response to a response to Meakin and Jamieson DNA transfer: Review and implications for casework', Forensic Science International: Genetics, vol. 22, pp. e5-e6.
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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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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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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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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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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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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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Australia's tropical waters represent predicted 'hotspots' for nitrogen (N2) 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 N2 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 N2 fixation rates ranged from <1 to 91 nmol l(-1) day(-1), and size fractionation indicated that unicellular organisms dominated N2 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 N2 fixation and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.The ISME Journal advance online publication, 27 November 2015; doi:10.1038/ismej.2015.205.

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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Abstract An 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.

Miller-Slough, RL, Dunsmore, JC, Ollendick, TH & Greene, RW 2016, 'Parent–Child Synchrony in Children with Oppositional Defiant Disorder: Associations with Treatment Outcomes', Journal of Child and Family Studies, vol. 25, no. 6, pp. 1880-1888.
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Oppositional defiant disorder (ODD), characterized by angry/irritable mood, and argumentative/defiant behavior, is associated with significant negative outcomes in childhood and beyond. Researchers posit that these behaviors arise from poor parenting and/or an incompatibility between characteristics of the child and the child’s parents, resulting in strained interaction styles. The present study examines parent–child synchrony, the inverse of parent–child incompatibility as a predictor of children’s emotional lability, aggression, and overall functioning following psychosocial treatment. Participants were 75 treatment-seeking families with children diagnosed with ODD (46 boys). Families received one of two empirically supported treatments for ODD (Parent Management Training or Collaborative and Proactive Solutions). Findings indicated that pre-treatment parent–child synchrony was associated with decreased emotional lability and aggression following both treatments, as well as improvement in overall functioning, irrespective of treatment condition. These results reflect the importance of parent–child relations at the onset of treatment in predicting response to treatment and suggest potential treatment targets within parent–child relationships.

Min, Q, Brown, J, Padmadas, S, Bohua, L, Jianan, Q & Falkingham, J 2016, 'Gender Inequalities in Employment and Wage-earning among Economic Migrants in Chinese Cities', Demographic Research, vol. 34, pp. 175-202.
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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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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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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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Mohanty, M, Asghar, MR & Russello, G 2016, '<inline-formula> <tex-math notation='LaTeX'>$2DCrypt$ </tex-math> </inline-formula>: Image Scaling and Cropping in Encrypted Domains', IEEE Transactions on Information Forensics and Security, vol. 11, no. 11, pp. 2542-2555.
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© 2016 IEEE. The evolution of cloud computing and a drastic increase in image size are making the outsourcing of image storage and processing an attractive business model. Although this outsourcing has many advantages, ensuring data confidentiality in the cloud is one of the main concerns. There are state-of-the-art encryption schemes for ensuring confidentiality in the cloud. However, such schemes do not allow cloud datacenters to perform operations over encrypted images. In this paper, we address this concern by proposing 2DCrypt, a modified Paillier cryptosystem-based image scaling and cropping scheme for multi-user settings that allows cloud datacenters to scale and crop an image in the encrypted domain. To anticipate a high storage overhead resulted from the naive per-pixel encryption, we propose a space-efficient tiling scheme that allows tile-level image scaling and cropping operations. Basically, instead of encrypting each pixel individually, we are able to encrypt a tile of pixels. 2DCrypt is such that multiple users can view or process the images without sharing any encryption keys - a requirement desirable for practical deployments in real organizations. Our analysis and results show that 2DCrypt is INDistinguishable under Chosen Plaintext Attack secure and incurs an acceptable overhead. When scaling a 512 × 512 image by a factor of two, 2DCrypt requires an image user to download approximately 5.3 times more data than the un-encrypted scaling and need to work approximately 2.3 s more for obtaining the scaled image in a plaintext.

Mohanty, M, Ooi, WT & Atrey, PK 2016, 'Secret sharing approach for securing cloud-based pre-classification volume ray-casting', Multimedia Tools and Applications, vol. 75, no. 11, pp. 6207-6235.
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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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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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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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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 others. W...

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 not others. ...

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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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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Moret, S, Becue, A & Champod, C 2016, 'Functionalised silicon oxide nanoparticles for fingermark detection', FORENSIC SCIENCE INTERNATIONAL, vol. 259, pp. 10-18.
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Over the past decade, the use of nanotechnology for fingermark detection has been attracting a lot of attention. A substantial number of nanoparticle types has thus been studied and applied with varying success. However, despite all efforts, few publications present clear supporting evidence of their superiority over standard and commonly used techniques. This paper focuses on a rarely studied type of nanoparticles that regroups all desired properties for effective fingermark detection: silicon oxide. These nanoparticles offer optical and surface properties that can be tuned to provide optimal detection. This study explores their potential as a new method for fingermark detection. Detection conditions, outer functionalisations and optical properties were optimised and a first evaluation of the technique is presented. Dye-doped silicon oxide nanoparticles were assessed against a one-step luminescent cyanoacrylate. Both techniques were compared on natural fingermarks from three donors collected on four different non-porous substrates. On average, the two techniques performed similarly but silicon oxide detected marks with a better homogeneity and was less affected by donor inter-variability. The technique remains to be further optimised and yet silicon oxide nanoparticles already show great promises for effective fingermark detection.

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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Abstract Winter 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.

Newland, TG, Moret, S, Becue, A & Lewis, SW 2016, 'Further investigations into the single metal deposition (SMD II) technique for the detection of latent fingermarks', FORENSIC SCIENCE INTERNATIONAL, vol. 268, pp. 62-72.
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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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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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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 (GC×GC-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 vs. stationary) and sample storage conditions (e.g. short-term vs. long-term storage at -18 °C). Future studies of CF-associated bacteria and exhaled breath condensate will benefit from the approaches presented in this study and further facilitate the p...

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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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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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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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.

Oar, EL, Farrell, LJ, Waters, AM & Ollendick, TH 2016, 'Blood-Injection-Injury Phobia and Dog Phobia in Youth: Psychological Characteristics and Associated Features in a Clinical Sample', Behavior Therapy, vol. 47, no. 3, pp. 312-324.
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Blood-Injection-Injury (BII) phobia is a particularly debilitating condition that has been largely ignored in the child literature. The present study examined the clinical phenomenology of BII phobia in 27 youths, relative to 25 youths with dog phobia-one of the most common and well-studied phobia subtypes in youth. Children were compared on measures of phobia severity, functional impairment, comorbidity, threat appraisals (danger expectancies and coping), focus of fear, and physiological responding, as well as vulnerability factors including disgust sensitivity and family history. Children and adolescents with BII phobia had greater diagnostic severity. In addition, they were more likely to have a comorbid diagnosis of a physical health condition, to report more exaggerated danger expectancies, and to report fears that focused more on physical symptoms (e.g., faintness and nausea) in comparison to youth with dog phobia. The present study advances knowledge relating to this poorly understood condition in youth.

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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Oliver, BGG & Black, J 2016, 'Asthma: Airways That Are Hyperactive by Design', American Journal of Respiratory and Critical Care Medicine, vol. 193, no. 6, pp. 596-598.
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Ollendick, TH 2016, 'A Commentary on Cognitive Behavior Therapy: Where We Have Been, Where We Are, and Where We Need to Go From Here', Cognitive and Behavioral Practice, vol. 23, no. 4, pp. 436-440.
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In this commentary, I use my own career and contributions to cognitive behavior therapy (CBT) as a point of departure and reflect upon where the field was when I obtained my graduate training in the late 60s, how it has changed over the past 50 years, and where it needs to go to remain alive and vibrant in the years ahead. Early on CBT was firmly and almost exclusively grounded in learning theory. Although learning theory remains our foundational core to this day, our primary allegiance these days is to broader evidence-based principles of change and the scientific pursuit of evidence-based interventions. Still, although we have accomplished much, we must do more in the years ahead of us. First we need to become more expansive in our attempts to understand the many and diverse problems we treat and, second, we must become more rigorous in the ways in which we assess and treat these problems. I conclude by indicating that although we are 50 years of age this year, and we have much reason to celebrate, we are really only in the adolescent period of our development. Growth is ahead of us.

Ollendick, TH & Grills, AE 2016, 'Perceived Control, Family Environment, and the Etiology of Child Anxiety—Revisited', Behavior Therapy, vol. 47, no. 5, pp. 633-642.
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In 1998, Chorpita, Brown, and Barlow published a now seminal study in Behavior Therapy examining the development of anxiety in children and adolescents using Barlow's 1988 model of the development of anxiety in adults. Mindful of developmental considerations, parental control and children's perceptions of control were considered key factors in this revised model. Since that study, mixed support has accumulated for the role of control, both parental control and children's perceptions of that control, in the development of childhood anxiety. As a result, the measurement of these constructs has been critically examined and refined in recent years and encouraging findings have been obtained. Unfortunately, however, the Chorpita and colleagues study as well as the studies that have followed have used cross-sectional designs and the directionality of effects has not been clearly established. Longitudinal studies are required. Here, we present a qualitative review of these developments and provide directions for future research.

Ollendick, TH, Greene, RW, Austin, KE, Fraire, MG, Halldorsdottir, T, Allen, KB, Jarrett, MA, Lewis, KM, Whitmore Smith, M, Cunningham, NR, Noguchi, RJP, Canavera, K & Wolff, JC 2016, 'Parent Management Training and Collaborative & Proactive Solutions: A Randomized Control Trial for Oppositional Youth', Journal of Clinical Child & Adolescent Psychology, vol. 45, no. 5, pp. 591-604.
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This study examined the efficacy of Collaborative & Proactive Solutions (CPS) in treating oppositional defiant disorder (ODD) in youth by comparing this novel treatment to Parent Management Training (PMT), a well-established treatment, and a waitlist control (WLC) group. One hundred thirty-four youth (ages 7–14, 61.9% male, 83.6% White) who fulfilled Diagnostic and Statistical Manual of Mental Disorders (4th ed.) criteria for ODD were randomized to CPS, PMT, or WLC groups. ODD was assessed with semistructured diagnostic interviews, clinical global severity and improvement ratings, and parent report measures. Assessments were completed pretreatment, posttreatment, and at 6 months following treatment. Responder and remitter analyses were undertaken using intent-to-treat mixed-models analyses. Chronological age, gender, and socioeconomic status as well as the presence of comorbid attention deficit/hyperactivity and anxiety disorders were examined as predictors of treatment outcome. Both treatment conditions were superior to the WLC condition but did not differ from one another in either our responder or remitter analyses. Approximately 50% of youth in both active treatments were diagnosis free and were judged to be much or very much improved at posttreatment, compared to 0% in the waitlist condition. Younger age and presence of an anxiety disorder predicted better treatment outcomes for both PMT and CPS. Treatment gains were maintained at 6-month follow-up. CPS proved to be equivalent to PMT and can be considered an evidence-based, alternative treatment for youth with ODD and their families.

Ollendick, TH, Jarrett, MA, White, BA, White, SW & Grills, AE 2016, 'Primary Versus Secondary Diagnosis of Generalized Anxiety Disorder in Youth: Is the Distinction an Important One?', Child Psychiatry & Human Development, vol. 47, no. 4, pp. 548-553.
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Examine whether children with a primary diagnosis of generalized anxiety disorder (GAD) differ from children with a secondary diagnosis of GAD on clinician, parent, teacher, and youth-report measures. Based on consensus diagnoses, 64 youth referred to a general outpatient assessment clinic were categorized as having either a primary or secondary diagnosis of GAD. A semi-structured diagnostic interview was used to guide diagnostic decisions and assign primary versus secondary diagnostic status. We predicted that youth with a primary GAD diagnosis would present with greater anxiety symptomatology and symptom impairment on a variety of anxiety-related measures than youth with a secondary GAD diagnosis. Contrary to our hypotheses, no differences were found between those with primary versus secondary GAD diagnoses on measures of symptom severity and clinical impairment, comorbid diagnoses, or youth and teacher-report measures. Our findings have potential implications for the current practice of requiring primary anxiety diagnostic status as an inclusion criterion in clinical research and treatment outcome studies. Assuming our findings are confirmed in larger samples and with other anxiety disorders, future clinical trials and basic psychopathology research might not exclude youth based on absence of a particular anxiety disorder as the primary disorder but rather include individuals for whom that anxiety disorder is secondary as well.

Orata, FD, Rosana, ARR, Xu, Y, Simkus, DN, Bramucci, AR, Boucher, Y & Case, RJ 2016, 'Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516', Genome Announcements, vol. 4, no. 4.
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ABSTRACT Strains of Sulfitobacter spp., Erythrobacter sp., and Marinobacter sp. were isolated from a polymicrobial culture of the naked (N-type) haptophyte Emiliania huxleyi strain CCMP1516. The genomes encode genes for the production of phytohormones, vitamins, and the consumption of their hosts' metabolic by-products, suggesting symbiotic interactions within this polymicrobial culture.

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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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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Paez-Espino, D, Chen, I-MA, Palaniappan, K, Ratner, A, Chu, K, Szeto, E, Pillay, M, Huang, J, Markowitz, VM, Nielsen, T, Huntemann, M, K. Reddy, TB, Pavlopoulos, GA, Sullivan, MB, Campbell, BJ, Chen, F, McMahon, K, Hallam, SJ, Denef, V, Cavicchioli, R, Caffrey, SM, Streit, WR, Webster, J, Handley, KM, Salekdeh, GH, Tsesmetzis, N, Setubal, JC, Pope, PB, Liu, W-T, Rivers, AR, Ivanova, NN & Kyrpides, NC 2016, 'IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses', Nucleic Acids Research, vol. 45, no. D1.
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AbstractViruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from &gt;6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.

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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Pangon, L, Ng, I, Giry-Laterriere, M, Currey, N, Morgan, A, Benthani, F, Tran, PN, Al-Sohaily, S, Segelov, E, Parker, BL, Cowley, MJ, Wright, DC, St Heaps, L, Carey, L, Rooman, I & Kohonen-Corish, MRJ 2016, 'JRK is a positive regulator of β-catenin transcriptional activity commonly overexpressed in colon, breast and ovarian cancer', Oncogene, vol. 35, no. 22, pp. 2834-2841.
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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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© 2016 The Fisheries Society of the British Isles. 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 150days) and rapid maturity (male S. argus 35days 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 2mmday-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.

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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Theophylline is an old drug experiencing a renaissance due to its beneficial anti-inflammatory effects in chronic respiratory diseases, such as asthma and COPD. Multiple modes of anti-inflammatory action have been reported, including inhibition of the enzymes that degrade cAMP - phosphodiesterase (PDE). Utilizing primary cultures of airway smooth muscle (ASM) cells, we recently revealed that PDE4 inhibitors can potentiate the anti-inflammatory action of β2-agonists by augmenting cAMP-dependent expression of the phosphatase that deactivates MAPK - 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 µM) did not increase formoterol-induced MKP-1 mRNA expression nor protein upregulation; consistent with the lack of cAMP generation. However, theophylline (at 10 µM) was anti-inflammatory and repressed secretion of the neutrophil chemoattractant cytokine, IL-8, produced in response to tumor necrosis factor α (TNFα). Because theophylline's effects were independent of PDE4 inhibition or anti-inflammatory MKP-1, we then wished to elucidate novel mechanisms responsible. We investigated the impact of theophylline on protein phosphatase 2A (PP2A), a master controller of multiple inflammatory signaling pathways, and show that theophylline increases TNFα-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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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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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 total changes in NPP, respectively, and the remaining 3% was attributed to LCC. Our results highlight the importance of rainfall supply on NPP variability in the TNSP zone.

Percy, A & Parrish, DR 2016, 'Editorial', Journal of University Teaching and Learning Practice, vol. 13, no. 5.

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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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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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 M. hyorhinis, M. hyosynoviae and M. 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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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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Pitt, FD, Millard, A, Ostrowski, M, Dervish, S, Mazard, S, Paulsen, IT, Zubkov, MV & Scanlan, DJ 2016, 'A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus', Frontiers in Microbiology, vol. 7.
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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.

Pokharel, D, Wijesinghe, P, Oenarto, V, Lu, JF, Sampson, DD, Kennedy, BF, Wallace, VP & Bebawy, M 2016, 'Deciphering Cell-to-Cell Communication in Acquisition of Cancer Traits: Extracellular Membrane Vesicles Are Regulators of Tissue Biomechanics', OMICS: A Journal of Integrative Biology, vol. 20, no. 8, pp. 462-469.
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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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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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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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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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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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Raijmakers, LHJ, Danilov, DL, Lammeren, JPMV, Lammers, TJG, Bergveld, HJ & Notten, PHL 2016, 'Non-Zero Intercept Frequency: An Accurate Method to Determine the Integral Temperature of Li-Ion Batteries', IEEE Transactions on Industrial Electronics, vol. 63, no. 5, pp. 3168-3178.
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© 2016 IEEE. A new impedance-based approach is introduced in which the integral battery temperature is related to other frequencies than the recently developed zero-intercept frequency (ZIF). The advantage of the proposed non-ZIF (NZIF) method is that measurement interferences, resulting from the current flowing through the battery (pack), can be avoided at these frequencies. This gives higher signal-to-noise ratios (SNRs) and, consequently, more accurate temperature measurements. A theoretical analysis, using an equivalent circuit model of a Li-ion battery, shows that NZIFs are temperature dependent in a way similar to the ZIF and can therefore also be used as a battery temperature indicator. To validate the proposed method, impedance measurements have been performed with individual LiFePO4 batteries and with large LiFePO4 battery packs tested in a full electric vehicle under driving conditions. The measurement results show that the NZIF is clearly dependent on the integral battery temperature and reveals a similar behavior to that of the ZIF method. This makes it possible to optimally adjust the NZIF method to frequencies with the highest SNR.

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, 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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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.

Rather, IA, Majumder, R, Alshammari, FH, Park, JG & Bajpai, VK 2016, 'Review-Ulcerative colitis and probiotics: An overview.', Pak J Pharm Sci, vol. 29, no. 5 Suppl, pp. 1877-1880.
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Ulcerative colitis is an inflammatory disease of the large intestine whose effects are bloody diarrhea, cramping and bloating. The disease is usually relapsing and remitting. However, the cause of ulcerative colitis is not yet known. Due to this reason, finding an effective treatment has been a great challenge. The suggested medical treatment is usually composed of two portions; keeping the flare up from happening and treating the flare up when it has happened. Active flare ups are treated with corticosteroids. There are several hypothesis which suggest that ulcerative colitis could be due to the micro flora present in gut. For this reason, several researchers tried to modify the gut microflora with probiotics. However, there is no probiotics found that can induce emission faster than the placebo. The ulcerative colitis patients taking probiotics showed fewer and less severe symptoms during the flare up. This means that even though the probiotics did not end up the flare up faster, it slowed up the severity of the symptoms of the patients.

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, Ca(2+) -regulated phospholipid-binding domains that regulate vesicle fusion in the synaptotagmin family. In humans, dysferlin mutations cause limb-girdle muscular dystrophy (LGMD2B) due to defective Ca(2+) -dependent, vesicle-mediated membrane repair and otoferlin mutations cause non-syndromic deafness due to defective Ca(2+) -triggered auditory neurotransmission. In this study, we describe the tissue-specific expression, subcellular localization and endocytic trafficking of the ferlin family. Dysferlin, myoferlin, and Fer1L6 are plasma membrane (PM) ferlins, whereas otoferlin and Fer1L5 localize predominantly to intracellular compartments. 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 plasma membrane residence, or rare incorporation of otoferlin molecules into the PM. Thus, type-I and type-II ferlins segregate as PM/late-endosomal or trans-Golgi/recycling ferlins, consistent with different ferlins mediating vesicle fusion events in specific subcellular locations.

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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Coral 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 ((1) O2 ) in Symbiodinium cultures. Inhibition of the Calvin-Benson cycle by thermal stress or high light promotes intracellular (1) O2 formation. Histidine addition, which decreases the amount of intracellular (1) O2 , provides partial protection against photosystem II photoinactivation and chlorophyll (Chl) bleaching. (1) O2 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 (1) O2 -sensitizing metabolites from the cells. Confocal microscopy imaging using SOSG showed most extracellular (1) O2 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 (1) O2 production in Symbiodinium cultures. Intracellular (1) O2 is associated with photosystem II photodamage and pigment bleaching, whereas extracellular (1) O2 has the potential to mediate the breakdown of symbiotic interaction between zooxanthellae and their animal host during coral bleaching.

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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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 guldoverflader En 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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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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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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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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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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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 asynchronous (e.g. Mediterran...

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 for third-year pharmacology students. A cohort of 167 students self-allocated into groups of four and were assigned a topic related to the pharmacology lecture material. A one-hour lecture was delivered to discuss digital media principles (visual design, video composition, multimedia learning principles, etc.) and how to apply these to create digital media projects. During practical classes, students developed a storyboard and received feedback and technical advice from tutors. Towards the end of the semester, students uploaded their preliminary presentations to a YouTube channel and received feedback from lecturers, tutors, and peers before submitting the final version. A marking rubric was developed and shared with students at the beginning of the semester. The study used a mixed-methods approach to 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 construction and skills gained. It also contained five open-ended questions. A high response rate was achieved for the voluntary survey (97/167). Additionally, students reviewed contributions of group members using SPARKPlus, and the marks attained were used to triangulate the questionnaire responses. In summary, the data shows that students found the assignment was engaging, fostered learning and creativity, and that they gained additional skills relevant to their future 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, pp. 1-13.
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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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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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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.
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Roberts, CL, Farrell, LJ, Waters, AM, Oar, EL & Ollendick, TH 2016, 'Parents’ Perceptions of Novel Treatments for Child and Adolescent Specific Phobia and Anxiety Disorders', Child Psychiatry & Human Development, vol. 47, no. 3, pp. 459-471.
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This study aimed to examine parents’ perceptions of established treatments, including cognitive behaviour therapy (CBT) and selective serotonin reuptake inhibitors (SSRIs), relative to novel treatments of d-cycloserine (DCS) and attention bias modification (ABM) augmented CBT to determine if novel treatments are perceived as more or less favorable than established treatments. Participants included parents of children with a specific phobia, enrolled in one of two randomized controlled trials of either one-session augmented DCS (n = 38, Gold Coast) or ABM augmented one-session treatment (n = 34, Brisbane), as well as parents from a community sample (n = 38). Parents of children with a specific phobia perceived CBT most favorably. There was no difference between the sites on perceptions of ABM. However, parents of children enrolled in the DCS trial perceived DCS more favorably than parents of children enrolled in the ABM trial and the community sample. These results demonstrate parents’ greater acceptance of psychological treatments over pharmacological treatments for the treatment of childhood phobias, highlighting the importance of educating parents to novel treatments.

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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Alzheimer'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.

Rosana, ARR, Orata, FD, Xu, Y, Simkus, DN, Bramucci, AR, Boucher, Y & Case, RJ 2016, 'Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217', Genome Announcements, vol. 4, no. 4.
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ABSTRACT Strains of Rhodobacteraceae , Sphingomonadales , Alteromonadales , and Bacteroidetes were isolated from a polymicrobial culture of the coccolith-forming (C-type) haptophyte Emiliania huxleyi strain M217 . The genomes encode genes for the production of algal growth factors and the consumption of their hosts' metabolic by-products, suggesting that the polymicrobial culture harbors many symbiotic interactions.

Roux, C 2016, 'Professional membership for the ANZFSS – is it time?', Australian Journal of Forensic Sciences, vol. 48, no. 3, pp. 245-247.
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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 antibiotic resi...

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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Cyclooxygenase 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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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 PGE₂secretion from airway smooth muscle cells: impact on β₂-adrenergic receptor desensitization', Allergy, vol. 71, no. 3, pp. 387-396.
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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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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), a bioactive sphingolipid that plays 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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Ryan, LM, Wand, MP & Malecki, AA 2016, 'Bringing coals to Newcastle', Significance, vol. 13, no. 6, pp. 32-37.
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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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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.The ISME Journal advance online publication, 31 July 2015; doi:10.1038/ismej.2015.123.

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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Salao, K, Jiang, L, Li, H, Tsai, VW-W, Husaini, Y, Curmi, PMG, Brown, LJ, Brown, DA & Breit, SN 2016, 'CLIC1 regulates dendritic cell antigen processing and presentation by modulating phagosome acidification and proteolysis', Biology Open, vol. 5, no. 5, pp. 620-630.
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ABSTRACT Intracellular chloride channel protein 1 (CLIC1) participates in inflammatory processes by regulating macrophage phagosomal functions such as pH and proteolysis. Here, we sought to determine if CLIC1 can regulate adaptive immunity by actions on dendritic cells (DCs), the key professional antigen presenting cells. To do this, we first generated bone marrow-derived DCs (BMDCs) from germline CLIC1 gene-deleted (CLIC1−/−) and wild-type (CLIC1+/+) mice, then studied them in vitro and in vivo. We found phagocytosis triggered cytoplasmic CLIC1 translocation to the phagosomal membrane where it regulated phagosomal pH and proteolysis. Phagosomes from CLIC1−/− BMDCs displayed impaired acidification and proteolysis, which could be reproduced if CLIC1+/+, but not CLIC1−/− cells, were treated with IAA94, a CLIC family ion channel blocker. CLIC1−/− BMDC displayed reduced in vitro antigen processing and presentation of full-length myelin oligodendrocyte glycoprotein (MOG) and reduced MOG-induced experimental autoimmune encephalomyelitis. These data suggest that CLIC1 regulates DC phagosomal pH to ensure optimal processing of antigen for presentation to antigen-specific T-cells. Further, they indicate that CLIC1 is a novel therapeutic target to help reduce the adaptive immune response in autoimmune diseases.

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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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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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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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.

Seligman, LD, Hovey, JD, Hurtado, G, Swedish, EF, Roley, ME, Geers, AL, Kene, P, Elhai, JD & Ollendick, TH 2016, 'Social cognitive correlates of attitudes toward empirically supported treatments.', Professional Psychology: Research and Practice, vol. 47, no. 3, pp. 215-223.
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Many clinicians report less than favorable attitudes regarding the use of Empirically Supported Treatments (ESTs). To better understand attitudes toward ESTs we examined the relationship among social-cognitive factors, career choices, and attitudes toward ESTs. Mental health professionals completed measures assessing need for cognition (NFC), decision-making style, career interests, and attitudes toward ESTs. Participants who reported spending the majority of their time in clinical practice reported significantly less favorable attitudes toward ESTs, a more intuitive decision-making style, and lower NFC than those spending the majority of their time doing research. Higher intuition and lower NFC were associated with less favorable attitudes toward ESTs. Moderation analyses testing the hypothesis that decision-making style and NFC would moderate the effects of career status on attitudes approached significance.

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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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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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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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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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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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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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 molecular complexity and valence orbital structure. Our findings improve 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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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.
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Simpson, JL, Baines, KJ, Horvat, JC, Essilfie, A-T, Brown, AC, Tooze, M, McDonald, VM, Gibson, PG & Hansbro, PM 2016, 'COPD is characterized by increased detection ofHaemophilus influenzae,Streptococcus pneumoniaeand a deficiency ofBacillusspecies', Respirology, vol. 21, no. 4, pp. 697-704.
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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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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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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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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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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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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.

Söderström, B, Mirzadeh, K, Toddo, S, von Heijne, G, Skoglund, U & Daley, DO 2016, 'Coordinated disassembly of the divisome complex inEscherichia coli', Molecular Microbiology, vol. 101, no. 3, pp. 425-438.
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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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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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Srivastava, A, Adamala, S & Kumar, S 2016, 'Development of process technology for making tomato powder and its quality evaluation', Indian Journal of Ecology, vol. 43, no. 2, pp. 533-536.
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The objective of this study was to analyse the physio-chemical and nutritional quality of a tray dried tomato powder with three chemical treatments namely potassium meta-bisulphite (KMS), calcium chloride (CaCI2) and combination of these two at different concentrations. The results indicated that the moisture content of tomato slices decreased rapidly with the increase in drying time from 1 hr to 10 hr using different concentrations of KMS, CaCI2 and KMS+CaCI2. At 11 hr, the moisture content attained a steady state for all the samples. Further, the quality of processed tomato powder with different KMS, CaCI2 and KMS+CaCI2 concentrations was tested in terms of lycopene (mg/100 gm), ash content (%), dehydration ratio, rehydration ratio, pH, % recovery, and vitamin C along with the raw controlled sample. It is concluded that overall quality of tomato powder was good in combination of KMS+CaCI2 as compared to KMS and CaCI2. Similarly, 0.2g KMS+1.0g CaCl2/100g concentration gave better quality than the 0.1 g KMS+0.5g CaCI2/100g and 0.3g KMS+1.5g CaCI2/100g.

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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Starkey, MR, Nguyen, DH, Brown, AC, Essilfie, A-T, Kim, RY, Yagita, H, Horvat, JC & Hansbro, PM 2016, 'Programmed Death Ligand 1 Promotes Early-Life Chlamydia Respiratory 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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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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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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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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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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Suen, H, Brown, R, Yang, S, Weatherburn, C, Ho, PJ, Woodland, N, Nassif, N, Barbaro, P, Bryant, C, Hart, D, Gibson, J & Joshua, D 2016, 'Multiple myeloma causes clonal T-cell immunosenescence: identification of potential novel targets for promoting tumour immunity and implications for checkpoint blockade', LEUKEMIA, vol. 30, no. 8, pp. 1716-1724.
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Sun, B, Guo, L, Ju, Y, Munroe, P, Wang, E, Peng, Z & Wang, G 2016, 'Unraveling the catalytic activities of ruthenium nanocrystals in high performance aprotic Li–O2 batteries', Nano Energy, vol. 28, pp. 486-494.
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Ruthenium (Ru)-catalyzed aprotic Li–O2 batteries have attracted a great deal of interests because of their excellent electrochemical performances including high specific energy and round-trip efficiency. However, it remains unclear how the incorporated Ru catalysts function to enhance the batteries’ performance. Herein, we report Ru nanocrystal-catalyzed carbon nanotube-based aprotic Li–O2 batteries with electrochemical performances that can match or even surpass some of the best literature results. The catalytic mechanism of Ru nanocrystals has been studied by a combination of Coulometry and in situ differential electrochemical mass spectrometry (DEMS). It has been found that through the synergy of water additive in electrolyte and Ru-based catalysts, the charging reaction overpotential can be brought down to 0.12 V (usually η>1 V). Moreover, an isotope-labeled DEMS study on the electrochemical oxidation of Li213CO3 indicated that Ru nanocrystals also have the capability to decompose Li2CO3, a detrimental by-product formed in almost all aprotic Li–O2 batteries, at a surprisingly low potential of ~3.5 V vs. Li/Li+ (usually >4.0 V). The capabilities of Ru nanocrystals to decompose Li2O2, LiOH, and Li2CO3 at low voltages, which drastically decreases the degradation of electrode and/or electrolyte, are crucial to achieve outstanding electrochemical performances for Li–O2 batteries.

Szpila, K & Wallman, JF 2016, 'Morphology and identification of first instar larvae of Australian blowflies of the genus Chrysomya of forensic importance', Acta Tropica, vol. 162, pp. 146-154.
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Tacchi, JL, Raymond, BBA, Haynes, PA, Berry, IJ, Widjaja, M, Bogema, DR, Woolley, LK, Jenkins, C, Minion, FC, Padula, MP & Djordjevic, SP 2016, 'Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae', OPEN BIOLOGY, vol. 6, no. 2.
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Tai, MC, Gentle, A, Arnold, MD & Cortie, MB 2016, 'Optical in situ study of de-alloying kinetics in nanoporous gold sponges', RSC Advances, vol. 6, no. 89, pp. 85773-85778.
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Nanoporous gold sponges are useful for a variety of applications but the kinetics of the dissolution process used to make them is not well understood.

Talbot-Wright, B, Baechler, S, Morelato, M, Ribaux, O & Roux, C 2016, 'Image processing of false identity documents for forensic intelligence', FORENSIC SCIENCE INTERNATIONAL, vol. 263, pp. 67-73.
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Tan, J, Walford, S-A, Dennis, ES & Llewellyn, D 2016, 'Trichomes control flower bud shape by linking together young petals', NATURE PLANTS, vol. 2, no. 7.
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Tan, KX, Lintang, HO, Maniam, S, Langford, SJ & Bakar, MB 2016, 'Synthesis and photophysical studies of fluorenone-armed porphyrin arrays', Tetrahedron, vol. 72, no. 35, pp. 5402-5413.
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Tan, SY, Ang, CY, Mahmood, A, Qu, Q, Li, P, Zou, R & Zhao, Y 2016, 'Doxorubicin-Loaded Metal-Organic Gels for pH and Glutathione Dual-Responsive Release', ChemNanoMat, vol. 2, no. 6, pp. 504-508.
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Tang, FSM, Hansbro, PM, Burgess, JK, Ammit, AJ, Baines, KJ & Oliver, BG 2016, 'A novel immunomodulatory function of neutrophils on rhinovirus-activated monocytes in vitro', Thorax, vol. 71, no. 11, pp. 1039-1049.
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Rhinovirus (RV) infections are the major precipitant of asthma exacerbations. While neutrophilic lung inflammation occurs during such infections, its role remains unclear. Neutrophilic inflammation is associated with increased asthma severity and steroid refractory disease. Neutrophils are vital for controlling infections but also have immunomodulatory functions. Previously, we found that neutrophils respond to viral mimetics but not replication competent RV. We aimed to investigate if neutrophils are activated and/or modulate immune responses of monocytes during RV16 infection.Primary human monocytes and autologous neutrophils were cocultured with or without RV16, in direct contact or separated by transwells. RV16-stimulated monocytes were also exposed to lysed neutrophils, neutrophil membrane components or soluble neutrophil intracellular components. Interleukin 6 (IL-6) and C-X-C motif (CXC)L8 mRNA and proteins were measured by quantitative PCR and ELISA at 24 hours.RV16 induced IL-6 and CXCL8 in monocytes, but not neutrophils. RV16-induced IL-6 and CXCL8 from monocytes was reduced in the presence of live neutrophils. Transwell separation abolished the inhibitory effects. Lysed neutrophils inhibited RV16-induced IL-6 and CXCL8 from monocytes. Neutrophil intracellular components alone effectively inhibited RV16-induced monocyte-derived IL-6 and CXCL8. Neutrophil intracellular components reduced RV16-induced IL-6 and CXCL8 mRNA in monocytes.Cell contact between monocytes and neutrophils is required, and preformed neutrophil mediator(s) are likely to be involved in the suppression of cytokine mRNA and protein production. This study demonstrates a novel regulatory function of neutrophils on RV-activated monocytes in vitro, challenging the paradigm that neutrophils are predominantly proinflammatory.

Tang, FSM, Van Ly, D, Spann, K, Reading, PC, Burgess, JK, Hartl, D, Baines, KJ & Oliver, BG 2016, 'Differential neutrophil activation in viral infections: Enhanced TLR ‐7/8‐mediated CXCL 8 release in asthma', Respirology, vol. 21, no. 1, pp. 172-179.
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Taudte, RV, Roux, C, Blanes, L, Horder, M, Kirkbride, KP & Beavis, A 2016, 'The development and comparison of collection techniques for inorganic and organic gunshot residues', ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 408, no. 10, pp. 2567-2576.
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Teo, WX, Kerr, MC, Huston, WM & Teasdale, RD 2016, 'Sortilin is associated with the chlamydial inclusion and is modulated during infection', Biology Open, vol. 5, no. 4, pp. 429-435.
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ABSTRACT Chlamydia species are obligate intracellular pathogens that have a major impact on human health. The pathogen replicates within an intracellular niche called an inclusion and is thought to rely heavily on host-derived proteins and lipids, including ceramide. Sortilin is a transmembrane receptor implicated in the trafficking of acid sphingomyelinase, which is responsible for catalysing the breakdown of sphingomyelin to ceramide. In this study, we examined the role of sortilin in Chlamydia trachomatis L2 development. Western immunoblotting and immunocytochemistry analysis revealed that endogenous sortilin is not only associated with the inclusion, but that protein levels increase in infected cells. RNAi-mediated depletion of sortilin, however, had no detectable impact on ceramide delivery to the inclusion or the production of infectious progeny. This study demonstrates that whilst Chlamydia redirects sortilin trafficking to the chlamydial inclusion, RNAi knockdown of sortilin expression is insufficient to determine if this pathway is requisite for the development of the pathogen.

Thomson, ACG, York, PH, Smith, TM, Sherman, CDH, Booth, DJ, Keough, MJ, Ross, DJ & Macreadie, PI 2016, 'Response to 'Comment on 'Seagrass Viviparous Propagules as a Potential Long-Distance Dispersal Mechanism' by A. C. G. Thomson et al'', ESTUARIES AND COASTS, vol. 39, no. 3, pp. 875-876.
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Thorburn, AN, Tseng, H-Y, Donovan, C, Hansbro, NG, Jarnicki, AG, Foster, PS, Gibson, PG & Hansbro, PM 2016, 'TLR2, TLR4 AND MyD88 Mediate Allergic Airway Disease (AAD) and Streptococcus pneumoniae-Induced Suppression of AAD', PLOS ONE, vol. 11, no. 6, pp. e0156402-e0156402.
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Tian, H, Liu, J, O’Donnell, K, Liu, T, Liu, X, Yan, Z, Liu, S & Jaroniec, M 2016, 'Revisiting the Stӧber method: Design of nitrogen-doped porous carbon spheres from molecular precursors of different chemical structures', Journal of Colloid and Interface Science, vol. 476, pp. 55-61.
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Tian, H, Saunders, M, Dodd, A, O'Donnell, K, Jaroniec, M, Liu, S & Liu, J 2016, 'Triconstituent co-assembly synthesis of N,S-doped carbon–silica nanospheres with smooth and rough surfaces', Journal of Materials Chemistry A, vol. 4, no. 10, pp. 3721-3727.
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This paper reports a facile synthesis of N,S-doped carbon–silica nanospheres with smooth and rough surfaces by using an extended Stöber method.

Tiberti, N, Latham, SL, Bush, S, Cohen, A, Opoka, RO, John, CC, Juillard, A, Grau, GE & Combes, V 2016, 'Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content', Scientific Reports, vol. 6, no. 1.
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AbstractCerebral malaria (CM) is a severe complication of Plasmodium falciparum infection responsible for thousands of deaths in children in sub-Saharan Africa. CM pathogenesis remains incompletely understood but a number of effectors have been proposed, including plasma microparticles (MP). MP numbers are increased in CM patients’ circulation and, in the mouse model, they can be localised within inflamed vessels, suggesting their involvement in vascular damage. In the present work we define, for the first time, the protein cargo of MP during experimental cerebral malaria (ECM) with the overarching hypothesis that this characterisation could help understand CM pathogenesis. Using qualitative and quantitative high-throughput proteomics we compared MP proteins from non-infected and P. berghei ANKA-infected mice. More than 360 proteins were identified, 60 of which were differentially abundant, as determined by quantitative comparison using TMTTM isobaric labelling. Network analyses showed that ECM MP carry proteins implicated in molecular mechanisms relevant to CM pathogenesis, including endothelial activation. Among these proteins, the strict association of carbonic anhydrase I and S100A8 with ECM was verified by western blot on MP from DBA/1 and C57BL/6 mice. These results demonstrate that MP protein cargo represents a novel ECM pathogenic trait to consider in the understanding of CM pathogenesis.

Titchener, JG, Solntsev, AS & Sukhorukov, AA 2016, 'Two-photon tomography using on-chip quantum walks', Optics Letters, vol. 41, no. 17, pp. 4079-4079.
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Tooze, JA, Freedman, LS, Carroll, RJ, Midthune, D & Kipnis, V 2016, 'The impact of stratification by implausible energy reporting status on estimates of diet-health relationships', Biometrical Journal, vol. 58, no. 6, pp. 1538-1551.
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© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.The food frequency questionnaire (FFQ) is known to be prone to measurement error. Researchers have suggested excluding implausible energy reporters (IERs) of FFQ total energy when examining the relationship between a health outcome and FFQ-reported intake to obtain less biased estimates of the effect of the error-prone measure of exposure; however, the statistical properties of stratifying by IER status have not been studied. Under certain assumptions, including nondifferential error, we show that when stratifying by IER status, the attenuation of the estimated relative risk in the stratified models will be either greater or less in both strata (implausible and plausible reporters) than for the nonstratified model, contrary to the common belief that the attenuation will be less among plausible reporters and greater among IERs. Whether there is more or less attenuation depends on the pairwise correlations between true exposure, observed exposure, and the stratification variable. Thus exclusion of IERs is inadvisable but stratification by IER status can sometimes help. We also address the case of differential error. Examples from the Observing Protein and Energy Nutrition Study and simulations illustrate these results.

Tovey, ER, Liu-Brennan, D, Garden, FL, Oliver, BG, Perzanowski, MS & Marks, GB 2016, 'Time-Based Measurement of Personal Mite Allergen Bioaerosol Exposure over 24 Hour Periods', PLOS ONE, vol. 11, no. 5, pp. e0153414-e0153414.
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Tran, N-AT, Padula, MP, Evenhuis, CR, Commault, AS, Ralph, PJ & Tamburic, B 2016, 'Proteomic and biophysical analyses reveal a metabolic shift in nitrogen deprived Nannochloropsis oculata', Algal Research, vol. 19, pp. 1-11.
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Tran, TN, Selinger, CI, Kohonen-Corish, MRJ, McCaughan, B, Kennedy, C, O'Toole, SA & Cooper, WA 2016, 'Alterations of MET Gene Copy Number and Protein Expression in Primary Non–Small-Cell Lung Cancer and Corresponding Nodal Metastases', Clinical Lung Cancer, vol. 17, no. 1, pp. 30-38.e1.
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Tran, TT, ElBadawi, C, Totonjian, D, Lobo, CJ, Grosso, G, Moon, H, Englund, DR, Ford, MJ, Aharonovich, I & Toth, M 2016, 'Robust multicolor single photon emission from point defects in hexagonal boron nitride', ACS NANO, vol. 10, no. 8, pp. 7331-7338.
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Hexagonal boron nitride (hBN) is an emerging two dimensional material for quantum photonics owing to its large bandgap and hyperbolic properties. Here we report a broad range of multicolor room temperature single photon emissions across the visible and the near infrared spectral ranges from point defects in hBN multilayers. We show that the emitters can be categorized into two general groups, but most likely possess similar crystallographic structure. We further show two approaches for engineering of the emitters using either electron beam irradiation or annealing, and characterize their photophysical properties. The emitters exhibit narrow line widths of sub 10 nm at room temperature, and a short excited state lifetime with high brightness. Remarkably, the emitters are extremely robust and withstand aggressive annealing treatments in oxidizing and reducing environments. Our results constitute the first step towards deterministic engineering of single emitters in 2D materials and hold great promise for the use of defects in boron nitride as sources for quantum information processing and nanophotonics.

Tran, TT, Zachreson, C, Berhane, AM, Bray, K, Sandstrom, RG, Li, LH, Taniguchi, T, Watanabe, K, Aharonovich, I & Toth, M 2016, 'Quantum Emission from Defects in Single Crystal Hexagonal Boron Nitride', PHYSICAL REVIEW APPLIED, vol. 5, no. 3.
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Bulk hexagonal boron nitride (hBN) is a highly nonlinear natural hyperbolic material that attracts major attention in modern nanophotonics applications. However, studies of its optical properties in the visible part of the spectrum and quantum emitters hosted by bulk hBN have not been reported to date. In this work we study the emission properties of hBN crystals in the red spectral range using sub-bandgap optical excitation. Quantum emission from defects is observed at room temperature and characterized in detail. Our results advance the use of hBN in quantum nanophotonics technologies and enhance our fundamental understanding of its optical properties.

Turnbull, L, Toyofuku, M, Hynen, AL, Kurosawa, M, Pessi, G, Petty, NK, Osvath, SR, Carcamo-Oyarce, G, Gloag, ES, Shimoni, R, Omasits, U, Ito, S, Yap, X, Monahan, LG, Cavaliere, R, Ahrens, CH, Charles, IG, Nomura, N, Eberl, L & Whitchurch, CB 2016, 'Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms', NATURE COMMUNICATIONS, vol. 7.
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Ueland, M, Blanes, L, Taudte, RV, Stuart, BH, Cole, N, Willis, P, Roux, C & Doble, P 2016, 'Capillary-driven microfluidic paper-based analytical devices for lab on a chip screening of explosive residues in soil', Journal of Chromatography A, vol. 1436, pp. 28-33.
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Ueland, M, Ewart, K, Troobnikoff, AN, Frankham, G, Johnson, RN & Forbes, SL 2016, 'A rapid chemical odour profiling method for the identification of rhinoceros horns', Forensic Science International, vol. 266, pp. e99-e102.
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Illegal poaching causes great harm to species diversity and conservation. A vast amount of money is involved in the trade of illegal or forged animal parts worldwide. In many cases, the suspected animal part is unidentifiable and requires costly and invasive laboratory analysis such as isotopic fingerprinting or DNA testing. The lack of rapid and accurate methods to identify wildlife parts at the point of detection represents a major hindrance in the enforcement and prosecution of wildlife trafficking. The ability of wildlife detector dogs to alert to different wildlife species demonstrates that there is a detectable difference in scent profile of illegally traded animal parts. This difference was exploited to develop a rapid, non-invasive screening method for distinguishing rhinoceros horns of different species. The method involved the collection of volatile organic compounds (VOC) by headspace solid-phase microextraction (HS-SPME) and analysis by comprehensive two-dimensional gas chromatography - time-of-flight mass spectrometry (GC×GC-TOFMS). It was hypothesised that the use of the specific odour profile as a screening method could separate and differentiate geographic origin or exploit the difference in diets of different species within a family (such as white rhinoceros and black rhinoceros from the Rhinocerotidae family). Known black and white rhinoceros horn samples were analysed using HS-SPME-GC×GC-TOFMS and multivariate statistics were applied to identify groupings in the data set. The black rhinoceros horn samples were distinctly different from the white rhinoceros horn samples. This demonstrated that seized rhinoceros horn samples can be identified based on their distinct odour profiles. The chemical odour profiling method has great potential as a rapid and non-invasive screening method in order to combat and track illegal trafficking of wildlife parts.

Umar, J, Hussain, T & Maqsood, M 2016, 'Modeling the mechanical and compression properties of polyamide/elastane knitted fabrics used in compression sportswear', The Journal of The Textile Institute, vol. 107, no. 10, pp. 1240-1252.
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Ung, AT, West, AN, Phillips, MJA & Williams, SG 2016, 'Synthesis of alkaloid-like compounds via the bridging Ritter reactions II', Monatshefte für Chemie - Chemical Monthly, vol. 147, no. 10, pp. 1737-1746.
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The bridging Ritter reactions are considered to be efficient synthetic methods rapidly providing access to alkaloid-like compounds in a few steps from inexpensive starting materials. In this manuscript, we report the synthesis of benzo[c]azepine derivatives bearing either amide or hydroxyl groups via the bridging Ritter reactions. These compounds are diastereoisomers of a known AChE inhibitor. All the structures were fully characterised by NMR spectroscopy and high-resolution mass spectrometry. NMR spectral analysis of diastereoisomers has allowed for the relative stereochemistry of the AChE inhibitor to be established.

van der Plaat, DA, de Jong, K, Lahousse, L, Faiz, A, Vonk, JM, van Diemen, CC, Nedeljkovic, I, Amin, N, Obeidat, M, van Duijn, CM, Boezen, HM & Postma, DS 2016, 'The Well-Known Gene HHIP and Novel Gene MECR Are Implicated in Small Airway Obstruction', American Journal of Respiratory and Critical Care Medicine, vol. 194, no. 10, pp. 1299-1302.
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Van Lent, S, Creasy, HH, Myers, GSA & Vanrompay, D 2016, 'The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences<b> </b>as well as the Most Conserved Pmp Protein Differ within and across <b><i>Chlamydia</i></b> Species', Microbial Physiology, vol. 26, no. 5, pp. 333-344.
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Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of <i>pmp</i> coding sequences differs between <i>Chlamydia</i> species, but it is unknown whether the number of <i>pmp</i> coding sequences is constant within a <i>Chlamydia</i> species. The level of conservation of the Pmp proteins has previously only been determined for <i>Chlamydia trachomatis.</i> As different Pmp proteins might be indispensible for the pathogenesis of different <i>Chlamydia </i>species, this study investigated the conservation of Pmp proteins both within and across <i>C. trachomatis,</i><i>C. pneumoniae,</i><i>C. abortus,</i> and <i>C. psittaci.</i> The <i>pmp</i> coding sequences were annotated in 16 <i>C. trachomatis,</i> 6 <i>C. pneumoniae,</i> 2 <i>C. abortus,</i> and 16 <i>C. psittaci</i> genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed <i>Chlamydia </i>species. The length of coding sequences of <i>pmpA,</i><i>pmpB,</i> and <i>pmpH</i> was conserved among all analyzed genomes, while the length of <i>pmpE/F</i> and <i>pmpG,</i> and remarkably also of the subtype <i>pmpD,</i> differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in <i>C. trachomatis,</i><i>C. pneumoniae,</i><i>C. abortus,</i> and <i>C. psittaci</i>, respectively. PmpB was the most conserved Pmp across the 4 analyzed <i>Chlamydia</i> species.

Varkey, D, Mazard, S, Ostrowski, M, Tetu, SG, Haynes, P & Paulsen, IT 2016, 'Effects of low temperature on tropical and temperate isolates of marine Synechococcus', The ISME Journal, vol. 10, no. 5, pp. 1252-1263.
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Venables, SJ, Daniel, R, Sarre, SD, Soedarsono, N, Sudoyo, H, Suryadi, H, van Oorschot, RAH, Walsh, SJ, Widodo, PT & McNevin, D 2016, 'Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations', FORENSIC SCIENCE INTERNATIONAL-GENETICS, vol. 20, pp. 45-52.
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Verma, A, Hoppenrath, M, Dorantes-Aranda, JJ, Harwood, DT & Murray, SA 2016, 'Molecular and phylogenetic characterization of Ostreopsis (Dinophyceae) and the description of a new species, Ostreopsis rhodesae sp. nov., from a subtropical Australian lagoon', Harmful Algae, vol. 60, pp. 116-130.
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Verma, A, Hoppenrath, M, Harwood, T, Brett, S, Rhodes, L & Murray, S 2016, 'Molecular phylogeny, morphology and toxigenicity of Ostreopsis cf. siamensis (Dinophyceae) from temperate south-east Australia', PHYCOLOGICAL RESEARCH, vol. 64, no. 3, pp. 146-159.
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Vivekanandarajah, A, Chan, YL, Chen, H & Machaalani, R 2016, 'Prenatal cigarette smoke exposure effects on apoptotic and nicotinic acetylcholine receptor expression in the infant mouse brainstem', NeuroToxicology, vol. 53, pp. 53-63.
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Infants exposed to cigarette smoked during pregnancy into infancy have increased respiratory and cardiac abnormalities. Nicotine, the major neurotoxic component of cigarette smoke, induces its actions by binding to nicotinic acetylcholine receptors (nAChR), with one downstream effect being increased apoptosis. Using a pre- into post- natal cigarette smoke exposure mouse model (SE), we studied the immunohistochemical expression of nAChR subunits α2, α3, α4, α5, α7, α9, β1 and β2 and two markers of apoptosis, active caspase-3 and TUNEL, in seven nuclei of the medulla and facial nucleus of the pons in male mice. Pups of dams exposed to two cigarettes (nicotine ≤1.2mg, CO ≤15mg) twice daily for six weeks prior to mating, during gestation and lactation (n=5; SE), were compared to pups exposed to air under the same condition (n=5; SHAM) at P20. Results showed that the hypoglossal nucleus had increased α3, α4, α7, α9, Casp-3 and TUNEL, dorsal motor nucleus of the vagus had increased α3, α5, α7, β1 and Casp-3, nucleus of the solitary tract had increased α3 but decreased α4, α5, β1 and apoptosis, cuneate nucleus had increased α3, β2 and Casp- 3, but decreased α5, nucleus of the spinal trigeminal tract had increased α3, α7, β1, lateral reticular nucleus had decreased β1, inferior olivary nucleus had increased β1 but decreased apoptosis, and the facial had increased α2, α3 and α7. This is the first study to demonstrate that nAChR subunits are affected following pre- into post-natal SE and that they simultaneously coincided with changes in apoptotic expression.

Waller, D, Mondy, P, Brama, T, Fisher, J, King, A, Malkov, K, Wall-Smith, D, Ryan, L & Irving, DO 2016, 'Determining the effect of vein visualization technology on donation success, vasovagal symptoms, anxiety and intention to re-donate in whole blood donors aged 18-30 years: A randomized controlled trial', Vox Sanguinis, vol. 111, no. 2, pp. 135-143.
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Wand, MP 2016, 'Fast Approximate Inference for Arbitrarily Large Semiparametric Regression Models via Message Passing', Journal of the American Statistical Association, vol. 112, no. 517, pp. 137-168.
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We show how the notion of message passing can be used to streamline the algebra and computer coding for fast approximate inference in large Bayesian semiparametric regression models. In particular, this approach is amenable to handling arbitrarily large models of particular types once a set of primitive operations is established. The approach is founded upon a message passing formulation of mean field variational Bayes that utilizes factor graph representations of statistical models. The underlying principles apply to general Bayesian hierarchical models although we focus on semiparametric regression. The notion of factor graph fragments is introduced and is shown to facilitate compartmentalization of the required algebra and coding. The resultant algorithms have ready-to-implement closed form expressions and allow a broad class of arbitrarily large semiparametric regression models to be handled. Ongoing software projects such as Infer.NET and Stan support variational-type inference for particular model classes. This article is not concerned with software packages per se and focuses on the underlying tenets of scalable variational inference algorithms.

Wang, C, Huang, Y, Pan, H, Jiang, J, Yang, X, Xu, Z, Tian, H, Han, S & Wu, D 2016, 'Nitrogen-Doped Porous Carbon/Graphene Aerogel with Much Enhanced Capacitive Behaviors', Electrochimica Acta, vol. 215, pp. 100-107.
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Wang, H, Sencadas, V, Gao, G, Gao, H, Du, A, Liu, H & Guo, Z 2016, 'Strong affinity of polysulfide intermediates to multi-functional binder for practical application in lithium–sulfur batteries', Nano Energy, vol. 26, pp. 722-728.
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Wang, W, Zhou, QT, Sun, S-P, Denman, JA, Gengenbach, TR, Barraud, N, Rice, SA, Li, J, Yang, M & Chan, H-K 2016, 'Effects of Surface Composition on the Aerosolisation and Dissolution of Inhaled Antibiotic Combination Powders Consisting of Colistin and Rifampicin', The AAPS Journal, vol. 18, no. 2, pp. 372-384.
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Wang, Y, Kretschmer, K, Zhang, J, Mondal, AK, Guo, X & Wang, G 2016, 'Organic sodium terephthalate@graphene hybrid anode materials for sodium-ion batteries', RSC ADVANCES, vol. 6, no. 62, pp. S7098-S7102.
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Wangpraseurt, D, Pernice, M, Guagliardo, P, Kilburn, MR, Clode, PL, Polerecky, L & Kuehl, M 2016, 'Light microenvironment and single-cell gradients of carbon fixation in tissues of symbiont-bearing corals', ISME JOURNAL, vol. 10, no. 3, pp. 788-792.
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Wark, P, Hsu, A, Starkey, M & Hansbro, P 2016, 'Micro-RNA-125a/b target A20 and MAVS to promote inflammatory and impair antiviral responses in chronic obstructive pulmonary disease', 3.2 Airway Cell Biology and Immunopathology, vol. 48.
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Watanabe, S, Kuzhiumparambil, U, Winiarski, Z & Fu, S 2016, 'Biotransformation of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans', FORENSIC SCIENCE INTERNATIONAL, vol. 261, pp. 33-42.
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Being marketed as “legal” smoking blends or mixtures, synthetic cannabinoids are abused widely owing to its cannabis-like effect. Due to the rapid introduction of new generation analogues of synthetic cannabinoids to escape from legislative/judicial control, the investigation of the metabolic pathways of these substances is of particular importance for drug control, abstinence and forensic toxicology purposes. In this study, the in vitro metabolism of JWH-018, JWH-073 and AM2201 by the fungus Cunninghamella elagans has been investigated with the purpose of validating its potential as a complementary model for investigating synthetic cannabinoid metabolism. JWH-018, JWH-073 and AM2201 were incubated for 72 h with C. elegans. Detection of metabolites was based on liquid chromatography–tandem mass spectrometry and high resolution mass spectrometry analysis. C. elegans was found capable of producing the majority of the phase I metabolites observed in earlier in vitro and in vivo mammalian studies as a result of monohydroxylation, dihydroxylation, carboxylation, dehydrogenation, ketone formation, dihydrodiol formation, dihydrodiol formation with N-dealkylation and combinations thereof. C. elegans can thus be a useful and economic model for studying synthetic cannabinoid metabolism.

Watanabe, S, Kuzhiumparambil, U, Winiarski, Z & Fu, S 2016, 'Data on individual metabolites of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans', Data in Brief, vol. 7, pp. 332-340.
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Synthetic cannabinoids JWH-018, JWH-073 and AM2201 were metabolised by the fungus Cunninghamella elegans. In this article, data on individual metabolites of their retention times, mass accuracies, major product ions and structures indicated by product ions are presented. The data in this article is related to “Biotransformation of synthetic cannabinoids JWH-018, JWH-073 and AM2201 by Cunninghamella elegans”

Wei, Y, Sun, B, Su, D, Zhu, J & Wang, G 2016, '3D Free-Standing NiCo2O4@graphene Foam for High-Performance Supercapacitors', ENERGY TECHNOLOGY, vol. 4, no. 6, pp. 737-743.
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Wenholz, DS, Luong, S, Philp, M, Forbes, SL, Stuart, BH, Drummer, OH & Fu, S 2016, 'A study to model the post-mortem stability of 4-MMC, MDMA and BZP in putrefying remains', FORENSIC SCIENCE INTERNATIONAL, vol. 265, pp. 54-60.
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Wheate, NJ, Dickson, K-A, Kim, RR, Nematollahi, A, Macquart, RB, Kayser, V, Yu, G, Church, WB & Marsh, DJ 2016, 'Host-Guest Complexes of Carboxylated Pillar[ n ]arenes With Drugs', Journal of Pharmaceutical Sciences, vol. 105, no. 12, pp. 3615-3625.
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White, SW, Richey, JA, Gracanin, D, Coffman, M, Elias, R, LaConte, S & Ollendick, TH 2016, 'Psychosocial and Computer-Assisted Intervention for College Students with Autism Spectrum Disorder: Preliminary Support for Feasibility.', Educ Train Autism Dev Disabil, vol. 51, no. 3, pp. 307-317.
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The number of young adults with Autism Spectrum Disorders (ASD) enrolled in higher education institutions has steadily increased over the last decade. Despite this, there has been little research on how to most effectively support this growing population. The current study presents data from a pilot trial of two novel intervention programs developed for college students with ASD. In this small randomized controlled trial, college students with ASD (n = 8) were assigned to one of two new programs - either an intervention based on a virtual reality-Brain-Computer Interface for ASD (BCI-ASD) or a psychosocial intervention, the College and Living Success (CLS) program. Preliminary evidence supports the feasibility and acceptability of both programs, although behavioral outcomes were inconsistent across participants and interventions. Results indicate that expanded research on psychosocial and computer-assisted intervention approaches for this population is warranted, given the preliminary support found in this pilot study.

Whyte, T, Gibson, T, Anderson, R, Eager, D & Milthorpe, B 2016, 'Mechanisms of Head and Neck Injuries Sustained by Helmeted Motorcyclists in Fatal Real-World Crashes: Analysis of 47 In-Depth Cases', Journal of Neurotrauma, vol. 33, no. 19, pp. 1802-1807.
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Despite an improved understanding of traumatic head and neck injury mechanisms, the impact tests required by major motorcycle helmet standards have remained unchanged for decades. Development of new test methods must reflect the specific impact loads causing injury in real crashes as well as test criteria appropriate for the observed injury profiles. This study analysed a collection of in-depth crash investigations of fatally injured helmeted riders in the Adelaide metropolitan region between 1983 and 1994 inclusive to review the head and neck injury patterns that resulted from specific types of impact. Inertial brain injury was sustained in 49% of examined cases, most often resulting from facial impacts but also in a large proportion of tangential, run over, and occipital impact cases. Focal brain and brainstem injury was also common (53%) and regularly associated with skull vault (11/12) and skull base fractures (22/31). Prevention of these fractures in impacts outside the area of required protection and in impacts with a straight edge would provide a significant increase in helmeted rider protection. Cervical spinal cord injury was sustained in facial, straight edge, and tangential impacts on the head. Motorcycle helmets are effective for preventing local skull fractures in impacts for which they are designed, whereas other serious injuries such as basilar skull fracture (BSF) and inertial brain injury persist despite helmet protection. Further impact test procedures should be developed for injurious impact types not currently assessed by major helmet standards, in particular facial impacts, and using test criteria based on commonly observed injuries. This study provides the necessary link, from impact load to injury, for guiding impact test development.

Whyte, T, Gibson, T, Eager, D & Milthorpe, B 2016, 'Response of a full-face motorcycle helmet FE model to the UNECE 22.05 chin bar impact test', International Journal of Crashworthiness, vol. 21, no. 6, pp. 555-565.
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Wieckowski, AT, Coffman, MC, Kim-Spoon, J, White, SW, Richey, JA & Ollendick, TH 2016, 'Impaired Fear Recognition and Social Anxiety Symptoms in Adolescence', Journal of Child and Family Studies, vol. 25, no. 11, pp. 3381-3386.
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This study represents the first examination of adolescent anxiety in relation to peer emotion recognition, rather than adult emotion recognition. Additionally, we examine potential mechanisms for the development of social anxiety in females. Facial emotion recognition (FER) is important for accurate social cognition, which is impaired in individuals with various disorders, including anxiety disorders. Social anxiety often onsets during adolescence, is observed more commonly in females, and is often associated with FER difficulties. Given the importance of peer interaction during adolescence, and some evidence that FER may differ as a function of the stimuli (adolescent or adult faces), we sought to study FER in relation to social anxiety symptoms using stimuli portraying adolescent faces. Male and female adolescents (N = 64) completed an online survey in which they rated 257 child and adolescent emotional faces and completed a self-report measure of social anxiety symptoms. We examined differences in emotion recognition (e.g., fear, anger, sadness) between individuals with high and low levels of social anxiety symptoms. Adolescents with high social anxiety symptoms were more likely to have problems correctly identifying fearful expressions (90.55 % accuracy) compared to adolescents with low social anxiety symptoms (96.00 % accuracy; t = 2.375, p = .021, d = 0.594), and this effect was observed exclusively in female adolescents. The observed sex difference in accurate identification of fearful faces in relation to social anxiety could suggest a potential mechanism for social anxiety development in adolescent females.

Wijesinghe, P, K. Shankar, S, T. Chickabasaviah, Y, Gorrie, C, Amaratunga, D, Hulathduwa, S, Sunil Kumara, K, Samarasinghe, K, Hun Suh, Y, W. Steinbusch, H & Ranil D. De Silva, K 2016, 'Cytoskeletal Pathologies of Age-Related Diseases between Elderly Sri Lankan (Colombo) and Indian (Bangalore) Brain Samples', Current Alzheimer Research, vol. 13, no. 3, pp. 268-280.
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© 2016 Bentham Science Publishers. Within South Asia, Sri Lanka represents fastest aging with 13% of the population was aged over 60’s in 2011, whereas in India it was 8%. Majority of the Sri Lankan population based genetic studies have confirmed their origin on Indian mainland. As there were inadequate data on aging cytoskeletal pathologies of these two nations with their close genetic affiliations, we performed a comparison on their elderly. Autopsy brain samples of 50 individuals from Colombo, Sri Lanka (mean age 72.1yrs ± 7.8, mean ± S.D.) and 42 individuals from Bangalore, India (mean age 65.9yrs ± 9.3) were screened for neurodegenerative pathologies using immunohistochemical techniques. A total of 79 cases with incomplete clinical history (Colombo- 47 and Bangalore- 32) were subjected to statistical analysis and 13 cases, clinically diagnosed with dementia and/or Parkinsonism disorders were excluded. As per National Institute on Aging Alzheimer’s Association guidelines, between Colombo and Bangalore samples, Alzheimer’s disease neuropathologic change for intermediate/ high level was 4.25% vs. 3.12% and low level was 19.15% vs. 15.62% respectively. Pathologies associated with Parkinsonism including brainstem predominant Lewy bodies-6.4% and probable progressive supra nuclear palsy2.13% were found solely in Colombo samples. Alzheimer related pathologies were not different among elders, however, in Colombo males, neurofibrillary tangle grade was significantly higher in the region of hippocampus (odds ratio = 1.46, 95% confidence interval = 0.07-0.7) and at risk in midbrain substantia nigra (p = 0.075). Other age-related pathologies including spongiform changes (p < 0.05) and hippocampus cell loss in dentate gyrus region (p < 0.05) were also identified prominently in Colombo samples. Taken together, aging cytoskeletal pathologies are comparatively higher in elderly Sri Lankans and this might be due to their genetic, dietary and/ or environmental variations.

Wijesinghe, P, Shankar, SK, Yasha, TC, Gorrie, C, Amaratunga, D, Hulathduwa, S, Kumara, KS, Samarasinghe, K, Suh, Y-H, Steinbusch, HWM & De Silva, KRD 2016, 'Vascular Contributions in Alzheimer’s Disease-Related Neuropathological Changes: First Autopsy Evidence from a South Asian Aging Population', Journal of Alzheimer's Disease, vol. 54, no. 4, pp. 1607-1618.
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BACKGROUND: Evidence from various consortia on vascular contributions has been inconsistent in determining the etiology of sporadic Alzheimer's disease (AD). OBJECTIVE: To investigate vascular risk factors and cerebrovascular pathologies associated in manifestation of AD-related neuropathological changes of an elderly population. METHODS: Postmortem brain samples from 76 elderly subjects (≥50 years) were used to study genetic polymorphisms, intracranial atherosclerosis of the circle of Willis (IASCW), and microscopic infarcts in deep white matters. From this cohort, 50 brains (≥60 years) were subjected to neuropathological diagnosis using immunohistopathological techniques. RESULTS: Besides the association with age, the apolipoproteinE ɛ4 allele was significantly and strongly associated with Thal amyloid-β phases ≥1 [odds ratio (OR) = 6.76, 95% confidence interval (CI) 1.37-33.45] and inversely with Braak neurofibrillary tangle (NFT) stages ≥III (0.02, 0.0-0.47). Illiterates showed a significant positive association for Braak NFT stages ≥IV (14.62, 1.21-176.73) and a significant negative association for microscopic infarcts (0.15, 0.03-0.71) in deep white matters. With respect to cerebrovascular pathologies, cerebral small vessel lesions (white matter hyperintensities and cerebral amyloid angiopathy) showed a higher degree of associations among them and with AD-related neuropathological changes (p < 0.05) compared to large vessel pathology (IASCW), which showed a significant association only with Braak NFT stages ≥I (p = 0.050). CONCLUSION: These findings suggest that besides age, education, and genetic factors, other vascular risk factors were not associated with AD-related neuropathological changes and urge prompt actions be taken against cerebral small vessel diseases since evidence for effective prevention is still lacking.

Wolff, C, Laer, RV, Steel, MJ, Eggleton, BJ & Poulton, CG 2016, 'Brillouin resonance broadening due to structural variations in nanoscale waveguides', New Journal of Physics, vol. 18, no. 2, pp. 025006-025006.
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Wong, EHH, Khin, MM, Ravikumar, V, Si, Z, Rice, SA & Chan-Park, MB 2016, 'Modulating Antimicrobial Activity and Mammalian Cell Biocompatibility with Glucosamine-Functionalized Star Polymers', Biomacromolecules, vol. 17, no. 3, pp. 1170-1178.
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Wonoputri, V, Gunawan, C, Liu, S, Barraud, N, Yee, LH, Lim, M & Amal, R 2016, 'Iron Complex Facilitated Copper Redox Cycling for Nitric Oxide Generation as Nontoxic Nitrifying Biofilm Inhibitor', ACS Applied Materials & Interfaces, vol. 8, no. 44, pp. 30502-30510.
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Wood, B, Padula, MP, Marks, DC & Johnson, L 2016, 'Refrigerated storage of platelets initiates changes in platelet surface marker expression and localization of intracellular proteins', Transfusion, vol. 56, no. 10, pp. 2548-2559.
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Wood, RJ, Mitrovic, SM, Lim, RP & Kefford, BJ 2016, 'How benthic diatoms within natural communities respond to eight common herbicides with different modes of action', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 557, pp. 636-643.
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Wood, RJ, Mitrovic, SM, Lim, RP & Kefford, BJ 2016, 'THE INFLUENCE OF REDUCED LIGHT INTENSITY ON THE RESPONSE OF BENTHIC DIATOMS TO HERBICIDE EXPOSURE', ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, vol. 35, no. 9, pp. 2252-2260.
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Herbicide pollution events in aquatic ecosystems often co-occur with increased turbidity and reduced light intensity. It is therefore important to determine whether reduced light intensity can influence herbicide toxicity, especially to primary producers such as benthic diatoms. Benthic diatoms collected from four rivers were exposed to herbicides in 48 h rapid toxicity tests under high light (100 µmol m(-2)  s(-1) ) and low light (20 µmol m(-2)  s(-1) ) intensities. The effects of two herbicides (atrazine and glyphosate) were assessed on 26 freshwater benthic diatom taxa. There was no significant interaction of light and herbicide effects at the community level or on the majority (22 of 26) of benthic diatom taxa. This indicates that low light levels will likely have only a minor influence on the response of benthic diatoms to herbicides. This article is protected by copyright. All rights reserved.

Woodcock, S 2016, 'Development of enquiry-oriented learning in the mathematical sciences', Australia and New Zealand Industrial and Applied Mathematics (ANZIAM) Journal, vol. 57, pp. C1-C13.
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Wu, J, Albert, LP, Lopes, AP, Restrepo-Coupe, N, Hayek, M, Wiedemann, KT, Guan, K, Stark, SC, Christoffersen, B, Prohaska, N, Tavares, JV, Marostica, S, Kobayashi, H, Ferreira, ML, Campos, KS, da Silva, R, Brando, PM, Dye, DG, Huxman, TE, Huete, AR, Nelson, BW & Saleska, SR 2016, 'Leaf development and demography explain photosynthetic seasonality in Amazon evergreen forests', Science, vol. 351, no. 6276, pp. 972-976.
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Leaf seasonality in Amazon forests Models assume that lower precipitation in tropical forests means less plant-available water and less photosynthesis. Direct measurements in the Amazon, however, show that production remains constant or increases in the dry season. To investigate this mismatch, Wu et al. use tower-based cameras to detect the phenology (i.e., the seasonal patterns) of leaf dynamics in tropical tree crowns in Amazonia, Brazil, and relate this to patterns of CO 2 flux. Accounting for age-dependent variation among individual leaves and crowns is necessary for understanding the seasonal dynamics of photosynthesis in the entire ecosystem. Leaf phenology regulates seasonality of the carbon flux in tropical forests across a gradient of climate zones. Science , this issue p. 972

Wu, M, Song, EH, Chen, ZT, Ding, S, Ye, S, Zhou, JJ, Xu, SQ & Zhang, QY 2016, 'Single-band red upconversion luminescence of Yb³⁺–Er³⁺via nonequivalent substitution in perovskite KMgF₃ nanocrystals', Journal of Materials Chemistry C, vol. 4, no. 8, pp. 1675-1684.
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Single-band red upconversion emission of Er³⁺ has been successfully achieved in Yb³⁺/Er³⁺ codoped KMgF₃ nanocrystals via a nonequivalent substitution strategy.

Wyrsch, ER, Roy Chowdhury, P, Chapman, TA, Charles, IG, Hammond, JM & Djordjevic, SP 2016, 'Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis', Frontiers in Microbiology, vol. 7, no. 843.
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Xia, W, Mahmood, A, Liang, Z, Zou, R & Guo, S 2016, 'ChemInform Abstract: Earth-Abundant Nanomaterials for Oxygen Reduction', ChemInform, vol. 47, no. 14.
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Xia, W, Mahmood, A, Liang, Z, Zou, R & Guo, S 2016, 'Earth-Abundant Nanomaterials for Oxygen Reduction', Angewandte Chemie International Edition, vol. 55, no. 8, pp. 2650-2676.
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Xia, W, Mahmood, A, Liang, Z, Zou, R & Guo, S 2016, 'Platinfreie Nanomaterialien für die Sauerstoffreduktion', Angewandte Chemie, vol. 128, no. 8, pp. 2698-2726.
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Xie, J, Danilov, DL, Eichel, R-A & Notten, PHL 2016, 'Modeling 3D-Deposition of TiO₂ Using a Monte Carlo Chemical Kinetics Approach', The Journal of Physical Chemistry C, vol. 120, no. 41, pp. 23823-23835.
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© 2016 American Chemical Society. 3D microbatteries are indispensable to cope with the increasing energy demand of autonomous smart devices. To synthesize 3D microbatteries, step-conformal deposition of thin films into 3D-substrates is vital, and low pressure chemical vapor deposition (LPCVD) is a technique that is capable of achieving this goal. In the present work, the 3D-deposition of TiO2 is investigated. It is shown that the growth of anatase TiO2 can be characterized by two rate-determining processes. In the diffusion-controlled temperature region, the TiO2 films deposited into 3D-substrates lack step-conformity. In contrast, in the kinetically controlled temperature region, uniform films were deposited inside these microstructures. To understand and improve the LPCVD deposition process, the experimental results were simulated using a Monte Carlo chemical kinetics (MCCK) model. Good agreement between the model and experiments was achieved in all cases. It was found that the deposition probability is low in the kinetically controlled deposition region, while this probability was found to be high in the diffusion-controlled region. It is also shown that the reflections of precursor molecules inside the trenches play an important role in achieving homogeneous 3D deposition. To show the strength of the MCCK model, the optimized deposition parameters are applied to predict the film thickness profiles in narrower microstructures.

Xie, J, Harks, P-PRML, Li, D, Raijmakers, LHJ & Notten, PHL 2016, 'Planar and 3D deposition of Li4Ti5O12 thin film electrodes by MOCVD', Solid State Ionics, vol. 287, pp. 83-88.
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© 2016 Elsevier B.V. All rights reserved. Li4Ti5O12 is well known to be a safe and efficient anode material for Li-ion batteries. A metal-organic chemical vapor deposition process has been developed for the synthesis of Li4Ti5O12 thin film anodes on planar and 3D substrates. The influences of various deposition parameters, including precursor flow rates and post-annealing temperatures, have been investigated by material and electrochemical analyses. Li4Ti5O12 thin films deposited at the optimized process parameters showed a high crystallinity and high electrochemical activity. A reversible storage capacity of 151 mAh/g was achieved at a current of 0.5 C, corresponding to 86.3% of the theoretical specific capacity of Li4Ti5O12. Up to almost 600 cycles, the electrodes showed no significant capacity loss. Furthermore, the deposited thin film anodes also showed excellent rate performance. Compared to the storage capacity at 0.5 C, 93% of the capacity was maintained at 10 C. Thin films were also deposited on highly structured substrates to investigate the uniformity and electrochemical performance. With the same footprint area, the 3D Li4Ti5O12 film anode showed a 2.5 times higher storage capacity than planar electrode.

Xie, J, Oudenhoven, JFM, Li, D, Chen, C, Eichel, R-A & Notten, PHL 2016, 'High Power and High Capacity 3D-Structured TiO₂Electrodes for Lithium-Ion Microbatteries', Journal of The Electrochemical Society, vol. 163, no. 10, pp. A2385-A2389.
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© The Author(s) 2016. An on-chip compatible method to fabricate high energy density TiO2 thin film electrodes on 3D-structured silicon substrates was demonstrated. 3D-structured electrodes are fabricated by combining reactive ion etching (RIE) with low pressure chemical vapor deposition (LPCVD), enabling accurate control of the aspect ratio of substrates and the subsequent deposition of TiO2 thin film electrodes onto these structured substrates. The prepared 3D-TiO2 electrodes exhibit a current-dependent increase in storage capacity of a factor up to 16 as compared to conventional planar electrodes. In addition, these 3D electrodes also reveal excellent power and cycling performance. This work demonstrates that LPCVD is capable of depositing homogeneous film electrodes on highly structured substrates and the prepared 3D-electrodes also shows significant improve in storage capacity and power density.

Xie, Q, Huang, W, Zhang, B, Chen, P, Song, X, Pascucci, S, Pignatti, S, Laneve, G & Dong, Y 2016, 'Estimating Winter Wheat Leaf Area Index From Ground and Hyperspectral Observations Using Vegetation Indices', IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, vol. 9, no. 2, pp. 771-780.
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Xie, Z, Huete, A, Ma, X, Restrepo-Coupe, N, Devadas, R, Clarke, K & Lewis, M 2016, 'Landsat and GRACE observations of arid wetland dynamics in a dryland river system under multi-decadal hydroclimatic extremes', Journal of Hydrology, vol. 543, pp. 818-831.
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Xie, Z, Huete, A, Restrepo-Coupe, N, Ma, X, Devadas, R & Caprarelli, G 2016, 'Spatial partitioning and temporal evolution of Australia's total water storage under extreme hydroclimatic impacts', REMOTE SENSING OF ENVIRONMENT, vol. 183, pp. 43-52.
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Australia experienced one of the worst droughts in history during the early 21st-century (termed the ‘big dry’), exerting negative impacts on food production and water supply, with increased forest die-back and bushfires across large areas. Following the ‘big dry’, one of the largest La Niña events in the past century, in conjunction with an extreme positive excursion of the Southern Annular Mode (SAM), resulted in dramatic increased precipitation from 2010 to 2011 (termed the ‘big wet’), causing widespread flooding and a recorded sea level drop. Despite these extreme hydroclimatic impacts, the spatial partitioning and temporal evolution of total water storage across Australia remains unknown. In this study we investigated the spatial-temporal impacts of the recent ‘big dry’ and ‘big wet’ events on Australia's water storage dynamics using the total water storage anomaly (TWSA) data derived from the Gravity Recovery and Climate Experiment (GRACE) satellites. Results showed widespread, continental-scale decreases in TWS during the ‘big dry’, resulting in a net loss of 3.89 ± 0.47 cm (299 km3) total water, while the ‘big wet’ induced a sharp increase in TWS, equivalent to 11.68 ± 0.52 cm (898 km3) of water, or three times the total water loss during the ‘big dry’. We found highly variable continental patterns in water resources, involving differences in the direction, magnitude, and duration of TWS responses to drought and wet periods. These responses clustered into three distinct geographic zones that correlated well with the influences from multiple large-scale climate modes. Specifically, a persistent increasing trend in TWS was recorded over northern and northeastern Australia, where the climate is strongly influenced by El Niño-Southern Oscillation (ENSO). By contrast, western Australia, a region predominantly controlled by the Indian Ocean Dipole (IOD), exhibited a continuous decline in TWS during the ‘big dry’ and only a subtle increase during the ‘big wet’,...

Xu, B, Li, J, Liu, Q, Huete, AR, Yu, Q, Zeng, Y, Yin, G, Zhao, J & Yang, L 2016, 'Evaluating Spatial Representativeness of Station Observations for Remotely Sensed Leaf Area Index Products', IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, vol. 9, no. 7, pp. 3267-3282.
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Continuous leaf area index (LAI) observations from global ground stations are an important reference dataset for the validation of remotely sensed LAI products. In this study, a pragmatic approach is presented for evaluating the spatial representativeness of station-observed LAI dataset in the product pixel grid. Three evaluation indicators, including dominant vegetation type percent (DVTP), relative absolute error (RAE) and coefficient of sill (CS), were established to quantify different levels of spatial representativeness. The DVTP was used to evaluate whether the station-observed vegetation type was the dominant one in the pixel grid, and the RAE and CS were applied to quantify the point-to-area consistency for a given station observation and the spatial heterogeneity caused by the different density of vegetation within the pixel, respectively. The proposed approach was applied to 25 stations from the Chinese Ecosystem Research Network, and results show significant differences of representativeness errors at different levels. The spatial representativeness for different stations varied seasonally with different vegetation growth stages due to temporal changes in heterogeneity, but the spatial representativeness remained consistent at interannual timeframes due to the relatively stable vegetation structure and pattern between adjacent years. A large error can occur in MOD15A2 product validation when the representativeness level of station LAI observations is low. This approach can effectively distinguish various levels of spatial representativeness for the station-observed LAI dataset at the pixel grid scale, which can consequently improve the reliability of LAI product validation by selecting LAI observations with a high degree of representativeness.

Xu, J, Su, D, Bao, W, Zhao, Y, Xie, X & Wang, G 2016, 'Rose flower-like NiCo2O4 with hierarchically porous structures for highly reversible lithium storage', Journal of Alloys and Compounds, vol. 684, pp. 691-698.
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Xu, J, Su, D, Zhang, W, Bao, W & Wang, G 2016, 'A nitrogen–sulfur co-doped porous graphene matrix as a sulfur immobilizer for high performance lithium–sulfur batteries', Journal of Materials Chemistry A, vol. 4, no. 44, pp. 17381-17393.
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The combination of the physical adsorption of lithium polysulfides onto porous graphene and the chemical binding of polysulfides to N and S sites promotes reversible Li₂S/polysulfide/S conversion, realizing high performance Li–S batteries with long cycle life and high-energy density.

Yang, C-N, Lin, BMT, Hwang, FJ & Wang, M-C 2016, 'Acquisition planning and scheduling of computing resources', Computers & Operations Research, vol. 76, pp. 167-182.
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Yang, CS, Zhang, J, Zhang, L, Huang, J & Wang, Y 2016, 'Mechanisms of body weight reduction and metabolic syndrome alleviation by tea', Molecular Nutrition & Food Research, vol. 60, no. 1, pp. 160-174.
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Yang, X, Xie, H, Alonas, E, Liu, Y, Chen, X, Santangelo, PJ, Ren, Q, Xi, P & Jin, D 2016, 'Mirror-enhanced super-resolution microscopy', Light: Science & Applications, vol. 5, no. 6, pp. e16134-e16134.
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Axial excitation confinement beyond the diffraction limit is crucial to the development of next-generation, super-resolution microscopy. STimulated Emission Depletion (STED) nanoscopy offers lateral super-resolution using a donut-beam depletion, but its axial resolution is still over 500 nm. Total internal reflection fluorescence microscopy is widely used for single-molecule localization, but its ability to detect molecules is limited to within the evanescent field of ~ 100 nm from the cell attachment surface. We find here that the axial thickness of the point spread function (PSF) during confocal excitation can be easily improved to 110 nm by replacing the microscopy slide with a mirror. The interference of the local electromagnetic field confined the confocal PSF to a 110-nm spot axially, which enables axial super-resolution with all laser-scanning microscopes. Axial sectioning can be obtained with wavelength modulation or by controlling the spacer between the mirror and the specimen. With no additional complexity, the mirror-assisted excitation confinement enhanced the axial resolution six-fold and the lateral resolution two-fold for STED, which together achieved 19-nm resolution to resolve the inner rim of a nuclear pore complex and to discriminate the contents of 120 nm viral filaments. The ability to increase the lateral resolution and decrease the thickness of an axial section using mirror-enhanced STED without increasing the laser power is of great importance for imaging biological specimens, which cannot tolerate high laser power.

Yeoh, GH, Gu, X, Timchenko, V, Valenzuela, SM & Cornell, BA 2016, 'High order accurate dual-phase-lag numerical model for microscopic heating in multiple domains', International Communications in Heat and Mass Transfer, vol. 78, pp. 21-28.
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Yu, X, Lim, CED & Cheng, NCL 2016, 'A systematic review and meta-analysis of acupuncture and related therapies for palliative cancer care', Focus on Alternative and Complementary Therapies, vol. 21, no. 2, pp. 97-98.
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Yu, X, Lim, CED & Cheng, NCL 2016, 'Meta-analysis of the Chinese herbal bath therapy for knee osteoarthritis', Focus on Alternative and Complementary Therapies, vol. 21, no. 1, pp. 36-37.
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Yu, X, Lim, CED & Cheng, NCL 2016, 'Role of compound Danshen dripping pill in early diabetic retinopathy', Focus on Alternative and Complementary Therapies, vol. 21, no. 1, pp. 38-39.
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Yu, X, Lim, CED & Zaslawski, C 2016, 'Moxibustion for diarrhoea-predominant irritable bowel syndrome: what is the current evidence?', Focus on Alternative and Complementary Therapies, vol. 21, no. 2, pp. 118-119.
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Yu, X, Lim, CED, Zaslawski, C & Cheng, YW 2016, 'Tai chi for chronic pain conditions: what does the meta-analysis tell us?', Focus on Alternative and Complementary Therapies, vol. 21, no. 3-4, pp. 180-182.
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Zaslawski, C, Berle, C, Gadau, M, Li, WH, Li, T, Wang, FC, Bangrazi, S, Li, L, Liguori, S, Liu, YS, Tan, YS & Zhang, SP 2016, 'Protocol for Acupuncture Treatment of Lateral Elbow Pain: A Multisite Randomised Controlled Trial in China, Hong Kong, Australia, and Italy', EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 2016, pp. 1-9.
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Background. Lateral elbow pain is one of the most common musculoskeletal pains associated with the upper limb and has an estimated population incidence of 1–3%. Methods/Design. This study protocol is for a multisite randomised controlled study and is designed to evaluate the clinical efficacy of acupuncture in the treatment of chronic (over three months’ duration) lateral elbow pain. Four study sites, in the People’s Republic of China, Hong Kong, Italy, and Australia, will recruit 24 participants each. A total of 96 participants will be randomised to either an acupuncture group or a sham laser control group. The primary outcome measure will be the Disabilities of Arm, Shoulder, and Hand questionnaire with secondary outcome measures of Pain-Free Grip Strength Test, Muscle Tension Test, and a pain visual analogue scale. Discussion. Key features for conducting a multisite international acupuncture randomised clinical trial have been detailed in this protocol. Trial Registration. This trial is registered at Australian and New Zealand Clinical Trial Registry ACTRN12613001138774 on 11 October, 2013.

Zavřel, T, Červený, J, Knoop, H & Steuer, R 2016, 'Optimizing cyanobacterial product synthesis: Meeting the challenges', Bioengineered, vol. 7, no. 6, pp. 490-496.
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Zavřel, T, Knoop, H, Steuer, R, Jones, PR, Červený, J & Trtílek, M 2016, 'A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry', Bioresource Technology, vol. 202, pp. 142-151.
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Zeng, Y, Li, J, Liu, Q, Huete, AR, Xu, B, Yin, G, Zhao, J, Yang, L, Fan, W, Wu, S & Yan, K 2016, 'An Iterative BRDF/NDVI Inversion Algorithm Based on <italic>A Posteriori</italic> Variance Estimation of Observation Errors', IEEE Transactions on Geoscience and Remote Sensing, vol. 54, no. 11, pp. 6481-6496.
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Zeng, Y, Li, J, Liu, Q, Huete, AR, Yin, G, Xu, B, Fan, W, Zhao, J, Yan, K & Mu, X 2016, 'A Radiative Transfer Model for Heterogeneous Agro-Forestry Scenarios', IEEE Transactions on Geoscience and Remote Sensing, vol. 54, no. 8, pp. 4613-4628.
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Landscape heterogeneity is a common natural phenomenon but is seldom considered in current radiative transfer (RT) models for predicting the surface reflectance. This paper developed an analytical RT model for heterogeneous Agro-Forestry scenarios (RTAF) by dividing the scenario into nonboundary regions (NRs) and boundary regions (BRs). The scattering contribution of the NRs can be estimated from the scattering-by-arbitrarily-inclined-leaves-with-the-hot-spot-effect model as homogeneous canopies, whereas that of the BRs is calculated based on the bidirectional gap probability by considering the interactions and mutual shadowing effects among different patches. The multiangular airborne observations and discrete-anisotropic-RT model simulations were used to validate and evaluate the RTAF model over an agro-forestry scenario in the Heihe River Basin, China. The results suggest that the RTAF model can accurately simulate the hemispherical–directional reflectance factors (HDRFs) of the heterogeneous scenarios in the red and near-infrared (NIR) bands. The boundary effect can significantly influence the angular distribution of the HDRFs and consequently enlarge the HDRF variations between the backward and forward directions. Compared with the widely used dominant cover type (DCT) and spectral linear mixture (SLM) models, the RTAF model reduced the maximum relative error from 25.7% (SLM) and 23.0% (DCT) to 9.8% in the red band and from 19.6% (DCT) and 13.7% (SLM) to 8.7% in the NIR band. The RTAF model provides a promising way to improve the retrieval of biophysical parameters (e.g., leaf area index) from remote sensing data over heterogeneous agro-forestry scenarios.

Zhang, C, Tian, H, Yang, D, Sunarso, J, Liu, J & Liu, S 2016, 'Enhanced CO₂ Resistance for Robust Oxygen Separation Through Tantalum-doped Perovskite Membranes', ChemSusChem, vol. 9, no. 5, pp. 505-512.
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Zhang, J, Sun, B, Xie, X, Zhao, Y & Wang, G 2016, 'A Bifunctional Organic Redox Catalyst for Rechargeable Lithium-Oxygen Batteries with Enhanced Performances', ADVANCED SCIENCE, vol. 3, no. 4.
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Zhang, L, Cheng, Q, Zhang, L, Wang, Y, Merrill, GF, Ilani, T, Fass, D, Arnér, ESJ & Zhang, J 2016, 'Serum thioredoxin reductase is highly increased in mice with hepatocellular carcinoma and its activity is restrained by several mechanisms', Free Radical Biology and Medicine, vol. 99, pp. 426-435.
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Zhang, S, Zhou, J, Wu, R, Lei, L, Xiao, Z, Zhang, J & Xu, S 2016, 'Controlling red upconversion luminescence in Gd₂O₃:Yb³⁺–Er³⁺nanoparticles by changing the different atmosphere', RSC Advances, vol. 6, no. 103, pp. 101707-101713.
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Upconversion luminescence properties were investigated by emission intensityvs.excitation power (double logarithmic relationship) and temperature dependent emission spectroscopy.

Zhang, Y, Čejka, J, Lumpkin, GR, Tran, TT, Aharonovich, I, Karatchevtseva, I, Price, JR, Scales, N & Lu, K 2016, 'Hydrothermal synthesis, structures and properties of two uranyl oxide hydroxyl hydrate phases with Co(ii) or Ni(ii) ions', New Journal of Chemistry, vol. 40, no. 6, pp. 5357-5363.
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Two new iso-structured uranyl oxide hydroxyl hydrate phases with hydroxyl Co²⁺or Ni²⁺ions at the interlayers have been synthesised under hydrothermal conditions and structurally characterised.

Zhang, Y, Clegg, JK, Lu, K, Lumpkin, GR, Tran, TT, Aharonovich, I, Scales, N & Li, F 2016, 'Uranium(VI) hybrid materials with [(UO₂)₃(µ₃-O)(µ₂-OH)₃]⁺as the sub-building unit via uranyl-cation interactions', ChemistrySelect, vol. 1, no. 1, pp. 7-12.
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Zhang, Y, Karatchevtseva, I, Bhadbhade, M, Tran, TT, Aharonovich, I, Fanna, DJ, Shepherd, ND, Lu, K, Li, F & Lumpkin, GR 2016, 'Solvothermal synthesis of uranium(VI) phases with aromatic carboxylate ligands: A dinuclear complex with 4-hydroxybenzoic acid and a 3D framework with terephthalic acid', Journal of Solid State Chemistry, vol. 234, pp. 22-28.
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Zhang, Y, Wen, S, Zhao, L, Li, D, Liu, C, Jiang, W, Gao, X, Gu, W, Ma, N, Zhao, J, Shi, X & Zhao, Q 2016, 'Ultrastable polyethyleneimine-stabilized gold nanoparticles modified with polyethylene glycol for blood pool, lymph node and tumor CT imaging', Nanoscale, vol. 8, no. 10, pp. 5567-5577.
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Facile formed ultrastable Au PSNPs with excellent biocompatibility for in vivo CT imaging.

Zhanghao, K, Chen, L, Yang, X-S, Wang, M-Y, Jing, Z-L, Han, H-B, Zhang, MQ, Jin, D, Gao, J-T & Xi, P 2016, 'Super-resolution dipole orientation mapping via polarization demodulation', Light: Science & Applications, vol. 5, no. 10, pp. e16166-e16166.
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Zhao, J, Zheng, X, Schartner, EP, Ionescu, P, Zhang, R, Nguyen, T, Jin, D & Ebendorff‐Heidepriem, H 2016, 'Glass Fibers: Upconversion Nanocrystal‐Doped Glass: A New Paradigm for Photonic Materials (Advanced Optical Materials 10/2016)', Advanced Optical Materials, vol. 4, no. 10, pp. 1419-1419.
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Zhao, J, Zheng, X, Schartner, EP, Ionescu, P, Zhang, R, Nguyen, T, Jin, D & Ebendorff‐Heidepriem, H 2016, 'Upconversion Nanocrystal‐Doped Glass: A New Paradigm for Photonic Materials', Advanced Optical Materials, vol. 4, no. 10, pp. 1507-1517.
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The integration of novel luminescent nanomaterials into glassy matrix can lead to new hybrid materials and photonic devices with promising material performance and device functions. Lanthanide-containing upconversion nanocrystals have become unique candidates for sensing, bioimaging, photon energy management, volumetric displays, and other photonic applications. Here, a versatile direct-doping approach is developed to integrate bright upconversion nanocrystals in tellurite glass with tailored nanoscale properties. Following our two-temperature glass-melting technique, the doping temperature window of 550-625 °C and a 5 min dwell time at 577 °C are determined as the key to success, which balances the survival and dispersion of upconversion nanocrystals in glass. It is identified that the fine spectra of upconversion emissions can be used to diagnose the survival and dissolution fraction of doped nanocrystals in the glass. Moreover, 3D dispersion of nanocrystals in the glass is visualized by upconversion scanning confocal microscopy. It is further demonstrated that a low-loss fiber, drawn from the highly transparent nanocrystals-doped glass retains the distinct optical properties of upconversion nanocrystals. These results suggest a robust strategy for fabrication of high-quality upconversion nanocrystal-doped glasses. The new class of hybrid glasses allows for fiber-based devices to be developed for photonic applications or as a useful tool for tailoring light-nanoparticles interactions study.

Zhao, Y, Zhang, J, Li, K, Ao, Z, Wang, C, Liu, H, Sun, K & Wang, G 2016, 'Electrospun cobalt embedded porous nitrogen doped carbon nanofibers as an efficient catalyst for water splitting', JOURNAL OF MATERIALS CHEMISTRY A, vol. 4, no. 33, pp. 12818-12824.
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Zheng, X, Lu, Y, Zhao, J, Zhang, Y, Ren, W, Liu, D, Lu, J, Piper, JA, Leif, RC, Liu, X & Jin, D 2016, 'High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis', Analytical Chemistry, vol. 88, no. 2, pp. 1312-1319.
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Zheng, X, Zhu, X, Lu, Y, Zhao, J, Feng, W, Jia, G, Wang, F, Li, F & Jin, D 2016, 'High-Contrast Visualization of Upconversion Luminescence in Mice Using Time-Gating Approach', Analytical Chemistry, vol. 88, no. 7, pp. 3449-3454.
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Zhou, B, Huang, F, Cai, M, Tian, Y, Zhou, J, Xu, S & Zhang, J 2016, 'Mid-Infrared 2.86-$\mu \text{m}$ Emission Characteristics in Highly Dy³⁺ Doped Fluoroaluminate Glass', IEEE Photonics Technology Letters, vol. 28, no. 4, pp. 429-432.
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A highly Dy3+ doped (10 mol%) fluoroaluminate glass was successfully fabricated by melt-quenching method for the first time. The intensity of 2.86-μm emission increases with the Dy3+ ions concentration without fluorescence quenching because of the large dispersibility of Dy3+ ions in this glass network without clustering. Radiative and emission parameters were calculated based on the Judd-Ofelt theory, which show that the 10 mol% highly doped sample possesses a high calculated spontaneous transition probability (32.01 S-1) together with a large emission cross section (5.94 × 10-21 cm2) of Dy3+: 6H13/2 →6H15/2 transition. In addition, the increasing Qt (t = 2,4,6) values, which caused by a complex outermost electron configuration of Dy3+ ions, have been further discussed to analyze the partial glass structure.

Zhou, H, Che, X, Bao, G, Wang, N & Bai, X 2016, 'Design, Synthesis and Structure-Activity Relationship Study of Pyri-midine-Fused Diazepine Derivatives as L3MBTL3 Inhibitors', Chinese Journal of Organic Chemistry, vol. 36, no. 12, pp. 2948-2948.
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Zhou, H, Che, X, Bao, G, Wang, N, Peng, L, Barnash, KD, Frye, SV, James, LI & Bai, X 2016, 'Design, synthesis, and protein methyltransferase activity of a unique set of constrained amine containing compounds', Bioorganic & Medicinal Chemistry Letters, vol. 26, no. 18, pp. 4436-4440.
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Zhou, J, Gu, F, Liu, X & Qiu, J 2016, 'Enhanced Multiphoton Upconversion in Single Nanowires by Waveguiding Excitation', Advanced Optical Materials, vol. 4, no. 8, pp. 1174-1178.
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40-Fold enhancement of upconversion luminescence in a single NaGdF4–LiF hybrid nanowire is reported, along with a series of unique characteristics. These include four-photon upconversion from Er3+:2P3/2 excited state, a low excitation power threshold, and high optical-imaging resolution by waveguiding excitation compared to free-space spot excitation.

Zhou, K, Zhang, J, Xu, L, Wu, T & Lim, CED 2016, 'Chinese herbal medicine for subfertile women with polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, vol. 2016, no. 10.
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© 2016 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. Background: Polycystic ovarian syndrome (PCOS) is one of the most common reproductive endocrinology abnormalities, and affects 5% to 10% of women of reproductive age. Western medicines, such as oral contraceptives, insulin sensitizers and laparoscopic ovarian drilling (LOD), have been used to treat PCOS. Recently, many studies have been published that consider Chinese herbal medicine (CHM) as an alternative treatment for women with PCOS. Objectives: To assess the efficacy and safety of CHM for subfertile women with PCOS. Search methods: We searched sources, including the following databases, from inception to 9 June 2016: the Cochrane Gynaecology and Fertility Group Specialized Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Allied and Complementary Medicine (AMED), PsycINFO, Chinese National Knowledge Infrastructure (CNKI), VIP, Wanfang and trial registries. In addition, we searched the reference lists of included trials and contacted experts in the field to locate trials. Selection criteria: Randomized controlled trials (RCTs) that considered the use of CHM for the treatment of subfertile women with PCOS. Data collection and analysis: Two review authors independently screened appropriate trials for inclusion, assessed the risk of bias in included studies and extracted data. We contacted primary study authors for additional information. We conducted meta-analyses. We used the odds ratios (ORs) to report dichotomous data, with 95% confidence intervals (CI). We assessed the quality of the evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methods. Main results: We included five RCTs with 414 participants. The comparisons in the included trials were as follows: CHM versus clomiphene, CHM plus clomiphene versus clomiphene (with or without ethinyloestradiol cyproterone acetate (CEA)), CHM plus follicle aspiration...

Zhu, A, Greaves, IK, Liu, P-C, Wu, L, Dennis, ES & Peacock, WJ 2016, 'Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour', The Plant Journal, vol. 88, no. 4, pp. 597-607.
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Zhu, S, Xiao, L & Cortie, MB 2016, 'Surface enhanced Raman spectroscopy on metal nitride thin films', Vibrational Spectroscopy, vol. 85, pp. 146-148.
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ZHU, S-P & NOVIKOV, A 2016, 'EDITORIAL: STOCHASTIC AND COMPUTATIONAL METHODS IN FINANCE', The ANZIAM Journal, vol. 57, no. 3, pp. 205-206.
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Zhu, Y, Ishizaka, J, Tripathy, SC, Wang, S, Mino, Y, Matsuno, T & Suggett, DJ 2016, 'Variation of the photosynthetic electron transfer rate and electron requirement for daily net carbon fixation in Ariake Bay, Japan', Journal of Oceanography, vol. 72, no. 5, pp. 761-776.
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The Oceanographic Society of Japan and Springer Japan Fast repetition rate fluorometry (FRRf) provides a potential means to examine marine primary productivity; however, FRRf-based productivity estimations require knowledge of the electron requirement (K) for carbon (C) uptake (KC) to scale an electron transfer rate (ETR) to the CO2 uptake rate. Most previous studies have derived KC from parallel measurements of ETR and CO2 uptake over relatively short incubations, with few from longer-term daily-integrated periods. Here we determined KC by comparing depth-specific, daily ETRs and CO2-uptake rates obtained from 24-h on-deck incubation experiments undertaken on seven cruises in Ariake Bay, Japan, from 2008 to 2010. The purpose of this study was to determine the extent of variability of KC and to what extent this variability could be reconciled with the prevailing environmental conditions and ultimately to develop a method for determining net primary productivity (NPP) based on FRRf measurements. Both daily ETR and KC of the upper layer varied considerably, from 0.5 to 115.7 mmol e− mg Chl-a−1 day−1 and 4.1–26.6 mol e− (mol C)−1, respectively, throughout the entire data set. Multivariate analysis revealed a strong correlation between daily photosynthetically active radiation (PAR) and KC (r2 = 0.94). A simple PAR-dependent relationship derived from the data set was used for generating KC, and this relationship was validated by comparing the FRRf-predicted NPP with the 13C uptake measured in 2007. These new observations demonstrate the potential application of FRRf for estimating regional NPP from ETR.

Zinger, A, Latham, SL, Combes, V, Byrne, S, Barnett, MH, Hawke, S & Grau, GE 2016, 'Plasma levels of endothelial and B-cell-derived microparticles are restored by fingolimod treatment in multiple sclerosis patients', Multiple Sclerosis Journal, vol. 22, no. 14, pp. 1883-1887.
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Background: No molecular marker can monitor disease progression and treatment efficacy in multiple sclerosis (MS). Circulating microparticles represent a potential snapshot of disease activity at the blood brain barrier. Objectives and methods: To profile plasma microparticles by flow cytometry in MS and determine how fingolimod could impact endothelial microparticles production. Results: In non-treated MS patients compared to healthy and fingolimod-treated patients, endothelial microparticles were higher, while B-cell-microparticle numbers were lower. Fingolimod dramatically reduced tumour necrosis factor (TNF)-induced endothelial microparticle release in vitro. Conclusion: Fingolimod restored dysregulated endothelial and B-cell-microparticle numbers, which could serve as a biomarker in MS.

Zoh, RS, Mallick, B, Ivanov, I, Baladandayuthapani, V, Manyam, G, Chapkin, RS, Lampe, JW & Carroll, RJ 2016, 'PCAN: Probabilistic correlation analysis of two non‐normal data sets', Biometrics, vol. 72, no. 4, pp. 1358-1368.
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Abdo, P, Huynh, BP, Avakian, V, Nguyen, T, Gammon, J, Torpy, FR & Irga, PJ 1970, 'Measurement of air flow through a green-wall module', Proceedings of the 20th Australasian Fluid Mechanics Conference, AFMC 2016, Australasian Fluid Mechanics Conference, Australasian Fluid Mechanics Society, Perth.
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© 2006 Australasian Fluid Mechanics Society. All rights reserved. Green or living walls are active bio-filters developed to enhance air quality. Often, these walls form the base from which plants are grown; and the plant-wall system helps to remove both gaseous and particulate air pollutants. A green wall can be found indoors as well as outdoors, and could be assembled from modules in an arrangement similar to tiling. Measurement of air flow through such a module has been conducted in this work. The module is essentially a rectangular plastic box (dimensions about 500 mm x 500 mm x 130 mm) that holds a permeable bag containing a plant-growing medium (replacement for soil). The front face of the module has multiple openings for plants to protrude out from the bag inside. Plant roots are imbedded in the medium. A fan positioned at a central opening on the module‟s back face drives air through the medium-plant-roots mix and then onward through the plants‟ canopy; and these would help to remove both gaseous and particulate pollutants from the air. Drip-irrigation water is dispensed from a tube running along the open top-face of the module. The module has also a small drainage hole on its bottom face. Pressure drop across the module, air-flow distribution through it as well as flow rate have been obtained, in terms of variable parameters which include moisture content, growing-medium-plant-roots mix and plant type. The measurements help to determine the pattern of flow resistances which in turn will be used in a future CFD (Computational Fluid Dynamics) analysis for improving the design of the module, such that more appropriate flow distribution and flow rate would be achieved. All this is in addition to the better understanding of air flow through complex moist porous media.

Aharonovich, I, Bray, K & Shimoni, O 1970, 'Florescent Nanodiamonds for Biomedical Applications', Conference on Lasers and Electro-Optics, CLEO: Applications and Technology, OSA, San Jose, CA.
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Ajani, PA 1970, 'Microalgae: coming into bloom (Invited Oral Presentation)', Science Week, Office of Environment and Heritage 2016, Sydney Australia.

Ajani, PA, Kohli, GS, Darling, AE, Liu, M & Ostrowski, M 1970, 'Genome variability in the ecologically significant marine diatom Leptocylindrus (Bacillariophyta) in a southern hemisphere upwelling system (Poster Presentation)', Sydney Bioinformatics Research Symposium 2016, Sydney, Australia.

Bathgate, E, Caprarelli, G, Xiao, H, Stuart, B & Pogson, R 1970, 'Raman, EPMA and SEM analysis of meteorites from the Australian Museum', 16th Australian Space Research Conference, Melbourne.

Berhane, AM, Choi, S, Kato, H, Makino, T, Mizuochi, N, Yamasaki, S, Toth, M & Aharonovich, I 1970, 'Defect luminescence in Diamond and GaN: towards single photon emitting devices', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, CA.
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Berhane, AM, Choi, S, Kato, H, Makino, T, Mizuochi, N, Yamasaki, S, Toth, M & Aharonovich, I 1970, 'Defect luminescence in Diamond and GaN: towards single photon emitting devices', Optics InfoBase Conference Papers.
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Narrow band single photon emitters in diamond and gallium nitride are investigated. The work provides foundation towards electrically driven sources at room temperature that are important prerequisites for solid state quantum technologies.

Blanes, L, Ueland, M, Taudte, R, Stuart, B, Cole, N, Willis, PA, Roux, C & Doble, P 1970, 'Capillary-driven microfluidic paper-based analytical devices for lab on a chip screening of explosive residues in soil', ANZFSS 23rd International Symposium on the Forensic Sciences, Auckland.

Booth, N, Imperia, P, Davidson, G, Lee, S, Stuart, B, Thomas, P, Komatsu, K, Yamane, R, Prescott, S, Maynard-Casely, H & Nelson, A 1970, 'Three impossible things before lunch or that sounds challenging, you want it when?', 9th International Workshop on Sample Environment at Scattering Facilities, Gettysburg.

Brown, AC, Essilfie, AT, Beckett, EL, Thorburn, AN, Hansbro, NG, Jarnicki, AG, Yagita, H, Foster, PS, Horvat, JC, Wark, PAB & Hansbro, PM 1970, 'The role of CD8 T-cells during anti-PD1 treatment of viral infection-induced secondary bacterial pneumonia', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 511-512.

Camacho-Morales, R, Rahmani, M, Kruk, S, Wang, L, Xu, L, Miroshnichenko, AE, Smirnova, D, Tan, H, Karouta, F, Naureen, S, Vora, K, Solntsev, AS, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 1970, 'Shaping the radiation pattern of second-harmonic generation from AlGaAs nonlinear nanoantennas', Optics InfoBase Conference Papers, Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), OSA Publishing, Sydney, Australia.
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We fabricate AlGaAs nanodisk antennas on a glass substrate and demonstrate experimentally the shaping of radiation patterns and polarization of the second harmonic emission in both forward and backward directions.

Camacho-Morales, R, Rahmani, M, Kruk, S, Wang, L, Xu, L, Miroshnichenko, AE, Smirnova, D, Tan, H, Karouta, F, Naureen, S, Vora, K, Solntsev, AS, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 1970, 'Shaping the radiation pattern of second-harmonic generation from AlGaAs nonlinear nanoantennas', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Australian Conference on Optical Fibre Technology, OSA, Sydney Australia.
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© OSA 2016.We fabricate AlGaAs nanodisk antennas on a glass substrate and demonstrate experimentally the shaping of radiation patterns and polarization of the second harmonic emission in both forward and backward directions.

Camacho-Morales, R, Rahmani, M, Kruk, S, Wang, L, Xu, L, Miroshnichenko, AE, Smirnova, D, Tan, H, Karouta, F, Naureen, S, Vora, K, Solntsev, AS, Carletti, L, De Angelis, C, Jagadish, C, Kivshar, YS & Neshev, DN 1970, 'Shaping the radiation pattern of second-harmonic generation from AlGaAs nonlinear nanoantennas', Optics InfoBase Conference Papers, Photonics and Fiber Technology 2016, OSA Publishing, Sydney, Australia.
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We fabricate AlGaAs nanodisk antennas on a glass substrate and demonstrate experimentally the shaping of radiation patterns and polarization of the second harmonic emission in both forward and backward directions.

Cheng, B, Sklibosios Nikitopoulos, C & Schlogl, E 1970, 'Empirical Hedging Performance on Long-Dated Crude Oil Derivatives', Quantitative Methods in Finance 2016, Sydney, Australia.

Cole, AJ, Dwight, T, Zhu, Y, Gill, AJ, Dickson, K-A, Clarkson, A, Gard, GB, Maidens, J, Valmadre, S, Clifton-Bligh, RJ & Marsh, DJ 1970, 'Abstract B05: Assessment of TP53 mutation status in primary high-grade serous ovarian cancer and cell line models: Comparison between immunohistochemistry and next-generation sequencing.', Clinical Cancer Research, Abstracts: AACR Special Conference: Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; October 17-20, 2015; Orlando, FL, American Association for Cancer Research (AACR), Orlando, FL, pp. B05-B05.
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Abstract Mutations in TP53 have been shown to occur in around 96% of high-grade serous ovarian cancer (HGSOC). Different TP53 mutations can lead to accumulation of mutant p53 in the cell that support gain of function effects, or loss or abrogation of both wild-type and mutant p53. Success of new therapeutic strategies for HGSOC that target mutant p53 will likely depend on detailed knowledge of the type of TP53 mutation present and its influence on mutant p53 levels in the cell. The aim of this study was to identify the spectrum of TP53 mutations in a cohort of primary HGSOCs and compare this with p53 immunostaining patterns. In addition, we sought to identify TP53 mutations in the previously uncharacterised HGSOC cell line models OV167 and OV202, as well as the clear cell adenocarcinoma line OV207. DNA from fresh frozen tumors and cell line samples were processed for next generation sequencing using The Fluidigm Access TP53 Array System run on the Fluidigm Biomark HD™ Real-Time PCR fluidics system (Fluidigm Corporation). Amplicon libraries were pooled and analyses performed in a single massively parallel sequencing run using the MiSeq Sequencing System (Illumina Inc.). Unaligned BAM files were analyzed within the Broad Institute's Genome Analysis Toolkit (GATK) best practice pipeline. The ANNOVAR software tool was used to generate an annotated variants list. Variants were further filtered based on their frequency in the 1000 Genome Database and predicted SIFT scores. Mutations were visualized using the Broad Institute's Integrative Genomics Viewer. All samples in which a mutation was identified underwent Sanger sequencing using primers recommended in the International Agency for Research on Cancer TP53 database. Immunohistochemistry for p53 was performed on formalin fixed paraffin embedded tissue sections using a commercially available mouse monoclonal anti-human antibody (Protein Clo...

Collison, A, Sokulsky, LA, Starkey, MR, Nightingale, S, Le Fevre, A, Percival, E, Hansbro, PM, Foster, PS & Mattes, J 1970, 'TRAIL regulates egg-allergen induced eosinophilic oesophagitis', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 461-462.

Czibula, OG, Gu, H & Zinder, Y 1970, 'A Lagrangian Relaxation-Based Heuristic to Solve Large Extended Graph Partitioning Problems', Lecture Notes in Computer Science, International Workshop on Algorithms and Computation (WALCOM), Springer International Publishing, Kathmandu, Nepal, pp. 327-338.
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The paper is concerned with the planning of training sessions in large organisations requiring periodic retraining of their staff. The allocation of students must take into account student preferences as well as the desired composition of study groups. The paper presents a bicriteria Quadratic Multiple Knapsack formulation of the considered practical problem, and a novel solution procedure based on Lagrangian relaxation. The paper presents the results of computational experiments aimed at testing the optimisation procedure on real world data originating from Australia’s largest electricity distributor. Results are compared and validated against a Genetic Algorithm based matheuristic

Czibula, OG, Gu, H & Zinder, Y 1970, 'Scheduling Personnel Retraining:Column Generation Heuristics', COMBINATORIAL OPTIMIZATION, ISCO 2016, International Symposium on Combinatorial Optimization, Springer, Vietri sul Mare, Italy, pp. 213-224.
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Many organisations need periodic retraining of staff. Due to certain requirements on the composition of study groups, the planning of training sessions is an NP-hard problem. The paper presents linear and nonlinear mathematical programming formulations of this problem together with three column generation based heuristic optimisation procedures. The procedures are compared by means of computational experiments that use data originating from a large Australian electricity distributor with several thousand employees.

Czibula, OG, Gu, H & Zinder, Y 1970, 'Timetabling of workplace training: A combination of mathematical programming and simulated annealing', PATAT 2016 - Proceedings of the 11th International Conference on the Practice and Theory of Automated Timetabling, International Conference of the Practice and Theory of Automated Timetabling, PATAT, Udine, Italy, pp. 95-107.
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The paper is concerned with the problem of scheduling workplace training, which arises in a broad range of organisations, from the hospital placements of nursing students to apprentice training at organisations such as electricity distributors. The problem can be viewed as a generalisation of the open shop scheduling problem. The paper discusses the complexity of the considered problem, and presents an optimisation procedure, which is a sequential application of integer linear programming and simulated annealing. The effectiveness of the proposed optimisation procedure was demonstrated by computational experiments using data with typical characteristics of a real-world problems arising at large electricity distributors. The computational experiments show that the proposed optimisation procedure produces superior solutions on average compared to those from a general purpose MIP solver.

Davila, YC & Griffiths, N 1970, 'Read to succeed: Developing Academic and Professional STEM Communication Practices', Proceedings of the Australian Conference on Science and Mathematics Education, Australian Conference on Science and Mathematics Education, The University of Queensland, pp. 60-61.

Davila, YC, Griffiths, N & Leigh, A 1970, 'A blended learning approach to supporting student learning of scientific writing skills with an embedded Academic Integrity Module', Higher Education Research and Development Society of Australasia, Fremantle.

Davila, YC, Reyna Zeballos, J, Huber, E & Meier, P 1970, 'Enhancing engagement in flipped learning across undergraduate Science using the Flipped Teacher and Flipped Learner Framework', Proceedings of the Australian Conference on Science and Mathematics Education, Australian Conference on Science and Mathematics Education, The University of Queensland, pp. 40-41.

de Chaisemartin, L, Jonsson, F, Granger, V, Gouel-Cheron, A, Neukirch, C, Nicaise-Roland, P, Gillis, C, Dib, F, Tubach, F, Longrois, D, Bruhns, P & Chollet-Martin, S 1970, 'Neutrophil activation in systemic anaphylaxis: results from the multicentric NASA study', ALLERGY, Meeting of the European-Academy-of-Allergy-and-Clinical-Immunology, WILEY-BLACKWELL, Vienna, AUSTRIA, pp. 41-42.

de Sterke, CM, Sturmberg, BCP, Chong, TK, Choi, D-Y, White, TP, Botten, LC, Dossou, KB, Poulton, CG, Catchpole, KR & McPhedran, RC 1970, 'Total absorption in Structured Ultrathin Semiconductor Layers', Light, Energy and the Environment, Optical Nanostructures and Advanced Materials for Photovoltaics, OSA.
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© OSA 2016. We show that essentially total absorption can be achieved in ultrathin layers of a modestly absorbing semiconductor using a grating geometry. Fabrication requires standard techniques and structured metal elements are not required.

de Vries, M, Faiz, A, Postma, DS, Sin, DD, Bossé, Y, Nickle, DC, Timens, W, van den Berge, M & Brandsma, C-A 1970, 'A potential role for extracellular matrix proteins in lung ageing in COPD', 3.1 Molecular Pathology and Functional Genomics, ERS International Congress 2016 abstracts, European Respiratory Society.
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Dixit, A, Donnelly, S, Lund, MA, Dalton, JP & Greer, JM 1970, 'Protection against development of a mouse model of multiple sclerosis by a parasite-derived 68-mer peptide', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 1042-1042.

Dossou, KB, Poulton, CG & Botten, LC 1970, 'Effective impedance modeling of metamaterial structures', 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), IEEE, AUSTRALIA, pp. 5-6.
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Du, K & Platen, E 1970, 'Benchmarked Risk Minimization', Mathematical Finance, AJOU Workshop in Financial Economics and Mathematics, Seoul, Korea, pp. 617-637.
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Elbadawi, C, Tran, TT, Shimoni, O, Totonjian, D, Lobo, CJ, Grosso, G, Moon, H, Englund, DR, Ford, MJ, Aharonovich, I & Toth, M 1970, 'Ultra-bright emission from hexagonal boron nitride defects as a new platform for bio-imaging and bio-labelling', SPIE Proceedings, SPIE BioPhotonics Australasia, SPIE, Adelaide, AUSTRALIA.
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Faiz, A, Postma, D, Koppelman, G, Hiemstra, P, Sterk, P, Timens, W, Steiling, K, Spira, A, Heijink, I & van den Berge, M 1970, 'LSC Abstract – Inducible expression quantitative trait loci: A novel method to identifying genetic variants associated with corticosteroid responsiveness in COPD', ERS Lung Science Conference 2016, ERS International Congress 2016 abstracts, European Respiratory Society.
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Faiz, A, Postma, DS, Koppelman, GH, Hiemstra, PS, Sterk, PJ, Timens, W, Steiling, K, Spira, A, Heijink, IH & van den Berge, M 1970, 'FKBP5 a candidate for corticosteroid insensitivity in COPD', 3.1 Molecular Pathology and Functional Genomics, ERS International Congress 2016 abstracts, European Respiratory Society.
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Fourment, Darling, AE & Matsen, E 1970, 'Phylogenetic inference with streaming data using sequential Monte Carlo', Sydney Bioinformatics Research Symposium, Sydney.

Fung, J, Zinder, Y & Singh, G 1970, 'Flexible Flow Shop with Storage: Complexity and Optimisation Methods', IFAC PAPERSONLINE, IFAC Conference on Manufacturing Modelling, Management and Control, Elsevier, Troyes, France, pp. 237-242.
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The paper is concerned with a two-stage flexible flow shop with a buffer under the assumption that all operations have the same processing time and that each job can be processed on a machine only if a certain amount of buffer space is allocated to this job. The amount of buffer space to be allocated differs from job to job. The buffer is shared by all machines and has limited size. The objective function is the makespan. The application area includes supply chains which involve loading and unloading operations, and problems arising in computer systems with shared memory. It is proven that in general, the problem is NP-hard in the strong sense, but in the case of two-machines, it is solvable in polynomial-time. For the general case, several integer linear programming models are presented and compared by means of computational experiments. The presented integer linear programming models implement various ideas such as symmetry breaking constraints, knapsack type cutting planes and the results of the analysis of the structure of optimal schedules.

Gellatly, S, Dennis, P, Jarnicki, A, Lachner, N, Wood, D, Fricker, M, Budden, K, Liu, G, Keely, S, Morrison, M, Willner, D, Cooper, M, Hugenholtz, P & Hansbro, P 1970, 'HEALTHY GUT MICROBIOTA AMELIORATES EXPERIMENTAL CHRONIC OBSTRUCTIVE PULMONARY DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 77-77.

Ghadiri, M, Young, P, Oliver, B, Jarolimek, W & Traini, D 1970, 'MODULATING TIGHT JUNCTIONS ON AIRWAY EPITHELIAL CELLS TO ENHANCE PARACELLULAR TRANSPORT OF ANTIFIBROTIC DRUGS', JOURNAL OF AEROSOL MEDICINE AND PULMONARY DRUG DELIVERY, MARY ANN LIEBERT, INC, pp. A11-A12.

Gillis, CM, Jonsson, F, Mancardi, D, Tu, N, Beutier, H, Van Rooijen, N, Macdonald, LE, Murphy, AJ & Bruhns, P 1970, 'Mechanisms of anaphylaxis in human low-affinity IgG receptor locus knock-in mice', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 782-783.

Gillis, CM, Zenatti, PP, Mancardi, DA, Beutier, H, Macdonald, LE, Murphy, AJ, Jonsson, F & Bruhns, P 1970, 'Phagocytic power of high-affinity mouse IgG receptor Fc gamma RI in disease and therapy models', EUROPEAN JOURNAL OF CLINICAL INVESTIGATION, WILEY-BLACKWELL, pp. 89-89.

Giovannini, L, Ma, X & Huete, A 1970, 'Drought resilience of Australian rangelands under intense hydroclimatic variability', 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IGARSS 2016 - 2016 IEEE International Geoscience and Remote Sensing Symposium, IEEE, Beijing, China, pp. 5467-5469.
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© 2016 IEEE.Rangelands comprise ∼81% of Australia's landmass, extend over a broad range of climates and vegetation types, and provide important social-economical functions (Fig. 1). The climate of Australia's rangelands is extremely variable. This variability was reflected in recent events of extreme flooding immediately following one of the most intense droughts in history over the early 21st century [1,2]. These extreme climatic events provide an opportunity to assess how Australian rangelands respond to hydroclimatic variations, and further generalise knowledge regarding resilience of these ecosystems to contrasting drought and wet extremes.

Gräfe, M, Antonosyan, DA, Solntsev, AS, Szameit, A & Sukhorukov, AA 1970, 'Photon-pair generation in nonlinear lossy waveguides: An optical emulation', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, California United States.
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© 2016 OSA.We demonstrate a coupled-waveguide platform which realizes classical optical simulation of quantum photon-pair generation through spontaneous parametric down-conversion in a nonlinear lossy waveguide. The photon-pair creation vs. the phase mismatch and loss are experimentally mapped.

Hansbro, P, Brown, A, Essilfie, A, Beckett, E, Thorburn, A, Hansbro, N, Jarnicki, A, Yagita, H, Foster, P & Horvat, J 1970, 'PROGRAMMED DEATH-1 (PD-1) PREDISPOSES TO RESPIRATORY VIRAL INFECTION-INDUCED SECONDARY BACTERIAL PNEUMONIA', RESPIROLOGY, WILEY-BLACKWELL, pp. 58-58.

Hansbro, P, Nair, P, Starkey, M, Haw, T, Liu, G, Clark, A & Ammit, A 1970, 'TRISTETRAPROLIN PROTECTS MICE AGAINST CIGARETTE-SMOKE INDUCED EXPERIMENTAL COPD', RESPIROLOGY, WILEY-BLACKWELL, pp. 125-125.

Hansbro, P, Sunkara, K, Jarnicki, A, Kim, R, Haw, T, Wark, P, Horvat, J & Foster, P 1970, 'ROLE OF MIR-21 IN THE PATHOGENESIS OF EXPERIMENTAL COPD', RESPIROLOGY, WILEY-BLACKWELL, pp. 125-125.

Hansbro, PM, Liu, G, Cooley, MA, Jarnicki, AG, Hsu, AC, Nair, PM, Haw, T, Fricker, M, Gellatly, SL, Kim, RY, Inman, MD, Tjin, G, Wark, PA, Horvat, JC, Oliver, BG, Argraves, WS, Knight, DA & Burgess, JK 1970, 'Fibulin-1 Plays Critical Roles In The Pathogenesis Of Pulmonary Diseases', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, San Francisco, CA.

Horvat, J, Kim, R, Pinkerton, J, Essilfie, A-T, Robertson, A, Baines, K, Mayall, J, Starkey, M, Wark, P, Gibson, P, O'Neill, L, Cooper, M & Hansbro, P 1970, 'NLRP3 inflammasome-mediated, IL-1β-dependent inflammatory responses drive steroid-resistant asthma', 5.3 Allergy and Immunology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Horvat, J, Kim, R, Pinkerton, J, Rae, B, Starkey, M, Essilfie, A, Mayall, J, Jones, B, Haw, T, Nguyen, H, Keely, S, Mattes, J, Adcock, I, Foster, P & Hansbro, P 1970, 'IDENTIFICATION OF NOVEL THERAPEUTIC TARGETS FOR STEROID-INSENSITIVE ASTHMA USING MODELS THAT REPRESENT DIFFERENT CLINICAL SUBTYPES OF DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 55-55.

Horvat, J, Kim, R, Pinkerton, J, Rae, B, Starkey, M, Essilfie, A-T, Mayall, J, Jones, B, Haw, TJ, Nguyen, H, Keely, S, Mattes, J, Adcock, I, Foster, P & Hansbro, P 1970, 'Identification of therapeutic targets for steroid-insensitive asthma using models that represent different clinical subtypes of disease', 5.3 Allergy and Immunology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Hossain, KR, Khamici, HA, Holt, SA & Valenzuela, SM 1970, 'Elucidating the Mechanism for Sterol Regulation of Chloride Intracellular Ion Channel Protein Interactions with Lipid Membranes', Biophysical Journal, 60th Annual Meeting of the Biophysical-Society, Elsevier BV, Los Angeles, CA, pp. 204a-204a.
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Hsu, A, Starkey, M, Hansbro, P & Wark, P 1970, 'Micro-RNA-125a/b target A20 and MAVS to promote inflammatory and impair antiviral responses in chronic obstructive pulmonary disease', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 462-462.

Huete, A, Restrepo-Coupe, N, Wu, J & Saleska, S 1970, 'Climate and leaf phenology controls on tropical forest photosynthesis', 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IGARSS 2016 - 2016 IEEE International Geoscience and Remote Sensing Symposium, IEEE, Beijing, China, pp. 1731-1733.
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© 2016 IEEE.Discerning photosynthetic seasonality in tropical forests is fundamental to both basic ecology (plant strategies for resource acquisition when resources are limiting) and the need to understand vegetation responses and feedbacks to a changing climate. The seasonality question provides an important threshold test to advance predictions of tropical forest response to future climate changes. Despite its importance, spatial and temporal photosynthesis patterns in tropical forests are highly uncertain and remain controversial as ecosystem models yield divergent results while satellite-based observations are subject to various artifacts associated with cloud leakage, aerosols, and sensor-sun observation geometries. In this research, in situ seasonal tower carbon flux and leaf-scale phenology measures from cameras were combined with satellite data to investigate the roles of climate drivers and biologic processes (leaf phenology and demography traits) on vegetation canopy photosynthesis. Our results show the importance of phenology traits on controls on seasonal photosynthesis.

Imkamp, K, Faiz, A, van der Wiel, E, Boudewijn, I, Koppelman, G, Brandsma, C-A, Kerstjens, H, Timens, W, Vroegop, S, Pasma, H, Boersma, W, Wielders, P, van den Elshout, F, Mansour, K, Steiling, K, Spira, A, Lenburg, M, Heijink, I, Postma, D & van den Berge, M 1970, 'Effects of ICS/LABA treatment on hyperinflation and genome wide gene-expression in upper airway epithelium in severe COPD', 6.4 Genes and Environment, ERS International Congress 2016 abstracts, European Respiratory Society.
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Irga, PJ & Torpy, FR 1970, 'A survey of aeromycota for urban Sydney and their relationships with environmental parameters', Australasian Mycological Society & Fungal Network of New Zealand Joint Meeting Conference, Queenstown, New Zealand..

Jaiswal, R, Pokharel, D & Bebawy, M 1970, 'Abstract 5114: The role of microvesicles on immune function in response to cancer', Cancer Research, Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA, American Association for Cancer Research (AACR), New Orleans, LA, pp. 5114-5114.
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Abstract Cell to cell communication is vital for the co-ordination of physiological process and the regulation of an organism's phenotype. More recently communication via extracellular membrane vesicles has gained recognition. We first described a novel mechanism for the spread and dominance of multidrug resistance (MDR) and enhanced metastatic capacity in cancer via submicron microparticles (MPs). MPs are plasma membrane vesicles released spontaneously from various cell types, carrying bioactive material and are implicated in different physiological and pathophysiological processes. Through this communication apparatus, cancer cells can acquire and secure a survival advantage by various mechanisms. This study aims to examine a role of MPs in altering immune cell function in cancer. The effects of MPs isolated from human breast cancer cells were examined on antigen presenting cells (APC) in vitro. MP-mediated effects on cell phenotype and functionality was assessed by cytokine profiling and migration assay. We observed a cancer cell induced change in immune cell phenotype and functionality which have the potential to support a reduced global immune response in cancer. The elucidation of this pathway provides novel therapeutic strategies which can be exploited for the treatment of cancer. Citation Format: Ritu Jaiswal, Deep Pokharel, Mary Bebawy. The role of microvesicles on immune function in response to cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5114.

Jamie, JF, Vemulpad, SR, Kichu, M, Kuzhiumparambil, U & Velmurugan, R 1970, 'Traditional medicine partnerships – fostering two way exchange of knowledge, skills and capacity strengthening', Acta Horticulturae, International Society for Horticultural Science (ISHS), pp. 21-30.
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Jha, S, Hannu, M, Newton, P, Gore, K, Wilhelm, K, Hayward, C, Jabbour, A, Kotlyar, E, Keogh, A, Dhital, K, Granger, E, Jansz, P, Spratt, P, Montgomery, E, Harkess, M, Tunnicliff, P & Macdonald, P 1970, 'Reversibility of frailty in heart transplant listed patients', The Transplantation Society of Australia and New Zealand 34th Annual Scientific Meeting, Sydney, Australia.

Jones, B, Harrison, C, Dua, K, Hsu, A, Starkey, M, Jarnicki, A, Smithers, N, Knight, D, Wark, P, Adcock, I & Hansbro, P 1970, 'Bromodomain inhibitors reverse inflammation and disease features in experimental chronic obstructive pulmonary disease', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 585-586.

Jones, B, Harrison, C, Waters, D, Dua, K, Starkey, M, Jarnicki, A, Smithers, N, Knight, D, Wark, P, Adcock, I & Hansbro, P 1970, 'BROMODOMAIN INHIBITORS REVERSE THE DISEASE FEATURES IN EXPERIMENTAL CHRONIC OBSTRUCTIVE PULMONARY DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 43-43.

Jonsson, F, de Chaisemartin, L, Granger, V, Gillis, C, Gouel-Cheron, A, Neukirch, C, Dib, F, Nicaise-Roland, P, Longrois, D, Tubach, F, Bruhns, P & Chollet-Martin, S 1970, 'Neutrophil activation in systemic anaphylaxis: results from the multicentric NASA study', EUROPEAN JOURNAL OF CLINICAL INVESTIGATION, WILEY-BLACKWELL, pp. 78-79.

Kalatzis, G, Lees, T, Nassif, N, Zaslawski, C & Lal, S 1970, 'Investigating cognitive function in diabetes and healthy samples using electroencephalography (EEG) and psychometric assessment: a comparative study.', Inter-University Neuroscience & Mental Health Conference.

Kim, R, Pinkerton, J, Essilfie, A, Robertson, A, Baines, K, Mayall, J, Starkey, M, Wark, P, Gibson, P, O'Neill, L, Cooper, M, Horvat, J & Hansbro, P 1970, 'NLRP3 INFLAMMASOME- MEDIATED, IL-1 beta-DEPENDENT INFLAMMATORY RESPONSES DRIVE SEVERE, STEROID-INSENSITIVE ASTHMA', RESPIROLOGY, WILEY-BLACKWELL, pp. 46-46.

Kim, R, Pinkerton, J, Essilfie, A-T, Robertson, A, Baines, K, Mayall, J, Starkey, M, Wark, P, Gibson, P, O'neill, L, Cooper, M, Horvat, J & Hansbro, P 1970, 'NLRP3 inflammasome-mediated, IL-1 beta-dependent inflammatory responses drive severe, steroid-resistant asthma', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 569-570.

Kim, RY, Pinkerton, JW, Essilfie, A-T, Robertson, AA, Baines, KJ, Mayall, JR, Starkey, MR, Wark, PA, Gibson, PG, O'Neill, LA, Cooper, MA, Horvat, JC & Hansbro, PM 1970, 'Nlrp3 Inflammasome-Mediated, Il-1 beta-Dependent Inflammatory Responses Drive Severe, Steroid-Insensitive Asthma', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, San Francisco, CA.

Koolaji, N, Murray, M & Rawling, T 1970, 'Aryl group modification in novel anti-cancer agents based on ω-3-17,18-epoxyeicosapentaenoic acid', European Journal of Cancer, 28th EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics, Elsevier BV, Munich, GERMANY, pp. S68-S68.
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Lapine, M 1970, 'Strong boundary effects in microwave metamaterial samples', 2016 IEEE Radio and Antenna Days of the Indian Ocean (RADIO), 2016 IEEE Radio and Antenna Days of the Indian Ocean (RADIO), IEEE, St. Gilles-les-Bains, Reunion, pp. 1-2.
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© 2016 IEEE.The majority of metamaterial ideas are expressed in terms of effective material parameters. However, in many cases that kind of description fails, for a number of reasons such as strong spatial dispersion. One of the less known problems stems from the finite size of realistic metamaterials, which makes the total number of individual elements insufficient for an effective medium description, and promotes significant boundary effects. We present an analysis of this situation and point out that even for ideally shaped metamaterial samples there is a remarkable difference from theoretical predictions. As an example, we report the implications of finite size for metamaterial lenses.

Lapine, M, Poulton, CG & McPhedran, RC 1970, 'On the deviation of metamaterial spheres from effective medium', 2016 10th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS), 2016 10th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS), IEEE, Chania, Greece, pp. 196-198.
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© 2016 IEEE.We analyse the convergence of the actual properties of finite subwavelength metamaterial samples where all the prerequisites for a reliable effective medium description, except for the finite size, are fulfilled, towards the effective medium predictions. We show that the convergence is rather slow and it is likely that hundreds of thousands of individual meta-atoms must be assembled together before the properties of the resulting structure can be claimed to correspond to those a bulk material. These observations are directly relevant for practical design of metamaterials and their future development.

Lenzini, F, Titchener, J, Fisher, P, Boes, A, Poddubny, AN, Kasture, S, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 1970, 'Measurement of photon-pair generation in waveguide arrays with specialized poling', Frontiers in Optics 2016, Frontiers in Optics, OSA.
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© OSA 2016. We present the realization of an inhomogeneously poled nonlinear waveguide array for the generation of photon pairs. The device is characterized by coincidence counting and a novel method based on reversed sum-frequency generation measurements.

Lenzini, F, Titchener, J, Kasture, S, Boes, A, Poddubny, AN, Fisher, P, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 1970, 'A nonlinear waveguide array with inhomogeneous poling pattern for the generation of photon pairs and its characterization in the quantum and classical regimes', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Nonlinear Photonics, OSA, Sydney, Australia.
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© 2016 OSA.We present the realization of an inhomogeneously poled nonlinear waveguide array for the generation of photon pairs. The device is characterized by coincidence counting and a novel method based on reversed sum-frequency generation measurements.

Lenzini, F, Titchener, J, Kasture, S, Poddubny, AN, Boes, A, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 1970, 'A nonlinear waveguide array with inhomogeneous poling pattern for the generation of photon pairs', 2016 Conference on Lasers and Electro-Optics, CLEO 2016, Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), OSA Publishing, Sydney, Australia.
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We present the realization of an inhomogeneously poled nonlinear waveguide array for the generation of photon pairs with integrated pump filtering. The biphoton wave-function produced from the device is characterized using reversed sum-frequency generation measurements.

Li, D, Shi, X & Jin, D 1970, 'Polydopamine-coated gold nanostars for CT imaging and enhanced photothermal therapy of tumors', SPIE Proceedings, SPIE BioPhotonics Australasia, SPIE, Adelaide.
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The advancement of biocompatible nanoplatforms with dual functionalities of diagnosis and therapeutics is strongly demanded in biomedicine in recent years. In this work, we report the synthesis and characterization of polydopamine (pD)-coated gold nanostars (Au NSs) for computed tomography (CT) imaging and enhanced photothermal therapy (PTT) of tumors. Au NSs were firstly formed via a seed-mediated growth method and then stabilized with thiolated polyethyleneimine (PEI-SH), followed by deposition of pD on their surface. The formed pD-coated Au NSs (Au-PEI@pD NSs) were well characterized. We show that the Au-PEI@pD NSs are able to convert the absorbed near-infrared laser light into heat, and have strong X-ray attenuation property. Due to the co-existence of Au NSs and the pD, the light to heat conversion efficiency of the NSs can be significantly enhanced. These very interesting properties allow their uses as a powerful theranostic nanoplatform for efficient CT imaging and enhanced phtotothermal therapy of cancer cells in vitro and the xenografted tumor model in vivo. With the easy functionalization nature enabled by the coated pD shell, the developed pD-coated Au NSs may be developed as a versatile nanoplatform for targeted CT imaging and PTT of different types of cancer. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Mangan, N, Mielke, L, De Geus, E, Gould, J, Cumming, H, Woodhouse, I, Gearing, J, Hansbro, P & Hertzog, P 1970, 'Type I interferons in the regulation of mucosal immune responses in the female reproductive tract', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 393-393.

Marshall, J, Kok, LF, Marsh-Wakefield, F, Gillis, C, Halliday, G & Byrne, S 1970, 'Immune suppressive doses of ultraviolet radiation activate a unique subset of B cells that are required for sunlight protection of mice from EAE', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 1134-1134.

Marsh-Wakefield, F, O'Sullivan, C, Leighton, S, Gillis, C, Halliday, G & Byrne, S 1970, 'IL-4-treated mast cells activate regulatory B cells in a cross-talk involving microvesicles', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 1080-1080.

Mayall, J, Mangan, N, Chevalier, A, Kim, R, Rae, B, Hertzog, P, Horvat, J & Hansbro, P 1970, 'Interferon-epsilon- regulated gene expression patterns in protection against female reproductive tract infection', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 280-280.

Merklein, M, Stiller, B, Kabakova, IV, Mutugala, US, Vu, K, Madden, SJ, Eggleton, BJ & Slavík, R 1970, 'Opto-electronic oscillator employing photonic-chip based stimulated Brillouin scattering', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Nonlinear Photonics, OSA.
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© 2016 OSA. We demonstrate an optoelectronic oscillator based on stimulated Brillouin scattering as an active filter on a photonic chip. An ultrahigh Brillouin gain chalcogenide rib waveguide is used to generate low-noise single-mode 10 GHz RF signals.

Merklein, M, Stiller, B, Kabakova, IV, Mutugala, US, Vu, K, Madden, SJ, Eggleton, BJ & Slavík, R 1970, 'Photonic-chip based widely tunable microwave source using a Brillouin opto-electronic oscillator', Frontiers in Optics 2016, Frontiers in Optics, OSA.
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© OSA 2016. We demonstrate the first widely tunable chip-based opto-electronic microwave source based on stimulated Brillouin scattering. The output frequency can be tuned over 40 GHz and the phase-noise performance is comparable to high-range laboratory RF sources.

Mitchell, A, Lam, H, Peters, M, Morgan, L & Oliver, B 1970, 'EXHALED VIRUSES ARE REPRESENTATIVE OF LOWER RESPIRATORY TRACT INFECTION', RESPIROLOGY, WILEY-BLACKWELL, pp. 82-82.

Mitchell, A, Lam, H, Peters, M, Morgan, L & Oliver, BG 1970, 'Concordance Between Rhinovirus Found In Exhaled Breath And Bronchoalveolar Lavage Fluid', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, San Francisco, CA.

Mitchell, A, Peters, M, Morgan, L & Oliver, B 1970, 'Baseline incidence of respiratory viruses in asymptomatic patients', 10.1 Respiratory Infections, ERS International Congress 2016 abstracts, European Respiratory Society.
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Mitchell, AB, Glanville, AR, Peters, M, Morgan, LC & Oliver, BG 1970, 'RESPIRATORY VIRUSES ARE COMMONLY DETECTED IN ASYMPTOMATIC ASTHMA AND COPD PATIENTS', RESPIROLOGY, WILEY-BLACKWELL, pp. 91-91.

Moeke, CH, Padula, MP, Beck, HC, Hansen, ML, Rasmussen, LM & Davies, MJ 1970, 'Detection of Pyruvate Kinase Isoform M2 (PKM2) in Arterial Wall Cells, Intact Arteries and Human Atherosclerotic Lesions', Free Radical Biology and Medicine, Elsevier BV, pp. S139-S139.
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Mohanty, M, Asghar, MR & Russello, G 1970, '3DCrypt: Privacy-preserving Pre-classification Volume Ray-casting of 3D Images in the Cloud', Proceedings of the 13th International Joint Conference on e-Business and Telecommunications, International Conference on Security and Cryptography, SCITEPRESS - Science and Technology Publications, pp. 283-291.
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Copyright © 2016 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved. With the evolution of cloud computing, organizations are outsourcing the storage and rendering of volume (i.e., 3D data) to cloud servers. Data confidentiality at the third-party cloud provider, however, is one of the main challenges. In this paper, we address this challenge by proposing - 3DCrypt - a modified Paillier cryptosystem scheme for multi-user settings that allows cloud datacenters to render the encrypted volume. The rendering technique we consider in this work is pre-classification volume ray-casting. 3DCrypt is such that multiple users can render volumes without sharing any encryption keys. 3DCrypt's storage and computational overheads are approximately 66.3 MB and 27 seconds, respectively when rendering is performed on a 256 x 256 x 256 volume for a 256 x 256 image space.

Moheimani, F, Koops, J, Williams, T, Reid, AT, Hansbro, PM, Wark, PA & Knight, DA 1970, 'ABNORMAL MICRORNAS EXPRESSION IN EPITHELIAL CELLS OF SEVERE ASTHMATICS', RESPIROLOGY, WILEY-BLACKWELL, pp. 26-26.

Montgomery, E, Macdonald, PS, Glanville, AR, Malouf, M, Havryk, A, Plit, M, Benzimra, M, Rigby, AL, Harkess, M, DeTullio, N, Smith, AL, Hogan, A, Tunnicliff, PS & Jha, S 1970, 'The Prevalence and Prognostic Significance of Frailty in Patients with Advanced Lung Disease Referred for Lung Transplantation', The Journal of Heart and Lung Transplantation, International Society of Heart and Lung Transplantation 35th Annual Meeting, Elsevier BV, Washington, USA, pp. S317-S317.
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Murrihy, R, Dedousis-Wallace, A, Ollendick, TH, Greene, RW, McAloon, J, Gill, S, Remond, L, Ellis, DM & Drysdale, S 1970, 'Parent Management Training and Collaborative & Proactive Solutions: A randomised comparison trial for oppositional youth within an Australian population', Eighth World Congress of Behavioural and Cognitive Therapies, Melbourne, Australia.

Patel, BS, Rahman, M, Rumzhum, N, Oliver, BG, Verrills, NM & Ammit, AJ 1970, 'Theophylline Represses Il-8 Secretion From Asm Cells Independently Of Pde Inhibition: Novel Role As A Pp2a Activator', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, International Conference of the American-Thoracic-Society (ATS), AMER THORACIC SOC, San Francisco, CA.

Pathinayake, PS, Hsu, AC-Y, Parsons, K, Loo, S-L, Fricker, M, Wood, LG, Hansbro, P & Wark, PAB 1970, 'Effect of oxidative stress and rhinovirus infection on mitochondrial/endoplasmic reticular function in human primary bronchial epithelial cells', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 694-694.

Phillips, ML 1970, 'Intentional Small-scale Disasters: Simulating Oil Spills to Develop Hands-on Remediation Experience', http://www.simulationcongress.com/wp-content/uploads/ASC_2016_Proceedings.pdf, Australasian Simulation Congress, Simulation Australasia, Melbourne Convention and Exhibition Centre, pp. 518-521.
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Oil spills pose substantial threats to ecosystem structure and function, and remediating ecosystems can be both time consuming and labour intensive. Crude oils contain hazardous heavy metal compounds, can be odorous, sticky and viscous, and may adhere easily to sand, rocks and biological tissues. Such properties make crude oil contamination immensely difficult to clean from shoreline communities. In order to provide an effective and memorable learning experience for university students enrolled in the subject 91159 Environmental Remediation, a laboratory simulation experiment was developed to realistically recreate both the impacts of an oceanic oil spill and the procedures required to remediate ecosystems at a microcosm scale. Students were tasked with creating their own miniature coastal ecosystems, complete with seawater, rocks, sediment, plants, small-scale model animals and a model shipping vessel. A small quantity of crude oil was then spilled from the model ship’s location and tidal forces were mimicked. Students were provided with an arsenal of remediation equipment in order to enact their own realistic management strategies for cleaning and extracting oil from their ecosystems, as well as protecting natural and assets. At the completion of the simulation, students were asked to reflect on their experience and to extrapolate their microcosm experiment to real world, full-scale oil spills. Learning and teaching educators noted a high level of enthusiasm and engagement from students. The Student Feedback Survey at the end of semester also revealed high student satisfaction and strong positive feedback from students in regard to managing the simulated oil spill. This laboratory simulation proved to be a very effective educational tool which also created a fun and memorable experience for university science students.

Pinkerton, J, Kim, R, Essilfie, A, Rae, B, Mayall, J, Ali, M, Starkey, M, Wood, L, Biswal, S, Horvat, J & Hansbro, P 1970, 'TARGETING OXIDATIVE STRESS FOR THE SUPPRESSION OF SEVERE, STEROID-INSENSITIVE ASTHMA', RESPIROLOGY, WILEY-BLACKWELL, pp. 105-105.

Pinkerton, J, Kim, R, Essilfie, A-T, Rae, B, Mayall, J, Ali, MK, Starkey, M, Wood, L, Biswal, S, Horvat, J & Hansbro, P 1970, 'Investigating antioxidant therapy for steroid-resistant asthma', 5.3 Allergy and Immunology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Piprek, J, Poulton, C, Steel, M & Sterke, MD 1970, 'Welcome', 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), IEEE, p. iii.
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Platen, E 1970, 'Numeraire Portfolio Investing', 9th World Congress of the Bachelier Finance Society, New York.

Platen, E 1970, 'On Interest Rate Term Structure Modelling under the Benchmark Approach', Seminar Institute Bachelier, Paris.

Reyna Zeballos, JL, Davila, YC & Meier, PC 1970, 'Enhancing the Flipped Classroom Experience with the Aid of Inclusive Design', Association for the Advancement of Computing in Education, EdMedia: World Conference on Educational Media and Technology, Association for the Advancement of Computing in Education (AACE), Vancouver, pp. 1789-1801.
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Flipped classrooms are increasingly used in tertiary institutions to engage students in active learning tasks and foster independent learning skills. The use of technology such as digital video, screencasts and interactive presentations is impacting the design of flipped classrooms. This creates an opportunity to apply the principles of Inclusive Design in the planning, development and deployment of resources used to flip the classroom. The aim of this paper is to discuss the integration of Inclusive Design into Flipped Classroom interventions to cater for a wider range of learners. For this purpose, we reviewed the pedagogical foundations of Flipped Classrooms, the advantages and disadvantages of its implementation, and discuss Inclusive Design enablers.

Rutting, S, Xenaki, D, Ge, Q, Wood, L, Hansbro, P & Oliver, B 1970, 'Interaction of dietary fatty acids with obesity induced cytokines in primary human pulmonary fibroblasts', 3.2 Airway Cell Biology and Immunopathology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Schulte, J & Griffiths, N 1970, 'Authentic Learning Experiences In A Theory Heavy Learning Context', Proceedings Of The Australian Conference On Science And Mathematics Education 2016 (22nd Annual UniServe Science Conference), Australian Conference on Science and Mathematics Education, UniServe Science, The University of Sydney, NSW 2006, Australia, Brisbane, Australia, pp. 1-6.
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Assessment in an undergraduate physics subject was re-designed to challenge and inspire students to develop and apply their disciplinary and non-disciplinary skills in a practice-based, authentic assignment task. The aims of the re-design were to expose students to workplace practice and increase their engagement in the subject. Traditionally, as a response to its emphasis on disciplinary theory, science is assessed by way of content focussed class tests and examinations, activities not reflected in workplace practice. These summative assessment types measure student attainment of knowledge rather than enable deeper understanding and learning. However, introducing students to ‘real-world’ practice-oriented assessment tasks can enhance student engagement and promote learning. To achieve these aims the assignment was carefully scaffolded to give students the opportunity to improve their scientific writing skills, develop an approach to systematic research, build a greater understanding of the peer-review process and acquire skills in self and team management. The task required students to work in groups to research and write a research paper based on a meta-study model. Their papers were then compiled and published in a student peer-reviewed research journal. The impact of this intervention was evaluated through a focus group discussion with the majority of the students commenting positively on their learning and engagement in the subject. This reflective article discusses the effectiveness of the assignment design, its scaffolding, the peer-review process and the authenticity of the workplace-setting. Suggestions are made as to how to further improve this type of assignment design. This workplace-focused intervention may be of interest to educators in other disciplines.

Shen, J, Tran, NN, Devadas, R, Huete, A, Zhang, H & Yu, Q 1970, 'Climate impacts on wheat phenology and production using mutisource data in NSW, Australia', 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IGARSS 2016 - 2016 IEEE International Geoscience and Remote Sensing Symposium, IEEE, Beijing, China, pp. 6296-6299.
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© 2016 IEEE.Wheat is the most important grain crop in Australia, which plays a significant role in world grain-trading market. However, climate warming, water shortage, as well as more frequent extreme weather events (e.g., heatwaves, droughts and floods), under pressure of food demand, would pose great risks to all aspects of wheat production worldwide, especially in Australia with high climate variability. This study aggregated multi-source observational data by using meteorological statistics, in-situ investigation data and the MODIS Enhanced Vegetation Index (EVI) product to explore and examine the correlation between climate variability and spatial-temporal patterns of wheat phenology metrics and productivity. The results from tests over 370 wheat trial sites showed: 1) narrower and earlier sowing and harvesting windows occurred in a drought year (2006) compared with a normal year (2005). Differences in sowing and harvesting window lengths were 9 and 5 days, respectively; 2) different weather patterns in each agro-climatic zone were followed by different remotely sensed crop EVI seasonality profiles. Crop growth was least affected by climate variability in agro-climate region E2, which is located in the south part of study area. This study reveals new information on cropland-climate relationships across the wheat belt in NSW in a changing climate.

Sidiqui, P, Huete, A & Devadas, R 1970, 'Spatio-temporal mapping and monitoring of Urban Heat Island patterns over Sydney, Australia using MODIS and Landsat-8', 2016 4th International Workshop on Earth Observation and Remote Sensing Applications (EORSA), 2016 4th International Workshop on Earth Observation and Remote Sensing Applications (EORSA), IEEE, Guangzhou, China, pp. 217-221.
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© 2016 IEEE.Most cities have become net sources of heat with well-documented examples of anthropogenic climate modification in urban areas driving the Urban Heat Island (UHI) effect. This is defined as having higher temperatures (air /surface) in the built environment of cities compared with the surrounding and in rural areas. In this study we integrated remotely sensed satellite data to map and monitor the UHI effect over the Sydney region in Australia. Terra/Aqua MODIS Land Surface Temperature (LST) time series data for 2003 to 2015 were analysed to determine the spatio-temporal dynamics of UHI intensity. Land cover data from the MODIS were used to delineate the urban, rural and water class for the Sydney region. The UHI intensities were extracted from LST images by normalising rural LST patterns for each date. A Gaussian approximation was then applied in order to quantify spatial extent, centre and magnitude of UHI intensities. The temporal analysis on seasonal and interannual variations of UHI, revealed maximum intensities in daytime periods, particularly during the summer season. The daytime UHI intensity in Sydney could be as large as 7 - 8 °C in summer days. However, relatively weak UHI intensities were observed in night-time periods during all seasons. It was observed from the time series data that there were slight non-significant increasing trend in daytime UHI magnitudes for Sydney. However, pixel based UHI intensities at dense urban suburbs showed significant increasing trends for daytime and no defined trend for night time observations. To better characterise the locational nature of UHI, Landsat-8 land surface temperature data were analysed for summer period. Landsat data were helpful in extracting the information on hot spots in urban area more precisely. Satellite data of MODIS and Landsat provided efficient results for monitoring, mapping and characterizing UHI patterns over time and space. Future work involves classification of urban areas using...

Smith, MJA, de Sterke, CM, Kuhlmey, BT, Poulton, CG, Lapine, M & Wolff, C 1970, 'Suppression of stimulated Brillouin scattering in composite media', 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), 2016 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), IEEE, Sydney, pp. 23-24.
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Overcoming stimulated Brillouin scattering (SBS) is a major challenge in optical telecommunications networks and in fiber lasers. We evaluate the SBS gain coefficient for an all-dielectric composite material comprising a cubic, subwavelength array of spheres in a uniform background. We demonstrate total SBS suppression in fused silica using GaAs spheres

Smith, MJA, Kuhlmey, BT, de Sterke, CM, Wolff, C, Lapine, M & Poulton, CG 1970, 'Elastic modelling of electrostriction in dielectric composite materials', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Australian Conference on Optical Fibre Technology, OSA, Sydney, Australia.
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The electrostriction of a composite material does not only depend on the electrostrictive properties of the constituents, but also includes an additional mechanical response term. We compare two different models to calculate this contribution

Solntsev, AS & Sukhorukov, A 1970, 'Quantum walks of photons on a non-linear chip(Conference Presentation)', Active Photonic Materials VIII, Active Photonic Materials VIII, SPIE.
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Solntsev, AS, Carletti, L, Xu, L, Poddubny, AN, De Angelis, C, Leo, G, Kivshar, YS, Neshev, DN & Sukhorukov, AA 1970, 'Photon-pair generation and sum-frequency conversion in nonlinear dielectric nanoresonators', Frontiers in Optics 2016, Frontiers in Optics, OSA.
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© OSA 2016. We predict photon-pair generation with non-classical angular correlations through spontaneous parametric down-conversion in quadratic nonlinear dielectric AlGaAs nanoresonators, and establish a quantum-classical correspondence with sum-frequency conversion.

Solntsev, AS, Carletti, L, Xu, L, Poddubny, AN, De Angelis, C, Leo, G, Kivshar, YS, Neshev, DN & Sukhorukov, AA 1970, 'Quantum-classical correspondence for photon-pair generation in nonlinear dielectric nano-resonators', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Nonlinear Photonics, OSA, Sydney, Australia.
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© 2016 OSA.We predict highly efficient sum-frequency conversion in quadratic nonlinear dielectric nano-resonators made of AlGaAs, and formulate a general quantum-classical correspondence with spontaneous parametric down-conversion, revealing a photon-pair generation regime with non-classical angular correlations.

Starkey, M, Haw, T, Pavlidis, S, Nair, MP, Liu, G, Hanish, I, Kim, R, Miyake, K, Adcock, I, Foster, P, Horvat, J & Hansbro, P 1970, 'TOLL-LIKE RECEPTOR 7 PROMOTES CIGARETTE-SMOKE INDUCED EMPHYSEMA-LIKE ALVEOLAR ENLARGEMENT IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 79-79.

Starkey, M, Nguyen, D, Kim, R, Haw, T, Nair, P, Essilfie, A, Horvat, J & Hansbro, P 1970, 'EARLY-LIFE RESPIRATORY BACTERIAL INFECTION-INDUCED CHRONIC LUNG DISEASE IS DRIVEN BY A NOVEL TLR2/IL-13/MIR-21/PI3K SIGNALLING PATHWAY', RESPIROLOGY, WILEY-BLACKWELL, pp. 37-37.

Starkey, MR, Dua, K, Hsu, AC, Nair, PM, Haw, TJ, Nguyen, DH, Kim, RY, Horvat, JC, Godfrey, D, McKenzie, AN, Lukacs, NW, Wark, PA, Foster, PS & Hansbro, PM 1970, 'Interleukin-13 predisposes to more severe influenza infection in mice and human epithelial cells by suppressing interferon responses and activating the microRNA-21/PI3K signaling pathway', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 322-322.

Starkey, MR, Nguyen, DH, Kim, RY, Haw, TJ, Nair, PM, Essilfie, AT, Horvat, JC, Foster, PS & Hansbro, PM 1970, 'Early-life respiratory bacterial infection-induced chronic lung disease is driven by a novel TLR2/IL-13/miR-21/PI3K signaling pathway', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 347-347.

Steptoe, R, Al-Kouba, J, Coleman, M, Jessup, C, Starkey, M, Overgaard, N, Bridge, J, Horvat, J, Werder, R, Walters, S, Coates, PT, Grey, S, Thomas, R, Wells, J, Hansbro, P, Phipps, S & Davies, J 1970, 'Ablation of pathogenic memory T-cell responses by bone marrow-mediated gene therapy under immune-preserving conditions', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 722-722.

Stuart, B, Thomas, P, Maynard-Casely, H, Booth, N & Leung, A 1970, 'A neutron diffraction investigation of shear forces on a model lipid for forensic application', ANZFSS 23rd International Symposium on the Forensic Sciences, Auckland.

Stützer, S, Solntsev, AS, Nolte, S, Sukhorukov, AA & Szameit, A 1970, 'Observation of Bloch oscillations with a threshold', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, Sydney, Australia.
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© 2016 OSA.We predict and demonstrate experimentally a metal-insulator phase transition from extended wave transport to localized Bloch oscillations at a critical effective potential strength in photonic lattices, which realize optical emulator of quantum photon squeezing.

Tang, F, Hansbro, P, Burgess, J, Baines, K & Oliver, B 1970, 'A NOVEL NEUTROPHIL SUPPRESSOR ROLE IN RHINOVIRUS INFECTIONS', RESPIROLOGY, WILEY-BLACKWELL, pp. 44-44.

Tang, V, Macer-Wright, J, Fu, S, Rayner, B & Hawkins, C 1970, 'Chlorinated Nucleosides - A Novel Inducer of Endothelial Dysfunction in Atherosclerosis?', Free Radical Biology and Medicine, Elsevier BV, pp. S152-S152.
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Taspinar, S, Mohanty, M & Memon, N 1970, 'PRNU based source attribution with a collection of seam-carved images', 2016 IEEE International Conference on Image Processing (ICIP), 2016 IEEE International Conference on Image Processing (ICIP), IEEE, Phoenix, AZ, pp. 156-160.
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Taspinar, S, Mohanty, M & Memon, N 1970, 'Source camera attribution using stabilized video', 2016 IEEE International Workshop on Information Forensics and Security (WIFS), 2016 IEEE International Workshop on Information Forensics and Security (WIFS), IEEE, NYU Abu Dhabi, Abu Dhabi, U ARAB EMIRATES.
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Tay, H, Yang, M, Hsu, A, Nguyen, T-H, Plank, M, Maltby, S, Bartlett, N, Hansbro, P & Foster, P 1970, 'Role of interleukin-36 gamma in regulating lung inflammation', EUROPEAN JOURNAL OF IMMUNOLOGY, International Congress of Immunology (ICI), WILEY-BLACKWELL, Melbourne, AUSTRALIA, pp. 17-18.

Titchener, J, Gräfe, M, Heilmann, R, Solntsev, AS, Szameit, A & Sukhorukov, AA 1970, 'Scalable on-chip quantum state tomography', Frontiers in Optics 2016, Frontiers in Optics, OSA, Munich, GERMANY.
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Titchener, JG, Solntsev, AS & Sukhorukov, AA 1970, 'Photonic cluster state generation in nonlinear waveguide arrays', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Nonlinear Photonics, OSA, Sydney, Australia.
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© 2016 OSA.We present a novel approach for all-optically reconfigurable integrated generation of quantum entangled photons in cluster states through spontaneous parametric down-conversion in coupled arrays of quadratic nonlinear waveguides with special poling patterns.

Tran, TT, Bray, K, Ford, MJ, Toth, M & Aharonovich, I 1970, 'Quantum Emission from Hexagonal Boron Nitride Monolayers', Optics InfoBase Conference Papers.
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We demonstrate first room temperature, and ultrabright single photon emission from a color center in two-dimensional multilayer hexagonal boron nitride. Density Functional Theory calculations indicate that vacancy-related centers are a likely source of the emission.

Troják, M, Šafránek, D, Hrabec, J, Šalagovič, J, Romanovská, F & Červený, J 1970, 'E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria', COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2016), 14th International Conference on Computational Methods in Systems Biology (CMSB), Springer International Publishing, Univ Cambridge, Comp Lab, Cambridge, ENGLAND, pp. 316-322.
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Umar, J, Hussain, T, Farooq, A & Nazir, A 1970, 'Development of wicking interfaces in single jersey knitted fabric for better moisture management properties', Fiber Society 2016 Spring Conference: Textile Innovations - Opportunities and Challenges.

Umar, J, Hussain, T, Farooq, A, Maqsood, M, Umer, D & Khan, J 1970, 'Comparison of Stretch and Recovery Properties of Polyester and Polyamide Knitted Fabrics for Compression Sportswear', http://thefibersociety.org/Portals/0/Past%20Conferences/2016_Fall_Abstracts.pdf, The Fiber Society 2016 Fall Meeting and Technical Conference – The Fiber Society—75 years in the Making, held October, Cornell University, Ithaca, New York, USA.

Unnikrishnan, A, Papaemmanuil, E, Beck, D, Verma, A, Kumari, A, Woll, P, Richards, L, Knezevic, K, Chandrakanthan, V, Thoms, J, Tursky, M, Huang, Y, Ali, Z, Olivier, J, Galbraith, S, Kulasekararaj, A, Tobiasson, M, Karimi, M, Pellagatti, A, Wilson, S, Lindeman, R, Young, B, Ramakrishna, R, Arthur, C, Stark, R, Crispin, P, Curnow, J, Warburton, P, Roncolato, F, Boultwood, J, Lynch, K, Jacobsen, S, Mufti, G, Hellstrom-Lindberg, E, MacKenzie, K, Wong, J, Campbell, P & Pimanda, J 1970, 'INTEGRATIVE GENOMICS IDENTIFIES THE MOLECULAR BASIS OF RESISTANCE TO AZACITIDINE THERAPY IN MYELODYSPLASTIC SYNDROMES', HAEMATOLOGICA, 21st Congress of the European-Hematology-Association, FERRATA STORTI FOUNDATION, Copenhagen, DENMARK, pp. 157-158.

Vaughan, A, Stevanovic, S, Rahman, M, Zare, A, Miljevic, B, Ristovski, Z, Bowman, R, Fong, K & Yang, I 1970, 'N-acetyl cysteine (NAC) intervention attenuates the effects of diesel and biodiesel emission exposure on human bronchial epithelial cells, 16HBE, at air-liquid interface', 3.2 Airway Cell Biology and Immunopathology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Vlachynska, A, Cerveny, J, Cmiel, V & Turecek, T 1970, 'Automatic Image-Based Method for Quantitative Analysis of Photosynthetic Cell Cultures', Hybrid Artificial Intelligent Systems, 11th International Conference on Hybrid Artificial Intelligence Systems (HAIS), Springer International Publishing, Seville, SPAIN, pp. 402-413.
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Wang, J, Bartlett, M & Ryan, L 1970, 'Housing transition and aging: 45 and Up Study', Joint Statistical Meetings, Chicago.

Wang, K, Shi, Y, Solntsev, AS, Fan, S, Sukhorukov, AA & Neshev, DN 1970, 'Controllable non-reciprocity induced by in-band photonic transitions in χ(2) nonlinear optics', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Nonlinear Photonics, OSA, Sydney, Australia.
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© 2016 OSA.We demonstrate a controllable non-reciprocity via in-band transitions of photons mediated by second-order parametric nonlinear processes, and propose a dynamic optical isolator based on directional geometric phase-shifts controlled by a single pump.

Wen, S, Li, D, Liu, D, Xu, X, Du, Y, Mitchell, DRG, Shi, B, Shi, X & Jin, D 1970, 'Seed mediated one-pot growth of versatile heterogeneous upconversion nanocrystals for multimodal bioimaging', SPIE Proceedings, SPIE BioPhotonics Australasia, SPIE, Adelaide, South Australia, Australia.
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© 2016 SPIE.The rapid development of a variety of molecular contrast agents makes the multimodality bioimaging highly attractive towards higher resolution, more sensitive, informative diagnosis. The key lies in the development of facile material synthesis that allows the integration of multiple contrast agents, ideally in a way that each of the components should be logically assembled to maximize their performances. Here, we report the one-pot programmable growth of multifunctional heterogeneous nanocrystal with tunable size, shape, composition, and properties. We demonstrated a facile one-pot hot-injection method to enable the highly selectively controlled growth of different sodium lanthanide fluoride nanomaterials in either longitudinal or transversal directions with atomic scale precision. This technique allows the upconversion luminescence signal, MRI signal and x-ray signal logically integrated and optimized within one single versatile nanoplatform for multimode bioimaging. These findings suggest that the facile strategy developed here have the promising to get the desired heterogeneous nanocrystals as an all-in-one contrast agent for integrated and self-correlative multimodal bioimaging.

Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 1970, 'Boundaries of practicability for integrated Stimulated Brillouin scattering devices', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA, San Jose, CA.
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Wood, BW, Padula, M, Marks, DC & Johnson, L 1970, 'Characterization and Comparison of the Surface Phenotype of Refrigerated and Cryopreserved Platelets', TRANSFUSION, AABB Annual Meeting, WILEY-BLACKWELL, Orlando, FL, pp. 37A-38A.

Xenaki, D, Deshpande, D, Oliver, B & Sharma, P 1970, 'Targeting ASK1 in preventing airway smooth muscle growth: Implications for airway remodeling in COPD', 3.2 Airway Cell Biology and Immunopathology, ERS International Congress 2016 abstracts, European Respiratory Society.
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Zhanghao, K, Chen, L, Yang, X, Wang, M, Jing, Z, Han, H, Zhang, MQ, Jin, D, Gao, J & Xi, P 1970, 'Super-resolution fluorescence dipole orientation microscopy', 2016 Progress in Electromagnetic Research Symposium (PIERS), 2016 Progress in Electromagnetic Research Symposium (PIERS), IEEE.
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Zhao, J, Zheng, X, Schartner, EP, Ionescu, P, Zhang, R, Nguyen, T-L, Jin, D & Ebendorff-Heidepriem, H 1970, 'Upconversion Nanocrystals Doped Glass: A New Paradigm for Integrated Optical Glass', Photonics and Fiber Technology 2016 (ACOFT, BGPP, NP), Australian Conference on Optical Fibre Technology, OSA.
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A new versatile method of integrating upconversion nanocrystals into a glassy matrix is presented, which opens up exciting possibilities for new hybrid glass materials and multifunctional fiber devices with tailored nanoscale properties and high transparency.

Zhao, L, Wen, S, Shi, X & Zhao, J 1970, '99mTc labeled multifunctional polyethylenimine-entrapped gold nanoparticles for dual mode SPECT and CT imaging', JOURNAL OF NUCLEAR MEDICINE, SOC NUCLEAR MEDICINE INC.

Zinder, Y, Lazarev, AA, Musatova, EG, Tarasov, IA & Khusnullin, NF 1970, 'Two-Station Single Track Scheduling Problem', IFAC PAPERSONLINE, IFAC Conference on Manufacturing Modelling, Management and Control, Elsevier, Troyes, France, pp. 231-236.
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Single track segments are common in various railway networks, in particular in various supply chains. For such a segment, connecting two stations, the trains form two groups, depending on what station is the initial station for the journey between these two stations. Within a group the trains differ by their cost functions. It is assumed that the single track is sufficiently long so several trains can travel in the same direction simultaneously. The paper presents polynomial-time algorithms for different versions of this two-station train scheduling problem with a single railway track. The considered models differ from each other by their objective functions.

Ajani, PA & Murray, S 2016, A Review of Toxic Algal Species towards Improving Management of Toxic Blooms in New South Wales, pp. 1-71.
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Murray, SA, Kohli, GS, Harwood, DT, Laczka, O & Boulter, M Fisheries Research and Development Corporation 2016, Safeguarding seafood consumers in NSW from ciguatera fish poisoning, no. ISBN 978-0-646-95465-3, pp. 1-51, Canberra, ACT, Australia.

Ruvindy, R, Ajani, P & Murray, S 2016, Microalgal Community Composition Assessment in Warringah Lagoons 2015-2016.

Wilkinson, SJ, Stoller, P, Ralph, P & Hamdorf, B UTS 2016, Feasibility of Algae Building Technology in Sydney, Feasibility of Algae Building Technology in Sydney, no. 1, pp. 1-56, Sydney Australia.

Ajani, PA 2016, 'Collecting data to help protect Australia's waters from toxic algal blooms.', The Conversation.
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Ever heard of Thalassiosira, Detonula, Leptocylindrus or Chaetoceros? No, they are not the names of Greek gods but arguably some of the most important and beautiful organisms on earth: the diatoms. https://theconversation.com/collecting-data-to-help-protect-australias-waters-from-toxic-algal-blooms-61298

Baldeaux, JF, Ignatieva, K & Platen, E 2016, 'Detecting Money Market Bubbles'.

Barash, M, Bayer, PE & van Daal, A 2016, 'Candidate gene scan for Single Nucleotide Polymorphisms involved in the determination of normal variability in human craniofacial morphology', Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory.
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AbstractDespite intensive research on genetics of the craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive. Recent development of novel digital methods for capturing the complexity of craniofacial morphology in conjunction with high-throughput genotyping methods, show great promise for unravelling the genetic basis of such a complex trait.As a part of our efforts on detecting genomic variants affecting normal craniofacial appearance, we have implemented a candidate gene approach by selecting 1,201 single nucleotide polymorphisms (SNPs) and 4,732 tag SNPs in over 170 candidate genes and intergenic regions. We used 3-dimentional (3D) facial scans and direct cranial measurements of 587 volunteers to calculate 104 craniofacial phenotypes. Following genotyping by massively parallel sequencing, genetic associations between 2,332 genetic markers and 104 craniofacial phenotypes were tested.An application of a Bonferroni–corrected genome–wide significance threshold produced significant associations between five craniofacial traits and six SNPs. Specifically, associations of nasal width with rs8035124 (15q26.1), cephalic index with rs16830498 (2q23.3), nasal index with rs37369 (5q13.2), transverse nasal prominence angle with rs59037879 (10p11.23) and rs10512572 (17q24.3), and principal component explaining 73.3% of all the craniofacial phenotypes, with rs37369 (5p13.2) and rs390345 (14q31.3) were observed.Due to over-conservative nature of the Bonferroni correction, we also report all the associations that reached the traditional genome-wide p-value threshold (<5.00E-08) as suggestive. Based on the genome-wide threshold, 8 craniofacial phenotypes demonstrated significant associations with 34 intergenic and extragenic SNPs. The majority of associations are novel, except

BARRY, A & HANSEN, D 2016, 'Naturally acquired immunity to malaria', Cambridge University Press (CUP), pp. 125-128.
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Cheng, B, Nikitopoulos Sklibosios, C & Schlogl, E 2016, 'Empirical Hedging Performance of Long dated Commodity Derivatives', Research Paper: 376, Quantitative Finance Research Centre, University of Technology Sydney.

Cheng, B, Nikitopoulos Sklibosios, C & Schlogl, E 2016, 'Empirical Pricing Performance on Long Dated Crude Oil Derivatives: Do Models with Stochastic Interest Rates Matter?', Research Paper: 367, Quantitative Finance Research Centre, University of Technology Sydney.

Cheng, B, Sklibosios Nikitopoulos, C & Schlogl, E 2016, 'Hedging Futures Options with Stochastic Interest Rates', Research Paper: 375, Quantitative Finance Research Centre, University of Technology Sydney.

Cheng, B, Sklibosios Nikitopoulos, C & Schlogl, E 2016, 'Pricing of Long-Dated Commodity Derivatives with Stochastic Volatility and Stochastic Interest Rates'.
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Aiming to study pricing of long-dated commodity derivatives, this paper presents a class of models within the Heath, Jarrow, and Morton (1992) framework for commodity futures prices that incorporates stochastic volatility and stochastic interest rate and allows a correlation structure between the futures price process, the futures volatility process and the interest rate process. The functional form of the futures price volatility is specified so that the model admits finite dimensional realisations and retains affine representations, henceforth quasi-analytical European futures option pricing formulae can be obtained. A sensitivity analysis reveals that the correlation between the interest rate process and the futures price process has noticeable impact on the prices of long-dated futures options, while the correlation between the interest rate process and the futures price volatility process does not impact option prices. Furthermore, when interest rates are negatively correlated with futures prices then option prices are more sensitive to the volatility of interest rates, an effect that is more pronounced with longer maturity options.

Chiarella, C, Sklibosios Nikitopoulos, C, Schlogl, E & Yang, H 2016, 'Pricing American Options Under Regime Switching Using Method of Lines'.
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This paper considers the American option pricing problem under regime-switching by using the method-of-lines (MOL) scheme. American option prices in each regime involve prices in all other regimes. We treat the prices from other regimes implicitly, thus guaranteeing consistency. Iterative procedures are required but very few iterative steps are needed in practice. Numerical tests demonstrate the robustness, accuracy and efficiency of the proposed numerical scheme. We compare our results with Buffington and Elliott (2002)’s analytical approximation under two regimes. Our MOL scheme provides improved results especially for out-of-the money options, possibly because they use a separation of variable approach to the PDEs which cannot hold around the early exercise region. We also compare our results with those of Khaliq and Liu (2009) and suggest that their implicit scheme can be improved.

Choi, Y, Cobbin, D, Walsh, S & Van reyk, D 2016, 'Does modern acupuncture address the clinical features of the original acupuncture theory?'.

DeMaere, MZ & Darling, AE 2016, 'Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)', PeerJ.
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Background. Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as viable means to generate 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. Methods. We developed a computational simulation pipeline for metagenomic 3C and Hi-C se- quencing 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. Results. When 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. Discussion. Previously, 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 considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further a...

DeMaere, MZ & Darling, AE 2016, 'Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)', PeerJ, PeerJ.
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Background. Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as viable means to generate 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. Methods. We developed a computational simulation pipeline for metagenomic 3C and Hi-C se- quencing 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. Results. When 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. Discussion. Previously, 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 considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further a...

DeMaere, MZ & Darling, AE 2016, 'Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)', PeerJ.
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Background. Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as viable means to generate 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. Methods. We developed a computational simulation pipeline for metagenomic 3C and Hi-C se- quencing 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. Results. When 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. Discussion. Previously, 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 considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further a...

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.
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Fourment, M, Darling, AE & Holmes, EC 2016, 'The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America', Cold Spring Harbor Laboratory.
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AbstractWild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby fostering opportunities for viruses to spread over long distances. However, the role played by such avian flyways in shaping the genetic structure of AIV populations has proven controversial. To assess the relative contribution of bird migration along flyways to the genetic structure of AIV we performed a large-scale phylogeographic study of viruses sampled in the USA and Canada, involving the analysis of 3805 to 4505 sequences from 36 to 38 geographic localities depending on the gene data set. To assist this we developed a maximum likelihood-based genetic algorithm to explore a wide range of complex spatial models, thereby depicting a more complete picture of the migration network than previous studies. Based on phylogenies estimated from nucleotide data sets, our results show that AIV migration rates within flyways are significantly higher than those between flyways, indicating that the migratory patterns of birds play a key role in pathogen dispersal. These findings provide valuable insights into the evolution, maintenance and transmission of AIVs, in turn allowing the development of improved programs for surveillance and risk assessment.Significance StatementAvian influenza viruses infect a wide variety of wild bird species and represent a potential disease threat to the poultry industry and hence to human and livestock populations. However, the ecological factors that drive the geographic spread and evolution of...

Gnoatto, A, Grasselli, M & Platen, E 2016, 'A Penny Saved is a Penny Earned: Less Expensive Zero Coupon Bonds'.
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In this paper we show how to hedge a zero coupon bond with a smaller amount of initial capital than required by the classical risk neutral paradigm, whose (trivial) hedging strategy does not suggest to invest in the risky assets. Long dated zero coupon bonds we derive, invest first primarily in risky securities and when approaching more and more the maturity date they increase also more and more the fraction invested in fixed income. The conventional wisdom of financial planners suggesting investor to invest in risky securities when they are young and mostly in fixed income when they approach retirement, is here made rigorous. The paper provides a strong warning for life insurers, pension fund managers and long term investors to take the possibility of less expensive products seriously to avoid the adverse consequences of the low interest rate regimes that many developed economies face.

Gorval, M, Lees, T, Elliott, J, Nassif, N, Simpson, A & Lal, S 2016, 'Investigation of the association between blood glucose levels, anxiety and depression'.

Jarman, L, Elliott, J, Lees, T, Nassif, N, Simpson, A, Clifton-Bligh, R & Lal, S 2016, 'Associations between heart rate variability and blood glucose levels'.

Lienhard, B, Schröder, T, Mouradian, S, Dolde, F, Tran, TT, Aharonovich, I & Englund, DR 2016, 'Bright and photostable single-photon emitter in silicon carbide'.

Macnamara, JR 2016, 'Review of J. Fawkes, Public Relations Ethics and Professionalism: The Shadow of Excellence', Abramis Academic, pp. 110-112.

Marcelino, VR, Cremen, MCM, Jackson, CJ, Larkum, AWD & Verbruggen, H 2016, 'Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green algaOstreobium quekettii', Cold Spring Harbor Laboratory.
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McInnes, AS, Messer, LF, Laiolo, L, Laverock, B, Laczka, O, Brown, M, Seymour, JR & Doblin, MA 2016, 'Microbial utilization of nitrogen in cold core eddies: size does matter'.
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As the base of the marine food web, and the first step in the biological carbon pump, understanding changes in microbial community composition is essential for predicting changes in the marine nitrogen (N) cycle. Climate change projections suggest that oligotrophic waters will become more stratified with a concomitant shift in microbial community composition based on changes in N supply. In regions of strong boundary currents, eddies could reduce this limitation through nutrient uplift and other forms of eddy mixing. Understanding the preference for different forms of N by microbes is essential for understanding and predicting shifts in the microbial community. This study aims to understand the utilization of different N species within different microbial size fractions as well as understand the preferred source of N to these groups across varying mesoscale and sub-mesoscale features in the East Australian Current (EAC). In June 2015 we sampled microbial communities from three depths (surface, chlorophyll-a maximum and below the mixed layer), in three mesoscale and sub-mesoscale eddy features, as well as two end-point water masses (coastal and oligotrophic EAC water). Particulate matter was analysed for stable C and N isotopes, and seawater incubations with trace amounts of 15NO3, 15NH4, 15N2, 15Urea and 13C were undertaken. All samples were size fractionated into 0.3-2.0 µm, 2.0-10 µm, and >10 µm size classes, encompassing the majority of microbes in these waters. Microbial community composition was also assessed (pigments, flow cytometry, DNA), as well as physical and chemical parameters, to better understand the drivers of carbon fixation and nitrogen utilization across a diversity of water masses and microbial size classes. We observed that small, young features have a greater abundance of larger size classes. We therefore predict that these microbes will preferentially draw down the recently pulsed NO3. Ultimately, the size and age of a feature will determin...

Nazrul Islam, SMK, Li, M, Frank, F, Sang, L & Wang, X 2016, 'High performance of thermoelectricity in doped and undoped Cu2Se'.

Palmer, C, Hall, G, Westerman, H, Henderson, J & Mountain, W 2016, 'The curious incentives and consequences of negative gearing', The Conversation.

Payne, M, Ung, AT, Harry, E & Bottomley, A 2016, 'Synthesis of FtsZ Inhibitors: Potential Antibiotic Agents'.
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Using the crystal structure of S. aureus FtsZ with a co-crystallised known inhibitor, a pharmacophore was developed that could be utilized in the design of novel inhibitors. A library of 19 molecules were synthesized and structurally elucidated that contain a pyrazole linker (Scheme 1). These molecules were screened against S. aureus ATCC 25923 and Escherichia coli (E. coli) MG1556 cells to determine their antibacterial activity.

Phillips, M & Ung, AT 2016, 'Alkaloid-like molecules: AChE inhibitors as a potential treatment for Alzheimer’s disease'.
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the process of neurotransmission across the synaptic cleft in neurons. Reversible AChE inhibitors are currently marketed for the treatment of Alzheimer’s disease for their ability to slow down the progression of symptom development such as memory loss. An example of a current treatment is Galantamine (Reminyl), an alkaloid derived from the Galanthus Nivalis species2. Enantiomers of (-)-2 and (-)-3were successfully prepared and screened for AChE inhibitory activity, along with a small library of novel compounds not observed in previous work. Furthermore, the influence of solvent choice was investigated between (R)-limonene and various nitriles under the Bridging Ritter reaction conditions. The concluding results from this project will be presented.

Platen, E & Taylor, D 2016, 'Loading Pricing of Catastrophe Bonds and Other Long-Dated, Insurance-Type Contracts'.
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Catastrophe risk is a major threat faced by individuals, companies, and entire economies. Catastrophe (CAT) bonds have emerged as a method to offset this risk and a corresponding literature has developed that attempts to provide a market-consistent pricing methodology for these and other long-dated, insurance-type contracts. This paper aims to unify and generalize several of the widely-used pricing approaches for long-dated contracts with a focus on stylized CAT bonds and market-consistent valuation. It proposes a loading pricing concept that combines the theoretically possible minimal price of a contract with its formally obtained risk neutral price, without creating economically meaningful arbitrage. A loading degree controls how much influence the formally obtained risk neutral price has on the market price. A key finding is that this loading degree has to be constant for a minimally fluctuating contract, and is an important, measurable characteristic for prices of long-dated contracts. Loading pricing allows long-dated, insurance-type contracts to be priced less expensively and with higher return on investment than under classical pricing approaches. Loading pricing enables insurance companies to accumulate systematically reserves needed to manage its risk of ruin in a market consistent manner.

Quiroz, M, Tran, M-N, Villani, M, Kohn, R & Dang, K-D 2016, 'The block-Poisson estimator for optimally tuned exact subsampling MCMC'.
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Speeding up Markov Chain Monte Carlo (MCMC) for datasets with many observations by data subsampling has recently received considerable attention. A pseudo-marginal MCMC method is proposed that estimates the likelihood by data subsampling using a block-Poisson estimator. The estimator is a product of Poisson estimators, allowing us to update a single block of subsample indicators in each MCMC iteration so that a desired correlation is achieved between the logs of successive likelihood estimates. This is important since pseudo-marginal MCMC with positively correlated likelihood estimates can use substantially smaller subsamples without adversely affecting the sampling efficiency. The block-Poisson estimator is unbiased but not necessarily positive, so the algorithm runs the MCMC on the absolute value of the likelihood estimator and uses an importance sampling correction to obtain consistent estimates of the posterior mean of any function of the parameters. Our article derives guidelines to select the optimal tuning parameters for our method and shows that it compares very favourably to regular MCMC without subsampling, and to two other recently proposed exact subsampling approaches in the literature.

Sang, L, Cao, Q, Yun, F, Jian, X, Nazrul Islam, SMK, Yu, Z & Wang, X 2016, 'A novel 2-Dimensional metallic systems, V1-xTixSe2 for low dimensional electronics and energy applications'.

Tran, M-N, Kohn, R, Quiroz, M & Villani, M 2016, 'The Block Pseudo-Marginal Sampler'.
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The pseudo-marginal (PM) approach is increasingly used for Bayesian inference in statistical models, where the likelihood is intractable but can be estimated unbiasedly. %Examples include random effect models, state-space models and data subsampling in big-data settings. Deligiannidis et al. (2016) show how the PM approach can be made much more efficient by correlating the underlying Monte Carlo (MC) random numbers used to form the estimate of the likelihood at the current and proposed values of the unknown parameters. Their approach greatly speeds up the standard PM algorithm, as it requires a much smaller number of samples or particles to form the optimal likelihood estimate. Our paper presents an alternative implementation of the correlated PM approach, called the block PM, which divides the underlying random numbers into blocks so that the likelihood estimates for the proposed and current values of the parameters only differ by the random numbers in one block. We show that this implementation of the correlated PM can be much more efficient for some specific problems than the implementation in Deligiannidis et al. (2016); for example when the likelihood is estimated by subsampling or the likelihood is a product of terms each of which is given by an integral which can be estimated unbiasedly by randomised quasi-Monte Carlo. Our article provides methodology and guidelines for efficiently implementing the block PM. A second advantage of the the block PM is that it provides a direct way to control the correlation between the logarithms of the estimates of the likelihood at the current and proposed values of the parameters than the implementation in Deligiannidis et al. (2016). We obtain methods and guidelines for selecting the optimal number of samples based on idealized but realistic assumptions.

Williams, SG, Rawling, T & Ung, AT 2016, 'Alkaloid-like Molecules for Drug Discovery'.
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The alkaloid class of natural compounds is extensively known for their variety of biological activities. A high percentage of currently employed chemotherapeutic drugs - more than 60% for cancer are of plant origin, and many are alkaloids.[1] Synthetic compounds that display similar structures to alkaloids are known as alkaloid-like molecules. Alkaloids are commonly documented to poses pharmacological properties such as antineoplasticity and acetylcholinesterase (AChE) inhibition. The Aristotelia alkaloids (1 and 2) have a broad spectrum of biological activities,[2] several of which contain the same 3-aza-bicyclo[3.3.1]nonane core structure architecture, seen in blue in Figure 2. Figure 1: Aristotelia alkaloids, 1 and 2. As these Alkaloids are both rare and require complex isolation, it is more resourceful to generate libraries of molecules with the same core scaffold through synthetic pathways, such as the Bridging Ritter reaction.[3] Through the use of the Bridging Ritter reaction with (-)-β-pinene (3) and various nitriles, a small library of alkaloid-like molecules has been synthesized. Figure 2: The bridging Ritter reaction of (-)-β-pinene with various nitriles. AChE inhibitors are currently the front line of drugs used for relieving the symptoms of Alzheimer’s disease (AD) by restoring natural levels neurotransmitter acetylcholine, found to be low in the synapse of AD suffers.[4] All of the currently approved AChE inhibitors have severe undesirable side-effects and with the diseases mortality rate expected to increase greatly, it is imperative that more suitable drug candidates be developed. Therefore, these alkaloid-like compounds were screened for AChE inhibitory activity using The TLC bioautographic method[5] and Ellman Assay[6]. A library of 27 alkaloid-like molecules has been synthesised. The library is currently undergoing in-house anticancer testing using the MTS assay[7] against the MDA-MB-231 breast cancer cell line. External screening has...

Woodcock, S 2016, 'A tip to win your office footy tipping? Don’t listen to the experts', The Conversation.

Woodcock, S 2016, 'The Melbourne Cup: why you didn’t win', Money Magazine.

Woodcock, S 2016, 'We need a fairer system for deciding rain-affected games in Twenty20 cricket', The Conversation.